Query psy16767
Match_columns 1020
No_of_seqs 216 out of 1885
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 21:29:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16767.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16767hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0262|consensus 100.0 6E-237 1E-241 2053.8 59.7 969 1-1011 601-1637(1640)
2 KOG0261|consensus 100.0 9E-180 2E-184 1536.9 42.9 844 1-1012 498-1364(1386)
3 PRK14977 bifunctional DNA-dire 100.0 9E-177 2E-181 1655.9 57.5 813 1-1013 474-1320(1321)
4 KOG0260|consensus 100.0 2E-163 3E-168 1427.2 42.2 898 1-1014 474-1424(1605)
5 PRK00566 DNA-directed RNA poly 100.0 7E-104 2E-108 970.8 27.6 628 1-1005 451-1139(1156)
6 TIGR02386 rpoC_TIGR DNA-direct 100.0 4E-103 8E-108 963.8 33.0 624 1-1003 443-1135(1140)
7 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 1E-103 3E-108 973.9 29.1 404 1-441 454-865 (868)
8 PRK08566 DNA-directed RNA poly 100.0 2E-103 5E-108 974.8 27.2 411 1-444 458-873 (882)
9 PRK14906 DNA-directed RNA poly 100.0 5.7E-95 1.2E-99 889.3 31.0 620 1-1004 539-1237(1460)
10 PRK09603 bifunctional DNA-dire 100.0 7.4E-91 1.6E-95 885.4 36.0 313 1-407 1850-2177(2890)
11 PRK14844 bifunctional DNA-dire 100.0 2.5E-91 5.5E-96 886.4 24.5 317 1-417 1894-2237(2836)
12 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 2.7E-83 5.9E-88 717.4 24.3 336 556-1009 25-367 (367)
13 cd02735 RNAP_I_Rpa1_C Largest 100.0 2.8E-83 6.1E-88 707.3 20.9 304 566-1007 1-309 (309)
14 cd02584 RNAP_II_Rpb1_C Largest 100.0 7.4E-82 1.6E-86 716.1 24.2 370 556-1009 8-410 (410)
15 PRK14897 unknown domain/DNA-di 100.0 4.4E-81 9.6E-86 711.6 24.4 337 556-1013 163-507 (509)
16 cd06528 RNAP_A'' A'' subunit o 100.0 7.8E-81 1.7E-85 698.8 24.1 335 556-1009 21-362 (363)
17 PRK04309 DNA-directed RNA poly 100.0 1.4E-79 2.9E-84 693.2 27.2 336 556-1012 40-382 (383)
18 cd02736 RNAP_III_Rpc1_C Larges 100.0 3.6E-79 7.8E-84 669.4 20.8 299 566-1004 1-300 (300)
19 PF04998 RNA_pol_Rpb1_5: RNA p 100.0 3.8E-73 8.2E-78 626.6 10.2 277 361-963 1-277 (277)
20 cd02737 RNAP_IV_NRPD1_C Larges 100.0 1.2E-68 2.6E-73 602.1 18.6 317 575-1008 1-381 (381)
21 PRK02597 rpoC2 DNA-directed RN 100.0 1.3E-63 2.9E-68 617.6 22.9 345 152-619 6-362 (1331)
22 PRK14898 DNA-directed RNA poly 100.0 2.4E-61 5.3E-66 597.0 21.0 303 590-1012 540-852 (858)
23 COG0086 RpoC DNA-directed RNA 100.0 2.7E-58 5.9E-63 561.3 14.8 380 1-435 405-796 (808)
24 TIGR02388 rpoC2_cyan DNA-direc 100.0 2.2E-54 4.8E-59 531.7 17.5 210 152-417 5-215 (1227)
25 CHL00117 rpoC2 RNA polymerase 100.0 7.2E-54 1.5E-58 537.2 16.1 345 151-618 11-365 (1364)
26 cd00630 RNAP_largest_subunit_C 100.0 2.3E-45 5.1E-50 366.9 7.9 109 895-1003 49-158 (158)
27 cd02655 RNAP_beta'_C Largest s 100.0 1.9E-41 4.1E-46 350.9 11.8 100 903-1003 65-204 (204)
28 PF04983 RNA_pol_Rpb1_3: RNA p 100.0 2.2E-32 4.7E-37 278.0 0.4 157 25-206 1-158 (158)
29 PF05000 RNA_pol_Rpb1_4: RNA p 99.8 1E-21 2.2E-26 186.8 7.5 94 257-354 15-108 (108)
30 COG0086 RpoC DNA-directed RNA 99.7 1.8E-18 3.8E-23 212.8 -3.1 325 569-1010 408-746 (808)
31 TIGR02388 rpoC2_cyan DNA-direc 99.6 3.2E-16 6.9E-21 195.5 8.0 111 893-1004 1057-1223(1227)
32 CHL00117 rpoC2 RNA polymerase 99.6 8.5E-16 1.8E-20 195.3 6.3 108 903-1011 1181-1325(1364)
33 CHL00018 rpoC1 RNA polymerase 99.5 1.6E-14 3.4E-19 171.3 4.9 54 1-54 490-547 (663)
34 PRK02625 rpoC1 DNA-directed RN 99.5 2.1E-14 4.6E-19 168.6 4.6 54 1-54 469-526 (627)
35 TIGR02387 rpoC1_cyan DNA-direc 99.5 2E-14 4.3E-19 168.7 4.1 53 1-53 462-518 (619)
36 PRK14898 DNA-directed RNA poly 98.6 1.9E-08 4E-13 126.8 4.7 41 557-597 39-79 (858)
37 PRK10738 hypothetical protein; 35.2 39 0.00084 33.6 3.5 59 360-426 32-93 (134)
38 COG3688 Predicted RNA-binding 25.4 93 0.002 31.9 4.1 39 867-918 4-42 (173)
39 KOG0260|consensus 23.7 3.3 7.1E-05 53.1 -7.6 134 875-1009 1124-1264(1605)
40 PF04990 RNA_pol_Rpb1_7: RNA p 22.2 52 0.0011 32.9 1.7 52 656-709 1-75 (135)
No 1
>KOG0262|consensus
Probab=100.00 E-value=6.1e-237 Score=2053.82 Aligned_cols=969 Identities=46% Similarity=0.769 Sum_probs=829.4
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeecccccccChHHHHHHHHHHhcccCccc
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCILNTEI 76 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d~fl~~~~~~~l~~~~~~~~~~~i 76 (1020)
|||||||+ |+.|||||++|+++.+||+.|++|.|++|||||||+++++||.||+||+|++|+||++.++....++|
T Consensus 601 FDGDEMN~HfPQse~araEa~~ian~dsqYLvPt~G~PlrGLIQDHiVsgv~LT~rd~Fftre~y~qLv~~~l~~~~~rI 680 (1640)
T KOG0262|consen 601 FDGDEMNVHFPQSEIARAEAYNIANTDSQYLVPTDGTPLRGLIQDHIVSGVLLTMRDSFFTREDYQQLVFAGLSDTFKRI 680 (1640)
T ss_pred CCcchhcccCCchhhHHHHHHHHhccCCceeccCCCCchhhhhhhheeeeEEEEecccccCHHHHHHHHHHhhhhhccce
Confidence 99999999 99999999999999999999999999999999999999999999999999999999999888877899
Q ss_pred ccCCCccccCCCCCCCcEEEEEEccccCCCCCccccccccccc-cccccccCccccCccccccCceEEEeccceeeeccC
Q psy16767 77 RTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSG-ILDKKQFGSTQYGLVHAVWDTHVTIRHGELLSGILD 155 (1020)
Q Consensus 77 ~l~~Pailkp~~lwTGKqv~s~~l~~~~P~~~~~in~~~~~~~-k~~~~~~~~~~~~~~~~~~d~~v~I~~Gell~G~Ld 155 (1020)
+++||+|+||.+|||||||||++|+|++|++++.||+ +++ |+|+++|.....- ..++++.|+||+||||+|+||
T Consensus 681 ~~lpPtIlkP~~LWTGKQVIsTil~Ni~P~~~p~iNl---~~kaKip~~~W~~~s~e--~~l~Es~v~ir~GellcGVLD 755 (1640)
T KOG0262|consen 681 KLLPPTILKPAPLWTGKQVISTILKNIIPEGHPPINL---ESKAKIPGKAWRVHSEE--PKLNESQVLIREGELLCGVLD 755 (1640)
T ss_pred eccCccccccccccccchHHHHHHHhcCCCCCCcccc---hhcccCchhhcCCCCCc--ccCCcceEEEecCceEEEeec
Confidence 9999999999999999999999999999999999999 999 9999999732211 247889999999999999999
Q ss_pred cccccCcchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHHHHHHHHHHHHHHHHHHHc
Q psy16767 156 KKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAACNAL 235 (1020)
Q Consensus 156 K~~lG~~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~~~i~~a~~~~~~~~~~~~ 235 (1020)
|+++|++.+||+|+||+.||+++++.+|+++.||++.||+.+|||||++|+++.++++++|+++|++++..+.++.++++
T Consensus 756 Ka~~Gat~yGLvH~~~ElYG~~~s~~lLs~~srlFT~ylq~~GFT~GvdDlll~~~~D~kR~~il~e~~~vG~qa~~~~~ 835 (1640)
T KOG0262|consen 756 KAQFGATAYGLVHCCHELYGGETSGKLLSVFSRLFTAYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKEAF 835 (1640)
T ss_pred hhhcCchhhhhhhhhhhhhCccchhhHHHHHHHHHHHHHHHhccccccceeeechhhhHHHHHHHHhhhcccHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCChhHHHHhhcCCcchhhHHHH
Q psy16767 236 GLPLDTDPEIISSQLQEAYASIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVNTMQI 315 (1020)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~N~~Qi 315 (1020)
+++.+.+.+++..+|+..+..+.+..+.||..+++.+|.++++|.+.|+|.|+.+.||.|++.+|+.||||||.+|++||
T Consensus 836 ~l~~da~~del~~~le~~y~~d~~~~~~LD~~~k~~~n~~ts~I~~~cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QI 915 (1640)
T KOG0262|consen 836 GLDVDAPPDELRSRLEAIYLKDADKLAMLDRVMKSELNGYTSEIVKKCVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQI 915 (1640)
T ss_pred CCCCCCCHHHHHHHHHHHHhcchhHHHHHHHHHHHHHhhhhHHHHhhhccchhhhcCCcchHHHHHHhcCCcccccHHHH
Confidence 99999999999999998888788889999999999999999999999999999999999999999999999999999999
Q ss_pred HhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhhhccccCCcchhHHHH
Q psy16767 316 SCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCL 395 (1020)
Q Consensus 316 ~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYLqRrL 395 (1020)
+||||||+|||+|+|+|.+|||||||.|+|.+|+|||||.++|++|+.|+|||||||||||||||||||||+||||||||
T Consensus 916 SclLGQqeLEGkRvPlMvSGKtLPsF~p~e~spraGGfI~~RFlTGi~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCL 995 (1640)
T KOG0262|consen 916 SCLLGQQELEGKRVPLMVSGKTLPSFAPYETSPRAGGFIDGRFLTGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCL 995 (1640)
T ss_pred HHhhhhHhhcCCccceeecCCccCCcCCCCCCCCCCCcccceeecCCCchHHhhhhhccccchhhhHHhcccchHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhcccccccchhhhhhHHHHhhHHHHHhhhccCchhHHHHHHHhh
Q psy16767 396 VKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYLTDKQFSFLEDNIKWICSYKVILNLLKKHPLSLALLLLLTF 475 (1020)
Q Consensus 396 vk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 475 (1020)
|||||+|+|+||.||||+||+||||.|||||+|.+|++|++. +.|..+|++.+-. +. +...+.+.+-..
T Consensus 996 iKhLEgl~V~YD~TVRDsDgsvVQF~YGEDglDitKssfl~~--~~f~~~Ny~avl~-----~~---~~~~v~s~~d~~- 1064 (1640)
T KOG0262|consen 996 IKHLEGLKVHYDLTVRDSDGSVVQFMYGEDGLDITKSSFLNK--KEFPTDNYEAVLL-----KY---KSESVLSAFDIK- 1064 (1640)
T ss_pred HHhhhhcEEeccceEEcCCCcEEEEeecCccccccHHhhcch--hhhhhhhHHHHHh-----hh---ChHHHhhhhhhH-
Confidence 999999999999999999999999999999999999999984 5566888776521 10 011111111000
Q ss_pred hcCCCCCcccCCCcchhHHHHH-----HHHHhhcHHHHHHHHHhccCCCCCCcccCCCCcccccchHHHHHHHHHHhhcc
Q psy16767 476 KSSGKPNFIFSPHRTKFTMDLL-----EQWYQLDDKARKKYRKKFKACPQPLISTFQPDAHFGSISENLADSVVKYTKGR 550 (1020)
Q Consensus 476 ~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~ 550 (1020)
......+.++ .+|.++ -++. .||+|+.++|+|..++|++||+++..++.|...+
T Consensus 1065 ------------~a~~~~k~i~kw~kk~~w~~~--------~k~~-~cpdpv~~k~~p~~y~gsvsekf~~~i~~f~~~~ 1123 (1640)
T KOG0262|consen 1065 ------------KASKYIKKILKWKKKHMWFEL--------DKKI-ACPDPVLAKYNPDKYLGSVSEKFRKKIDDFDDEN 1123 (1640)
T ss_pred ------------HHHHHHHHHHHHHhhhccchh--------hccc-CCCChhhhhcchhhhhccccHHHHHHHHHHHHHh
Confidence 0000001111 112221 2334 3999999999999999999999999999998776
Q ss_pred Ccc-----hhHHHHHHHHHHhhhcccCCCCCcchhhhhcccCCccccccccccccCCccccccccChhhHHHHHHHhhcC
Q psy16767 551 TDA-----SHVDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKA 625 (1020)
Q Consensus 551 ~~~-----~~~~~~~~~~~~ky~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~ASk~ 625 (1020)
+.. -+++.|+.++..||++||++|||+||+||||||||||||||||||||||+|+|||||||||||||||+||++
T Consensus 1124 ~k~~~s~~~~~~~lr~ll~~K~~~SLa~PGE~VGvlAAQSIGEPSTQMTLNTFHfAGrGemNVTLGIPRLREIlMtASan 1203 (1640)
T KOG0262|consen 1124 AKKEKSEEPSEEKLRRLLQLKYIRSLADPGEPVGVLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASAN 1203 (1640)
T ss_pred hhhhccccchHHHHHHHHHHHHHHHhcCCCCcceeeeecccCCCcceeehhheeeccccceeeeecchHHHHHHHHHhhc
Confidence 322 356789999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeEEEEcCCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecCCC-CCcceEEEEEEecccccccccCCChhhH
Q psy16767 626 IKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPE-PHMNYQMKFCFIPAHMYRDKTSVKPSKI 704 (1020)
Q Consensus 626 iKTP~mtv~L~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~-~~~~y~i~~~l~~~~~~~~~~~i~~~~i 704 (1020)
||||+||||+.++.+. ++|..++.+|.+++|+||++++.|.+.+...++ .++.|.++|+|++.+.|..+|++++++|
T Consensus 1204 IkTP~mt~pi~~g~s~--~ra~~i~~~l~rV~L~evlk~v~vte~~t~~~~~~~~~y~lr~~~~~~~~y~~e~~v~~e~i 1281 (1640)
T KOG0262|consen 1204 IKTPSMTVPIKNGVSD--ERADDITKELRRVTLKEVLKKVGVTEKITMVENQSCKKYKLRFDLLPREEYQEEYDVRPEDI 1281 (1640)
T ss_pred cCCCceeeeccCCccH--HHHHHHHHHHHHHHHHHHHhheeeeEEEEeeccccceEEEEEEeecCHHHhhhhcCCCHHHH
Confidence 9999999999999887 899999999999999999999999999887766 4689999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCC-CcCCCCccccchhhhhhhhhhcc
Q psy16767 705 IDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALG-RVDVSSDEERDEEDAVQSHKKVN 783 (1020)
Q Consensus 705 ~~~~~~~f~~~~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~d~~~~~~~~~ 783 (1020)
.+.++..|++.+..+|+|...+. ..+.....+.+ .++..+..+.+.+ .++..+ +.+.+++++.++.|+...++..+
T Consensus 1282 ~~~m~~~Flk~L~~aI~k~~~k~-~~~~~~~~dd~-~~~~~~~~~~~~~-~~~~~~~~~~~e~~~~~ddddas~~k~~~k 1358 (1640)
T KOG0262|consen 1282 EEVMENRFLKLLERAIKKKLKKA-KYTRGMSNDDA-DPDDGNEVDNNDE-VGGEDNEDSDDESEDDEDDDDASDAKLHKK 1358 (1640)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh-HHhhccccccC-CccccccCCcccc-ccCCccccccccccccCcccchhHHHHhhh
Confidence 99999999999999998877662 11222221111 1111111110000 001111 11111111122224555677777
Q ss_pred ccccCCCCCcchHHhhh-hcccccCCCc----ccccc-----hhh-cc--cc-----hhHHHHHHhhccccceeeecccc
Q psy16767 784 QEEDNDFEEPEDEERMS-EREEDDNTSN----IGERF-----KIE-FR--DS-----TNVFVKDVVNQHNIVHKYSYDKK 845 (1020)
Q Consensus 784 ~~~~~~~~~~d~~~~~~-~~~~~~~~~~----~~~~~-----~~~-~~--~~-----~~~~i~~v~~~~~~i~~~~~d~~ 845 (1020)
..++.+||++|+++... .+.+++++++ .++.. ..+ +. +. ...+++.++..++.|+.|+||.+
T Consensus 1359 ~~~~~dYe~~de~e~~~~~~~e~~~~~e~~e~d~e~g~dg~~~~~~~~~e~~~~~~~~er~~qs~~~~~~fi~~y~fd~~ 1438 (1640)
T KOG0262|consen 1359 TEEEADYESEDEDERVEEREDEGDEDEESDEDDEEVGLDGTPEPEEEDQEGQPEVNAVERREQSVKKRHDFISRYTFDKE 1438 (1640)
T ss_pred hccccCcCCCchhhhhhhhhcccccccccccchhhcccCCCCCcccccccCCchhhHHHHHHHHHHHHHHHhhhhccccc
Confidence 77889999888754431 1111111111 00000 000 00 00 23446677777778899999999
Q ss_pred CCceEEEEe-ccc------------------cee-----------ccC---CceEEEEEeccchhhhhccCCcccccccc
Q psy16767 846 NHMWCKLLF-LPS------------------NLF-----------EEK---ESKHLLKTDGINVNFISQYRHLLDLNKLY 892 (1020)
Q Consensus 846 ~~~~~~~~~-lp~------------------~~~-----------~~~---~~e~~l~teG~nl~~~~~~~~~iD~~r~~ 892 (1020)
.++||+|.+ +|. +++ ..+ ++.-+|.|+|+||.++|.+.+++|++++|
T Consensus 1439 ~~~wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~~l~TeGVnl~a~~~~~d~LDv~~ly 1518 (1640)
T KOG0262|consen 1439 SGKWCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKSVLLTEGVNLPALFDHADILDVNRLY 1518 (1640)
T ss_pred cCcEEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCcccccccceehhcCccHHHHHHHHhhhhhhhhc
Confidence 999999999 872 121 111 22238999999999999999999999999
Q ss_pred cccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceeeeeEEeeeccccccCcchhhhhcchhHHHHH
Q psy16767 893 VNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLNPSFIQKMTFEMPLEKI 972 (1020)
Q Consensus 893 sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~G~~~~~nR~G~~~~~spl~kaSFE~t~~~L 972 (1020)
||||++|+++|||||||++|++||.+||+.|||+||+|||+||||||||+|.|.||||+||..++|||+|||||+|+.||
T Consensus 1519 SNDI~ail~tyGVEAar~~Iv~Ev~~VF~vYGIsVd~RHLsLiADYMTf~G~y~pfnR~Gm~~ssSP~qkMsFETt~~Fl 1598 (1640)
T KOG0262|consen 1519 SNDIHAILNTYGVEAARNAIVNEVNNVFKVYGISVDIRHLSLIADYMTFEGGYQPFNRMGMESSSSPLQKMSFETTCQFL 1598 (1640)
T ss_pred cchHHHHHHHhhHHHHHHHHHHHHHHhhhheeeeecHHHHHHHHHHHhhccccccccccccccCCChhHhhhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCCccCCCcccceecCCccccCccceEEeeccc
Q psy16767 973 RQASMQGREDSLRAPSARVMLGQECRQGTGLFQLRNREK 1011 (1020)
Q Consensus 973 ~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~fdll~~~~ 1011 (1020)
.+||++|+.|.|++|||||+||++++.|||+|||++++.
T Consensus 1599 ~~Aa~~g~~D~L~sPSArLvvG~~~r~GTG~Fdll~~v~ 1637 (1640)
T KOG0262|consen 1599 KQAALFGEEDELSSPSARLVVGLPVRGGTGSFDLLQKVD 1637 (1640)
T ss_pred HHHHhcCcccccCCCcceeEeccccCCCcceeeeeccCC
Confidence 999999999999999999999999999999999999875
No 2
>KOG0261|consensus
Probab=100.00 E-value=8.6e-180 Score=1536.93 Aligned_cols=844 Identities=29% Similarity=0.428 Sum_probs=644.6
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeecccccccChHHHHHHHHHHhcccCccc
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCILNTEI 76 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d~fl~~~~~~~l~~~~~~~~~~~i 76 (1020)
|||||||+ ++||||||.+||.++||+++|++|+||++.+||+|+|+||||.+|+||+|+++.|++.. +.+-...|
T Consensus 498 FDGDEMNlHvPQTEEAraEA~~LMgvknNlvTPr~GEpiiAAtQDFiTg~YLlt~KDtF~dRa~~~ql~s~-~~d~~~~i 576 (1386)
T KOG0261|consen 498 FDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIAATQDFITGGYLLTHKDTFLDRAEFSQLCSY-MSDAMTHI 576 (1386)
T ss_pred CCcccccccCCchHHHHHHHHHHhccccccccCCCCCceeehhhhhhhcceeeecccccccHHHHHHHHHH-Hhcccccc
Confidence 99999999 99999999999999999999999999999999999999999999999999999999876 44444578
Q ss_pred ccCCCccccCCCCCCCcEEEEEEccccCCCCCc--cccccccccc-cccccccCccccCccccccCceEEEeccceeeec
Q psy16767 77 RTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKV--IIRHGELLSG-ILDKKQFGSTQYGLVHAVWDTHVTIRHGELLSGI 153 (1020)
Q Consensus 77 ~l~~Pailkp~~lwTGKqv~s~~l~~~~P~~~~--~in~~~~~~~-k~~~~~~~~~~~~~~~~~~d~~v~I~~Gell~G~ 153 (1020)
.+|||||+||..||||||+||.+++ |++.. .+|+ ..+ |..... .++ +..-+.+|++|+|+|+|+++|+
T Consensus 577 ~lppPaI~KP~~LwTGKQ~fsvlir---pn~~s~v~~Nl---~~k~k~~~~~-~~k--~~~mc~nDg~v~irns~l~sG~ 647 (1386)
T KOG0261|consen 577 DLPPPAILKPVELWTGKQLFSVLIR---PNDDSPVRVNL---DAKNKNFSLV-KGK--SFEMCPNDGYVIIRNSELISGV 647 (1386)
T ss_pred CCCChhhcCceeeeccCEEEEEEec---cCCCCceEEee---ccccceeecc-cCC--CcccCCCCCeEEEecchhhhcc
Confidence 9999999999999999999999995 76432 3565 433 211000 000 0112345999999999999999
Q ss_pred cCcccccCc-chhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHHHHHHHHHHHHHHHHH
Q psy16767 154 LDKKQFGST-QYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAAC 232 (1020)
Q Consensus 154 LdK~~lG~~-~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~~~i~~a~~~~~~~~~ 232 (1020)
+||+.+|++ +.+|++.+.++||+.+|++.|+++.+|+.+||..+||||||+|+.+.+...++|.++++.++..+++.+.
T Consensus 648 ldKs~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lgnrGFSIGi~DVqPg~~L~~~k~~lv~~gY~kc~~~I~ 727 (1386)
T KOG0261|consen 648 LDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGIDDVQPGEILSQEKEELVNRGYAKCDEKIE 727 (1386)
T ss_pred cccccccCCCccceEeeehhhcchHHHHHHHHHHHHhhhhhccccccccccCCCCccHHHHHHHHHHHHhHHHHHHHHHH
Confidence 999999986 5799999999999999999999999999999999999999999999999999999999999977665554
Q ss_pred HHcCCCCCCCHHHHHHHHHHhcc---CchhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCChhHHHHhhcCCcch
Q psy16767 233 NALGLPLDTDPEIISSQLQEAYA---SIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGST 309 (1020)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~ 309 (1020)
. ++++.+ ++...+++||+.+.+.||.+|+++++.|+.. +.|.|++++|+.||||||.
T Consensus 728 e----------------~~kG~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~e----L~~~NsPliMa~CGSKGS~ 787 (1386)
T KOG0261|consen 728 E----------------YNKGKLQLQPGCNEEETLEAEILSELSTIREEAGKICIRE----LHPRNSPLIMALCGSKGSK 787 (1386)
T ss_pred H----------------HhccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh----cCcccChHHHHHhcCCCCc
Confidence 3 223333 5677889999999999999999999999974 8899999999999999999
Q ss_pred hhHHHHHhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhhhccccCCcc
Q psy16767 310 VNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSG 389 (1020)
Q Consensus 310 ~N~~Qi~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~sG 389 (1020)
+|++||.+|||||.+.|.|+|.||..|+||||++.+..|+|+|||.|||++||+|.|||||+|||||||||||||||+||
T Consensus 788 INiSQMvACVGQQ~ISG~RvPdGf~dRsLPHF~r~Sk~P~aKGFV~NSFySGLTptEFfFHtm~GREGLVDTAVKTAETG 867 (1386)
T KOG0261|consen 788 INISQMVACVGQQIISGHRVPDGFEDRSLPHFERHSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETG 867 (1386)
T ss_pred ccHHHHHHHhhhhhhcCCcCCCccccccCccccccCCCccccchhhhhcccCCCchhhheeecccccchhhhhhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhcccc-cccchhhhhhHHHHhhHHHHHhhhccCchhHH
Q psy16767 390 YLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYLT-DKQFSFLEDNIKWICSYKVILNLLKKHPLSLA 468 (1020)
Q Consensus 390 YLqRrLvk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~~-~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~ 468 (1020)
||||||||+||||.++||+|||++.|.||||.||+||+||..++.-+ +.+|..+.+|...+.+ ....+....
T Consensus 868 YMqRRLmK~LEDL~~~YDgTVR~s~~~vvqF~YG~DglDPa~mEg~~~pv~f~r~~~~~~~~~~-------~~~~~~l~~ 940 (1386)
T KOG0261|consen 868 YMQRRLMKSLEDLSVQYDGTVRNSNGDVVQFTYGGDGLDPAMMEGKDQPVNFNRVFDHAKAIFP-------HRHDPPLSS 940 (1386)
T ss_pred hHHHHHHHHHHHHHHhhcCceecCCCcEEEEeecCCCCChhhhcCCCCchhHHHHHHHHHhcCC-------CCCCCCCCH
Confidence 99999999999999999999999999999999999999999776433 3334444444333211 000110000
Q ss_pred HHHHHhhhc-CCCCCcccCCCcchhHHHHHHHHHhhcHHHHHHHHHhccCCCCCCcccCCCCcccc--cchHHHHHHHHH
Q psy16767 469 LLLLLTFKS-SGKPNFIFSPHRTKFTMDLLEQWYQLDDKARKKYRKKFKACPQPLISTFQPDAHFG--SISENLADSVVK 545 (1020)
Q Consensus 469 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~e~~~~~l~~ 545 (1020)
.+.-..+.. +.. .+....+. ++..+.++....+.+..+.....++......-|...+. .+++
T Consensus 941 ~el~e~~~~~l~~--~f~~~~~~-----F~~~~~~~i~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~t~-------- 1005 (1386)
T KOG0261|consen 941 EELDETLEEELLR--KFTEKGDP-----FVHELREFIASLSKKIKKLQDKYGDECGPKFCPDLLYQISRLTE-------- 1005 (1386)
T ss_pred HHHHHHHHHHHHH--HhhhhhhH-----HHHHHHHHHHHHHHHHHHHhhhcccccCCccCccceeeeeeccH--------
Confidence 100000000 000 00000010 11111111111111111111111111111111111110 0111
Q ss_pred HhhccCcchhHHHHHHHHHHhhhcccCCCCCcchhhhhcccCCccccccccccccCCccccccccChhhHHHHHHHhhcC
Q psy16767 546 YTKGRTDASHVDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKA 625 (1020)
Q Consensus 546 ~~~~~~~~~~~~~~~~~~~~ky~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~ASk~ 625 (1020)
-+.+.|.+.|..||+++.++||.+||+|||||||||+|||||+|||||||++||+||||||++||| ||||+
T Consensus 1006 --------kql~~f~~~~~~ky~~a~~EpGTavGAi~aQSIGEPGTQMTLKTFHFAGVASMNiTlGVPRIkEII-NAsk~ 1076 (1386)
T KOG0261|consen 1006 --------KQLEKFVERCLDKYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEII-NASKT 1076 (1386)
T ss_pred --------HHHHHHHHHHHHHHHhhhcCCcchhhhhhcccCCCCCceeeeeeeeecceeeeeeccCcchHHHHH-hhhcc
Confidence 134568889999999999999999999999999999999999999999999999999999999999 89999
Q ss_pred CCCCeEEEEcCCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecCCCCCcceEEEEEEecccccccccCCChhhHH
Q psy16767 626 IKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMNYQMKFCFIPAHMYRDKTSVKPSKII 705 (1020)
Q Consensus 626 iKTP~mtv~L~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~~~~~y~i~~~l~~~~~~~~~~~i~~~~i~ 705 (1020)
|+||+|+..|.++.+. ..|+.|+.+|++++|+||++++++.+ .|+.. ...+.+.+..-.. -...+++..|.
T Consensus 1077 ISTPIItA~L~n~~d~--~~Ar~VKgRiEKt~L~dv~~yieeV~----~p~~~-fl~i~vd~~~I~~--l~L~i~~~~I~ 1147 (1386)
T KOG0261|consen 1077 ISTPIITAELENPHDE--RSARVVKGRIEKTTLGDVCSYIEEVY----GPDSC-FLLIRVDLKRISL--LQLEITIESIA 1147 (1386)
T ss_pred cCccceeeeecCchhH--HHHHHHhhhhhhhhHHHHHHHHHHHh----CCcce-EEEEEecHhHHhh--hhccccHHHHH
Confidence 9999999999988766 89999999999999999999987633 33211 1122222211000 02223333222
Q ss_pred HHHHHHHHHHHHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccchhhhhhhhhhcccc
Q psy16767 706 DHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQE 785 (1020)
Q Consensus 706 ~~~~~~f~~~~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 785 (1020)
..+. ++ . ..+....++.... .. .++....
T Consensus 1148 ~sI~----------------~s----~---~~k~~~~~v~v~~--------------------------~~--~~~v~~~ 1176 (1386)
T KOG0261|consen 1148 YSIL----------------KS----P---KRKVKPNDVRVVG--------------------------ET--TLRVTPV 1176 (1386)
T ss_pred HHHh----------------cC----C---ccccCCcceEEec--------------------------ce--eEEEeec
Confidence 2111 10 0 0000001111000 00 0000000
Q ss_pred ccCCCCCcchHHhhhhcccccCCCcccccchhhcccchhHHHHHHhhccccceeeeccccCCceEEEEe--ccc----ce
Q psy16767 786 EDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLF--LPS----NL 859 (1020)
Q Consensus 786 ~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~i~~~~~d~~~~~~~~~~~--lp~----~~ 859 (1020)
. +.+ .....+++.++...+ .+.+ +|. ++
T Consensus 1177 ~-----~~~--------------------------~S~~~~lq~lk~~L~---------------~Vvv~gip~vnr~vi 1210 (1386)
T KOG0261|consen 1177 S-----DTK--------------------------SSVYYNLQRLKRSLP---------------NVVVKGIPEVNRAVI 1210 (1386)
T ss_pred c-----ccc--------------------------chhhhhHHHHHhhCC---------------ceEEecCcchhhhhe
Confidence 0 000 001234444443222 1222 554 23
Q ss_pred e-ccCCceEEEEEeccchhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcchhhhhccc
Q psy16767 860 F-EEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADY 938 (1020)
Q Consensus 860 ~-~~~~~e~~l~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~ 938 (1020)
. ..+.+.|.|.+||.||+++++. ++|+-.||.||+|.+|.++|||||||.+||+||..+|..+|++||+||++||||+
T Consensus 1211 ~~de~~~~y~L~vEG~gLr~Vm~t-~GV~g~~TtsNnv~Ev~~vLGIEAAR~~II~EI~ytM~~HGmsiD~RHiMLLaDv 1289 (1386)
T KOG0261|consen 1211 NIDEKRGLYKLLVEGTGLRAVMNT-DGVKGRRTTSNNVLEVEKVLGIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADV 1289 (1386)
T ss_pred eecccCCceEEEEeccchHHHhcc-CCccccccccCceEEeehhhchHHHHHHHHHHHHHHHHhcCcccCHHHHHHHHHH
Confidence 2 2234449999999999999999 5789999999999999999999999999999999999999999999999999999
Q ss_pred ceeeeeEEeeecccccc-CcchhhhhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCccceEEeecccc
Q psy16767 939 MTHSGTYVAMNRNGIRL-NPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLFQLRNREKK 1012 (1020)
Q Consensus 939 MT~~G~~~~~nR~G~~~-~~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~fdll~~~~~ 1012 (1020)
|||+|++.||+|+|+.+ ..|.|+.||||+|.++|++||.+|.+|.+.|||+|||+|.|.++|||.|+|+|.-+.
T Consensus 1290 MTyrGEVlGITRfGl~KM~~SVL~lASFEkT~DhLF~AA~~~k~D~I~GVSEcIIlG~pm~iGTG~fkl~~~~~~ 1364 (1386)
T KOG0261|consen 1290 MTYRGEVLGITRFGLAKMKDSVLMLASFEKTADHLFDAAAYGKKDAIEGVSECIILGIPMCIGTGIFKLLQRTDD 1364 (1386)
T ss_pred hhhcceeeeeeehhhHHHHHHHHHHHhhhhhhHHHHHHHHhcCcccccchhhheecccceeccccHHHHHHhcCC
Confidence 99999999999999998 699999999999999999999999999999999999999999999999999997665
No 3
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=8.6e-177 Score=1655.93 Aligned_cols=813 Identities=26% Similarity=0.359 Sum_probs=631.3
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeecccccccChHHHHHHHHHHhcccCccc
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCILNTEI 76 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d~fl~~~~~~~l~~~~~~~~~~~i 76 (1020)
|||||||+ |++|||||++||++++||+||++|+|++|++||+|+|+|+||.+|+||+++++++|+|+ .+. ..
T Consensus 474 FDGDEMNlHvPQS~eArAEa~~Lm~v~~niisP~~G~Pi~gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~--~~~--~~ 549 (1321)
T PRK14977 474 FDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAML--AGI--TD 549 (1321)
T ss_pred cccceeeeecCCCHHHHHHHHHHHhhhhcEecCCCCCeeEEeehhhhhhhhhhccCcccCCHHHHHHHHHh--CCC--cc
Confidence 99999999 99999999999999999999999999999999999999999999999999999999997 222 13
Q ss_pred ccCCCccc-cCCCCCCCcEEEEEEccccCCCCCccccccccccc-cccccccCccccCccccccCceEEEeccceeeecc
Q psy16767 77 RTLPPTIW-KPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSG-ILDKKQFGSTQYGLVHAVWDTHVTIRHGELLSGIL 154 (1020)
Q Consensus 77 ~l~~Pail-kp~~lwTGKqv~s~~l~~~~P~~~~~in~~~~~~~-k~~~~~~~~~~~~~~~~~~d~~v~I~~Gell~G~L 154 (1020)
.+|+|||+ ||.+|||||||||++| |.+ +|+ ..+ +.+...|+. +..+.+..|++|+|+||||++|+|
T Consensus 550 ~lp~PaI~~kp~~lwTGKQi~s~iL----p~~---~n~---~~~~~~~~~~~~~--~~~~~~~~d~~v~I~~geLl~G~l 617 (1321)
T PRK14977 550 PLPEPAIKTKDGPAWTGKQLFSLFL----PKD---FNF---EGIAKWSAGKAGE--AKDPSCLGDGYVLIKEGELISGVI 617 (1321)
T ss_pred ccCCCceecCCCCeeeHHHHHHHHc----CCC---CCc---eeccccccccccc--ccccCCCCcceEEeecCeEEeeec
Confidence 58999999 9999999999999998 875 566 444 444444431 011123458999999999999999
Q ss_pred CcccccC---cchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHHHHHHHHHHHHHHHH
Q psy16767 155 DKKQFGS---TQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAA 231 (1020)
Q Consensus 155 dK~~lG~---~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~~~i~~a~~~~~~~~ 231 (1020)
||+++|+ +++||+|.+|++||+++|..||+++++|+++||+.+|||||++|++++++..+++.+.++++...+.+++
T Consensus 618 dK~~~G~~~~~~~~Lih~i~~~yG~~~a~~fL~~l~~l~~~~L~~~GFSigi~D~~~~~~~~~~i~~~i~~~~~~v~~l~ 697 (1321)
T PRK14977 618 DDNIIGALVEEPESLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLI 697 (1321)
T ss_pred chHhhccccCCCCcHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEEeeCcEecCHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999998 7889999999999999999999999999999999999999999999999988888888888877766655
Q ss_pred HHHcCCCCCCCHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCChhHHHHhhcCCcchhh
Q psy16767 232 CNALGLPLDTDPEIISSQLQEAYASIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVN 311 (1020)
Q Consensus 232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~N 311 (1020)
+.+. ...... .+.... ...++.+..+++|..+.+.|+++++.+++.+.. .+.|+|++++|+.||||||++|
T Consensus 698 ~~~~-~~~~i~--~~~~~~--~~~~G~~~~~~~e~~i~~~l~~~r~~~~~~~~~----~l~~~N~l~~Mv~SGAKGS~~N 768 (1321)
T PRK14977 698 DQRK-ITRKIT--IYKGKE--ELLRGMKEEEALEADIVNELDKARDKAGSSAND----CIDADNAGKIMAKTGARGSMAN 768 (1321)
T ss_pred HHHh-hhcccc--ccccch--hcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH----hcCCCCcHHHHhhcccccCHHH
Confidence 4321 000000 000000 012455677888999999999999988887654 2568999999999999999999
Q ss_pred HHHHHhhccceeec--------CCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhhhcc
Q psy16767 312 TMQISCLLGQIELE--------GKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAV 383 (1020)
Q Consensus 312 ~~Qi~~~lGQQ~l~--------G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiDTAv 383 (1020)
++||+||||||+++ |+|||.|++|||||||.++|.+|+|+|||.|||++||+|+||||||||||||||||||
T Consensus 769 i~Qi~~~lGQQ~ve~~~~~~~~G~Ri~~~~~~RtLPhF~~~d~~p~a~GfV~nsFl~GL~P~EfFFHaM~GREGLiDTAV 848 (1321)
T PRK14977 769 LAQIAGALGQQKRKTRIGFVLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKAR 848 (1321)
T ss_pred HHHHHhccccccccccccccCCCCCCcCCCCCCcCCCCCCCCCCcccccchhhhhcCCCCHHHHHHHhhccccccccccc
Confidence 99999999999999 9999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCcchhHHHHHhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhcccccccchhhhhhHHHHhhHHHHHhhhccC
Q psy16767 384 KTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYLTDKQFSFLEDNIKWICSYKVILNLLKKH 463 (1020)
Q Consensus 384 KTa~sGYLqRrLvk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~ 463 (1020)
|||+||||||||||+||||+|+||+||||++|+||||.||+||+||++.+++.+.+++.+..+.... ..
T Consensus 849 KTA~SGYLQRrLvk~lEDl~v~YD~TVR~s~g~iiQF~YGeDG~d~~~~~~~~~~n~~~~~~~~~~~---------~~-- 917 (1321)
T PRK14977 849 RTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKLDHGEAFNLERIIEKQKIE---------DR-- 917 (1321)
T ss_pred ccCcCchhHHHHHHHhcceEEecCCeEEeCCCCEEEEeecCCCcCHHHhccCCcccHHHHHHHhhhh---------cc--
Confidence 9999999999999999999999999999999999999999999999998765543333322221100 00
Q ss_pred chhHHHHHHHhhhcCCCCCcccCCCcch-hHHHHHHHHHhhcHHHHHHHHHhccCCCCCCcccCCCCcccccchHHHHHH
Q psy16767 464 PLSLALLLLLTFKSSGKPNFIFSPHRTK-FTMDLLEQWYQLDDKARKKYRKKFKACPQPLISTFQPDAHFGSISENLADS 542 (1020)
Q Consensus 464 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 542 (1020)
..+... ....+.+. |.+. +++ .+...+...
T Consensus 918 ----------------------~~~~~~~~~~~~~~~-----------~~~~-----------~~~-----~~~~~~~~~ 948 (1321)
T PRK14977 918 ----------------------GKGASKDEIEELAKE-----------YTKT-----------FNA-----NLPKLLADA 948 (1321)
T ss_pred ----------------------ccCCCHHHHHHHHHH-----------HHHh-----------hhh-----hhHHHHHHH
Confidence 000000 00011111 1000 000 000111111
Q ss_pred HHHHhhccCcchhHHHHHHHHHHhhhcccCCCCCcchhhhhcccCCccccccccccccCCccccccccChhhHHHHHHHh
Q psy16767 543 VVKYTKGRTDASHVDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMA 622 (1020)
Q Consensus 543 l~~~~~~~~~~~~~~~~~~~~~~ky~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~A 622 (1020)
+..+- -......+|...++.+|.+++|+||||||+|||||||||+|||||||||+||++++|||+|||||+||| +|
T Consensus 949 ~~~~~---~~~~~~~~~~~~~~~~~~~~~~~pGe~VG~iaAQSiGEP~TQmTLnTFH~AGv~~~nvt~GvpRl~Eii-~a 1024 (1321)
T PRK14977 949 IHGAE---LKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELV-DA 1024 (1321)
T ss_pred HHHcC---CCHHHHHHHHHHHHHHHHhcccCCcccchhhhhhhccCceeeecccccccccccccCcccCccchHHhh-hc
Confidence 11110 000123455666799999999999999999999999999999999999999999999999999999999 89
Q ss_pred hcCCCCCeEEEEcCCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecCCCCCcceEEEEEEecccccccccCCChh
Q psy16767 623 TKAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMNYQMKFCFIPAHMYRDKTSVKPS 702 (1020)
Q Consensus 623 Sk~iKTP~mtv~L~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~~~~~y~i~~~l~~~~~~~~~~~i~~~ 702 (1020)
+|+||||+|+++|.++...+++.|++++.+|++++|+||++++.+.+ +++ ...+ ..+......+.++++
T Consensus 1025 ~k~~~tp~m~~~l~~~~~~~~~~a~~v~~~ie~~~l~~~~~~~~i~~----~~~-----~~~i--~~d~~~i~~~~i~~~ 1093 (1321)
T PRK14977 1025 RAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDN----ANE-----IKLI--KPDKRALENGCIPME 1093 (1321)
T ss_pred ccCCCCCeEEEEeCCcccchHHHHHHHHhheeeeEHHHhhhheEeec----cCC-----ceEE--ecCHHHHHhcCCCHH
Confidence 99999999999999876666688999999999999999999887643 332 1122 223333344556554
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccchhhhhhhhhhc
Q psy16767 703 KIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKV 782 (1020)
Q Consensus 703 ~i~~~~~~~f~~~~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~ 782 (1020)
.|.+.+... ... ..+. +. .++ + ++..
T Consensus 1094 ~i~~~i~~~------------~~~--~~~~-----------~~--------------------~~~-----~----~i~~ 1119 (1321)
T PRK14977 1094 RFAEIEAAL------------AKG--KKFE-----------ME--------------------LED-----D----LIIL 1119 (1321)
T ss_pred HHHHHHHHh------------hcC--CceE-----------Ee--------------------ecC-----C----EEEE
Confidence 433321100 000 0000 00 000 0 0000
Q ss_pred cccccCCCCCcchHHhhhhcccccCCCcccccchhhcccchhHHHHHHhhccccceeeeccccCCceEEEEe--ccc---
Q psy16767 783 NQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLF--LPS--- 857 (1020)
Q Consensus 783 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~i~~~~~d~~~~~~~~~~~--lp~--- 857 (1020)
...+ .++.+. ....++.+..... .+++ +|.
T Consensus 1120 ~~~~---~~~~~~---------------------------~~~~l~~l~~~l~---------------~~~i~Gi~~I~r 1154 (1321)
T PRK14977 1120 DLVE---AADRDK---------------------------PLATLIAIRNKIL---------------DKPVKGVPDIER 1154 (1321)
T ss_pred ecCc---ccccch---------------------------HHHHHHHHHHhcC---------------CcEEecCCCceE
Confidence 0000 000000 0011222221100 1111 222
Q ss_pred -ce---eccCCceEEEEEeccchhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcchhh
Q psy16767 858 -NL---FEEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLS 933 (1020)
Q Consensus 858 -~~---~~~~~~e~~l~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~ 933 (1020)
++ .+.+.++|+|+|||+||.++|.++ .||+.||+||||++|+++|||||||++|++||++||+.||++||+|||.
T Consensus 1155 ~~i~~~~~~~~~e~~l~teG~nl~~vl~~~-~Vd~~rt~sN~i~ei~~~lGIEAaR~~ii~Ei~~v~~~~G~~V~~rHi~ 1233 (1321)
T PRK14977 1155 AWVELVEKDGRDEWIIQTSGSNLAAVLEMK-CIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIM 1233 (1321)
T ss_pred EEEEeeccCCCeeEEEEecCcCHHHHhCCC-CCcccccEECCHHHHHHhhhHHHHHHHHHHHHHHHHHHcCCccCHHHHH
Confidence 11 122346899999999999999995 6899999999999999999999999999999999999999999999999
Q ss_pred hhcccceeeeeEEeee------cccccc-CcchhhhhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCccceEE
Q psy16767 934 LVADYMTHSGTYVAMN------RNGIRL-NPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLFQL 1006 (1020)
Q Consensus 934 LlAD~MT~~G~~~~~n------R~G~~~-~~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~fdl 1006 (1020)
||||+||++|.+.++| ||||++ ++|||++||||+|+++|++||++|+.|.|+|||+|||+|+++|+|||+|||
T Consensus 1234 LlaD~MT~~G~~~~i~~~~~~~R~Gi~~~~~s~l~~asFE~t~~~L~~AA~~g~~D~l~gvsenii~G~~~~~GTG~~~L 1313 (1321)
T PRK14977 1234 LVADIMCSRGTIEAIGLQAAGVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDL 1313 (1321)
T ss_pred HHHHHHccCceEEeccccccccccccccCCCCHHHhcCHHHHHHHHHHHHHhcCcCccCChHHhhhcCCCccCccceEEE
Confidence 9999999999999999 999998 599999999999999999999999999999999999999999999999999
Q ss_pred eeccccc
Q psy16767 1007 RNREKKK 1013 (1020)
Q Consensus 1007 l~~~~~~ 1013 (1020)
+++..++
T Consensus 1314 l~~~~~~ 1320 (1321)
T PRK14977 1314 LMDFSGK 1320 (1321)
T ss_pred EeccccC
Confidence 9998775
No 4
>KOG0260|consensus
Probab=100.00 E-value=1.5e-163 Score=1427.23 Aligned_cols=898 Identities=31% Similarity=0.420 Sum_probs=649.6
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeecccccccChHHHHHHHHHHhcccCccc
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCILNTEI 76 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d~fl~~~~~~~l~~~~~~~~~~~i 76 (1020)
|||||||+ |++||||+.+|+++++||++||+|+|++|++||+|+|++++|.||+|++++++|||+|+ +..|++
T Consensus 474 FDGDemnlhvPQS~etkAEl~EL~~vpkQiispQsnkpvmgivQDTLta~R~~t~Rd~Fl~r~~vmnLlm~-~p~~d~-- 550 (1605)
T KOG0260|consen 474 FDGDEMNLHVPQSLETKAELEELAMVPKQIISPQSNKPVMGIVQDTLTAVRKMTKRDVFLNRAQVMNLLMY-VPDWDG-- 550 (1605)
T ss_pred CCCceeecccCcchhHHHHHHHHhhhhhhhcCCcCCCcceeeehhhHHHHHHHhhHhhhhcHHHHHHHHhh-ccccCC--
Confidence 99999999 99999999999999999999999999999999999999999999999999999999998 456655
Q ss_pred ccC-CCccccCCCCCCCcEEEEEEccccCCCCCccccccccccc-cccccccCccccCccccccCceEEEeccceeeecc
Q psy16767 77 RTL-PPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSG-ILDKKQFGSTQYGLVHAVWDTHVTIRHGELLSGIL 154 (1020)
Q Consensus 77 ~l~-~Pailkp~~lwTGKqv~s~~l~~~~P~~~~~in~~~~~~~-k~~~~~~~~~~~~~~~~~~d~~v~I~~Gell~G~L 154 (1020)
..| +|||+||+|||||||||++++ |.++.++-. .+. -.....|. ...|+.|+|.+|+++.|+|
T Consensus 551 ~~Pa~pai~Kp~PlWTGkQifslii----P~~in~~r~---~s~h~d~~~~~~--------~p~dt~~lie~g~l~~g~l 615 (1605)
T KOG0260|consen 551 PPPAKPAILKPKPLWTGKQIFSLII----PGGINYIRD---HSTHPDSEDELI--------SPGDTRVLIEGGELLIGVL 615 (1605)
T ss_pred CCCCCcccCCCCcccchhhheeeec----CCCcceecc---cccCcCCCcccc--------cCCCceEEEeCCceEEEEe
Confidence 567 899999999999999999999 987433322 211 11111222 2247899999999999999
Q ss_pred CcccccCcchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHHHHHHHHHHHHHHHHHHH
Q psy16767 155 DKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAACNA 234 (1020)
Q Consensus 155 dK~~lG~~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~~~i~~a~~~~~~~~~~~ 234 (1020)
+|+.+|++.++|+|++|.+.|++.|+.|.+.+|+|.+.||...|||+||+|.+..++....++..|.+|+..+.++++++
T Consensus 616 ~Kkt~G~s~g~lvh~i~~e~Gp~~~~~f~~~iQ~lin~wll~~gfsigIgDtiad~~t~~~iq~~I~~ak~dv~~vi~~a 695 (1605)
T KOG0260|consen 616 CKKTVGSSAGGLVHVIFLEKGPKIARGFFDSIQTLINSWLLREGFSIGIGDTIADAATMCVIQNTIKEAKRDVLAVIREA 695 (1605)
T ss_pred eccccccccCceEEEeehhhCHHHHHHHHHHHHHHHHHHHHhcCccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998888765
Q ss_pred cCCCCCCCHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCChhHHHHhhcCCcchhhHHH
Q psy16767 235 LGLPLDTDPEIISSQLQEAYASIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVNTMQ 314 (1020)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~N~~Q 314 (1020)
.+- +++ . -++.+..++++..++.+||+++++.+..... .+...|++..|+.+|||||.+||+|
T Consensus 696 ~~~-------~L~-----~-~pg~tlretfe~~v~~vlndArd~~gssA~~----sl~esNn~k~Mv~aGSKGs~inisQ 758 (1605)
T KOG0260|consen 696 QNN-------ELE-----P-TPGRTLRETFENKVNRVLNDARDKSGSSAQK----SLSESNNFKTMVVAGSKGSFINISQ 758 (1605)
T ss_pred hhc-------ccc-----C-CcchhHHHHHHHHHHHHHHHHHHhhhhHHHh----hhhhcccHHHHHhhcCCCcceehhh
Confidence 431 111 0 1456788999999999999999998765543 3556899999999999999999999
Q ss_pred HHhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhhhccccCCcchhHHH
Q psy16767 315 ISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRC 394 (1020)
Q Consensus 315 i~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYLqRr 394 (1020)
+++|+|||++||+|||+||.+||||||.++|++|+++|||.|||++||+|+|||||||||||||||||||||++||||||
T Consensus 759 ~saCVGqQnVEgkrIpFGF~~Rtlphf~kDdysPesrGfVENSyL~GLtP~EfFfHamggREglidtavktaEtGyiqRR 838 (1605)
T KOG0260|consen 759 VSACVGQQNVEGKRIPFGFPKRTLPHFSKDDYSPESRGFVENSYLTGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRR 838 (1605)
T ss_pred hhhhhccccccccccccCCCcccccccccCCCCccccceeecccccCCCHHHHHHHHhcccchhhhhhhcccccchHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhcccccccchhhhhhHHHHhh---HHHHH-hhhcc------C-
Q psy16767 395 LVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYLTDKQFSFLEDNIKWICS---YKVIL-NLLKK------H- 463 (1020)
Q Consensus 395 Lvk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~~~~~~~~~~~n~~~~~~---~~~~~-~~~~~------~- 463 (1020)
|||+|||++|+|||||||+-|++|||.||+||+|..-.++.+ ++.+.-....++. |..+. ++... .
T Consensus 839 L~kameDimv~yDgTVRNs~gqviQf~YGeDG~d~~~vE~q~---~~~l~~~~a~f~~~~~~d~ld~~~~~~~~~~~~e~ 915 (1605)
T KOG0260|consen 839 LMKAMEDIMVAYDGTVRNSLGQVIQFKYGEDGLDGHPVEFQN---GETLGSLNACFESEFAYDALDEPISLSSEEVVNEI 915 (1605)
T ss_pred HHHHHHHHHhhcCcceecccceeEEEEeccCccccceeeccc---cccccchHHHHHhhhhhhhhcCcccchhhhHhhhh
Confidence 999999999999999999999999999999999987655433 3333322222211 11111 01000 0
Q ss_pred --chhHHHHHHHhhhcCCCCC----cccCCCcch-----hHHHHHH-HHHhhcHHHHH-------HHHHhccCCCCCCcc
Q psy16767 464 --PLSLALLLLLTFKSSGKPN----FIFSPHRTK-----FTMDLLE-QWYQLDDKARK-------KYRKKFKACPQPLIS 524 (1020)
Q Consensus 464 --~~~~~~~~~~~~~~~~~~~----~~~~~~~~~-----~~~~~~~-~~~~~~~~~~~-------~~~~~~~~~~~~~~~ 524 (1020)
...+...+...|.++...+ .+...+..+ ..+.++. +...+.-+.+. +..+-...+..++.+
T Consensus 916 ~~~~~l~~lle~e~~~l~~dr~~l~~i~~~g~~k~~lp~n~~r~I~Na~~~f~~~~r~~t~l~~~~v~~g~~~l~e~l~i 995 (1605)
T KOG0260|consen 916 SELLKLQNLLECEYKKLVRDRRVLLYIFEYGDAKWPLPENLQRIIWNALKKFSIDERKPTDLIPFKVVKGVKELAEKLVI 995 (1605)
T ss_pred hhhHHHHHHHHHHHHhhhhhhhhhhhhcccCCcccccchhHHHHHHHHHhhcccccccccccchhhhhhhhhhhhheeEE
Confidence 0001122222233322111 112222211 0111111 00000000000 000000001111111
Q ss_pred cCCCCcccccchHHHHHHHHH------HhhccCcchhHHHHHHH---HHHhhhcccCCCCCcchhhhhcccCCccccccc
Q psy16767 525 TFQPDAHFGSISENLADSVVK------YTKGRTDASHVDKFYDM---IFYKNLLSLANPGENVGVLAAQSIGEPSTQMTL 595 (1020)
Q Consensus 525 ~~~~~~~~~~~~e~~~~~l~~------~~~~~~~~~~~~~~~~~---~~~ky~~slv~pGe~VG~iAAQSIGEP~TQmTL 595 (1020)
. +-..++......|+-+|+- .+..+. ++.++|.++ ++.+|.++.+.|||+||++||||||||+|||||
T Consensus 996 v-~g~~~~sraqrl~~~lLrs~l~~krv~~e~r--ls~eaf~w~~~~Ie~~f~qa~a~pgemvg~lAaqsvgePatqmTl 1072 (1605)
T KOG0260|consen 996 V-RGEDYISRAQRLFNILLRSTLATKRVLEEYR--LSSEAFEWVLGEIEARFLQAEASPGEMVGALAAQSVGEPATQMTL 1072 (1605)
T ss_pred e-eCchhHHHHHHHHHHHHHhhHHHHHHHHHhc--ccHHHHHHHhhhhhhheeeeecCccchHhHHHHHHhCCchhhccc
Confidence 0 0010111101111112211 111111 466666554 788999999999999999999999999999999
Q ss_pred cccccCCccccccccChhhHHHHHHHhhcCCCCCeEEEEcCCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecCC
Q psy16767 596 NTFHFAGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISP 675 (1020)
Q Consensus 596 nTFH~AG~~~~nvTlGvPRLkEIi~~ASk~iKTP~mtv~L~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~ 675 (1020)
||||+|||+++|||+||||||||+ |.+|++|||+++|+|..+.....+.|+.|+.+|++++|+++.....+ +|+|
T Consensus 1073 ntfh~aGVssknVt~gvprlkei~-Nv~k~~ktpsLtV~l~g~~~k~~e~ak~v~~~le~ttl~~vt~~t~i----~ydp 1147 (1605)
T KOG0260|consen 1073 NTFHYAGVSSKNVTLGVPRLKEII-NVAKNAKTPSLTVYLTGEAAKDNEWAKLVQCCLEHTTLKDVTRATEI----YYDP 1147 (1605)
T ss_pred chhcccceeeeeeeccCcchhhhh-hhhccCCCceEEEEecchhhcchHHHHHHhhhcccccHHhhhccCcc----eecC
Confidence 999999999999999999999999 77899999999999998776666899999999999999999877666 4455
Q ss_pred CCCcceEEE--EEEecccccccccCCChhhHHHHHHHHHHHHHHHHHHHHHHccccccccccccccc--cCCCCcccCCc
Q psy16767 676 EPHMNYQMK--FCFIPAHMYRDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQM--EDDVEDDEGEG 751 (1020)
Q Consensus 676 ~~~~~y~i~--~~l~~~~~~~~~~~i~~~~i~~~~~~~f~~~~~~~i~k~~~k~~~~~~~~~~~~~~--~~~~~~~~~~~ 751 (1020)
+... +.|. .+|+. .|.+--..+..+|..+ +++..+++.+. ..+ ...++++..++.. ..++..
T Consensus 1148 dp~~-tvI~ed~e~v~--a~~e~pd~D~~~ispw----lLrlelDr~~m-~dk-~ltm~~ia~~i~~~f~~d~~~----- 1213 (1605)
T KOG0260|consen 1148 DPQS-TVIDEDREFVV--AYYEMPDEDVGRISPW----LLRLELDRASM-TDK-KLTMEQIAEKINRGFGSDLAC----- 1213 (1605)
T ss_pred CCcc-eeeccchhhHH--hhhcCcccchhhcChH----HHHhhhhhhhc-ccc-cccHHHHHHHHHhhccCCCce-----
Confidence 4322 1211 11110 0111111122223332 22333322111 111 1223332222211 112111
Q ss_pred cccccccCCCcCCCCccccchhhhhhhhhhccccccCCCCCcchHHhhhhcccccCCCcccccchhhcccchhHHHHHHh
Q psy16767 752 AEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVV 831 (1020)
Q Consensus 752 ~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~ 831 (1020)
..+|+++ +....++|.-+ + + +++.. ...+....
T Consensus 1214 ------------i~~ddna---~klv~r~ri~~--~----~-e~D~~-------------------------l~~Ie~~m 1246 (1605)
T KOG0260|consen 1214 ------------IFSDDNA---EKLVLRLRIAK--E----E-EDDVF-------------------------LKCIEANM 1246 (1605)
T ss_pred ------------eecccCC---cceEEEEEecC--c----c-chhHH-------------------------HHHHHHhh
Confidence 1122222 11222333211 1 0 11000 01111111
Q ss_pred hccccceeeeccccCCceEEEEecc---cceeccCCceEEEEEeccchhhhhccCCcccccccccccHHHHHHhhhHHHH
Q psy16767 832 NQHNIVHKYSYDKKNHMWCKLLFLP---SNLFEEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAA 908 (1020)
Q Consensus 832 ~~~~~i~~~~~d~~~~~~~~~~~lp---~~~~~~~~~e~~l~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAa 908 (1020)
-. .+.-.... ...+|.+.| +.. +.-++|+|+|+|+||..++..++ ||..||+|||+-+|++++||||+
T Consensus 1247 l~--~~~l~G~~----~i~kV~m~~~~~G~f--~~~~ew~LeTdg~~l~~v~s~~~-vD~~rt~sn~l~ei~~vlgIea~ 1317 (1605)
T KOG0260|consen 1247 LG--DMTLRGIP----DIFKVYMSPTEDGEF--KPVDEWDLETDGVNLRRVLSEPD-VDPARTTSNDLVEIAEVLGIEAV 1317 (1605)
T ss_pred hh--hcccCCcc----ccceEEEeecCCCce--eecceeEEecCchhHHhhhccCC-CCcccccccchhhhhhhhcHHHH
Confidence 00 00000000 001111100 011 13478999999999999999975 89999999999999999999999
Q ss_pred HHHHHHHHHhhhhccCcccCcchhhhhcccceeeeeEEeeecccccc-CcchhhhhcchhHHHHHHHHHhcCCCccCCCc
Q psy16767 909 NRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRL-NPSFIQKMTFEMPLEKIRQASMQGREDSLRAP 987 (1020)
Q Consensus 909 r~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~G~~~~~nR~G~~~-~~spl~kaSFE~t~~~L~~AA~~g~~D~l~sv 987 (1020)
|.++++|+..|...+|.+||+||+.|++|+||++|.+++++|||+++ .+++|+|||||+|++.|++||+++++|.++|+
T Consensus 1318 r~a~~~e~~~vi~f~gsyVnyrhlaLl~dvmT~~g~lm~itRhg~nr~~tgaLmrcSfEetv~il~~aa~~~ekd~~rgv 1397 (1605)
T KOG0260|consen 1318 RKALLRELLNVISFDGSYVNYRHLALLCDVMTARGHLMAITRHGINRQDTGALMRCSFEETVDILMDAAAHAEKDPCRGV 1397 (1605)
T ss_pred HhhhhhhhhheEeecccchhHHHHHHHHHHHhcccceeeeeccccchhhccccccccHHHHHHHHHHHHhhhccCCCccc
Confidence 99999999999999999999999999999999999999999999999 49999999999999999999999999999999
Q ss_pred ccceecCCccccCccceEEeecccccc
Q psy16767 988 SARVMLGQECRQGTGLFQLRNREKKKK 1014 (1020)
Q Consensus 988 Sa~Ii~Gk~~~~GTG~fdll~~~~~~~ 1014 (1020)
|++|++||.+++|||+|||+.+.++-+
T Consensus 1398 sEnImlgqlap~gTg~~d~~ld~e~l~ 1424 (1605)
T KOG0260|consen 1398 SENIMLGQLAPMGTGCFDLMLDAEKLK 1424 (1605)
T ss_pred eeeeeecccccCCCcceeeeccHHhhh
Confidence 999999999999999999999976644
No 5
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=7.2e-104 Score=970.82 Aligned_cols=628 Identities=25% Similarity=0.374 Sum_probs=435.0
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeecccc--------cccChHHHHHHHHHH
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRD--------TFLTRAEYMNLVYQA 68 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d--------~fl~~~~~~~l~~~~ 68 (1020)
|||||||| |++|||||+.||++++||+||++|+|+++|+||+|+|+|+||.++ .|+++++++++.+.+
T Consensus 451 FDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~ 530 (1156)
T PRK00566 451 FDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENG 530 (1156)
T ss_pred cccceeEEecCCCHHHHHHHHHHhCCcccEEecCCCCeeEEeehhhhhhhheeecccccccCCCceeCCHHHHHHHHHcC
Confidence 99999999 999999999999999999999999999999999999999999988 899999999876543
Q ss_pred hcccCcccccCCCccccCCCCCCCcEEEEEEccccCCCCCccccccccccccccccccCccccCccccccCceEEEeccc
Q psy16767 69 LCILNTEIRTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSGILDKKQFGSTQYGLVHAVWDTHVTIRHGE 148 (1020)
Q Consensus 69 ~~~~~~~i~l~~Pailkp~~lwTGKqv~s~~l~~~~P~~~~~in~~~~~~~k~~~~~~~~~~~~~~~~~~d~~v~I~~Ge 148 (1020)
..+.+..+.+++|.. +....|||||+|+.+| |++++++|.
T Consensus 531 ~i~l~~~i~~~~~~~-~~i~tt~Gk~if~~il----P~~~~~~n~----------------------------------- 570 (1156)
T PRK00566 531 EVDLHARIKVRITSK-KLVETTVGRVIFNEIL----PEGLPFINV----------------------------------- 570 (1156)
T ss_pred CCCCCCeEEecCCCC-ceEEcCcHHHHHHhhc----cccceeecc-----------------------------------
Confidence 233333333333310 1234799999999888 886543221
Q ss_pred eeeeccCcccccCcchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHHHHHHHHHHHHH
Q psy16767 149 LLSGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGT 228 (1020)
Q Consensus 149 ll~G~LdK~~lG~~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~~~i~~a~~~~~ 228 (1020)
+|++||+++| +|||.+|+.||++.|+.|||++++|+++|++.+|||||++|+.+|++ |.++++++++++.
T Consensus 571 --~g~ldKk~Lg----~LI~~i~~~yG~~~t~~~LD~ik~Lgf~yat~~GfSigi~Dl~ip~~----K~~ii~~a~~~v~ 640 (1156)
T PRK00566 571 --NKPLKKKEIS----KIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPE----KKEIIEEAEKEVA 640 (1156)
T ss_pred --cceecHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEeehhhcCcChH----HHHHHHHHHHHHH
Confidence 5799999998 79999999999999999999999999999999999999999999986 5789999887765
Q ss_pred HHHHHHcCCCCCCCHHHHHHHHHHhcc-CchhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCChhHHHHhhcCCc
Q psy16767 229 EAACNALGLPLDTDPEIISSQLQEAYA-SIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKG 307 (1020)
Q Consensus 229 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~N~~~~M~~SGAKG 307 (1020)
++ +..++.+.+ ..+++.+.++.| +++.+.+.+.+.+.+-+ ..+|.||+++|+.|||||
T Consensus 641 ~i----------------~~~y~~G~lt~~er~~kvi~~w-~~~~d~v~~~~~~~l~~----~~~~~N~i~mMa~SGARG 699 (1156)
T PRK00566 641 EI----------------EKQYRRGLITDGERYNKVIDIW-SKATDEVAKAMMKNLSK----DQESFNPIYMMADSGARG 699 (1156)
T ss_pred HH----------------HHHHHcCCCCchHHHHHHHHHH-HHHHHHHHHHHHHhCcc----ccCCCCChheeeeccCCc
Confidence 44 334445545 334454554443 55555555444443311 256899999999999999
Q ss_pred chhhHHHHHhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhhhccccCC
Q psy16767 308 STVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSR 387 (1020)
Q Consensus 308 S~~N~~Qi~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~ 387 (1020)
|+.|++||+||+|||. ..+|+++|. ||.|||++||+|+|||||||||||||+|||||||+
T Consensus 700 S~~ni~QL~GmrGlma--------~p~G~iie~------------pI~ssFreGLt~~EyFfst~GaRkGLiDTALKTAd 759 (1156)
T PRK00566 700 SASQIRQLAGMRGLMA--------KPSGEIIET------------PIKSNFREGLTVLEYFISTHGARKGLADTALKTAD 759 (1156)
T ss_pred CHHHHHHHHhhcCccc--------cCCCCEeeh------------hhhhhhhcCCCHHHHhhcCcchhhcccchheeecc
Confidence 9999999999999973 356777763 49999999999999999999999999999999999
Q ss_pred cchhHHHHHhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhcccccccchhhhhhHHHHhhHHHHHhhhccCchhH
Q psy16767 388 SGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYLTDKQFSFLEDNIKWICSYKVILNLLKKHPLSL 467 (1020)
Q Consensus 388 sGYLqRrLvk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~ 467 (1020)
|||||||||+++||+ +||..||.. ..|+........ ......+.+. +
T Consensus 760 SGYLtRRLVdvaqDv------iV~~~DCgT------~~gi~~~~~~~~-~~~i~~l~~~---~----------------- 806 (1156)
T PRK00566 760 SGYLTRRLVDVAQDV------IVREDDCGT------DRGIEVTAIIEG-GEVIEPLEER---I----------------- 806 (1156)
T ss_pred ceeeehhHHHhhCce------EEEECCCCC------cCCEEEEEeccC-CEEEeEhhhe---e-----------------
Confidence 999999999955555 555666543 233322111000 0000000000 0
Q ss_pred HHHHHHhhhc--CCCCCcccCCCcchhHHHHHHHHHhhcHHHHHHHHHhccCCCCCCcccCCCCcccccchHHHHHHHHH
Q psy16767 468 ALLLLLTFKS--SGKPNFIFSPHRTKFTMDLLEQWYQLDDKARKKYRKKFKACPQPLISTFQPDAHFGSISENLADSVVK 545 (1020)
Q Consensus 468 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~ 545 (1020)
+ .++.+ +.++ .+++.. ...-..++.+...++.+.. .....+. +|-
T Consensus 807 ---~-GR~~~~di~~~----~t~~~i-----~~~~~~i~~~~~~~i~~~~-i~~v~iR---S~l---------------- 853 (1156)
T PRK00566 807 ---L-GRVLAEDVVDP----ETGEVI-----VPAGTLIDEEIADKIEEAG-IEEVKIR---SVL---------------- 853 (1156)
T ss_pred ---E-eEEEhhheecC----CCCcEE-----EcCCCccCHHHHHHHHHcC-CCEEEEc---CCe----------------
Confidence 0 00000 0000 000000 0000000111111111100 0000000 000
Q ss_pred HhhccCcchhHHHHHHHHHHhhh--cccCCCCCcchhhhhcccCCccccccccccccCCccccccccChhhHHHHHHHhh
Q psy16767 546 YTKGRTDASHVDKFYDMIFYKNL--LSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMAT 623 (1020)
Q Consensus 546 ~~~~~~~~~~~~~~~~~~~~ky~--~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~AS 623 (1020)
.| .+...+|..|+.+-+ ..+|+.|||||+|||||||||+||+||+|||..|+ ++|.|+||+.|++ -|
T Consensus 854 -----tC-~s~~gvC~~CYG~~La~~~~v~iGeaVGiIAAQSIGEPGTQLTmRTFHtGGv---dIT~Glprv~elf-ea- 922 (1156)
T PRK00566 854 -----TC-ETRHGVCAKCYGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVAELF-EA- 922 (1156)
T ss_pred -----ee-cCCCcccHhhhCccccCCCCcccCcceeEEeeeecCCCccceeeeeeeecce---eccCCccchhhhe-ee-
Confidence 01 133457777876643 68999999999999999999999999999999999 9999999999999 55
Q ss_pred cCCCCCeEEEEcCCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecCCCCCcceEEEEEEecccccccccCCChhh
Q psy16767 624 KAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMNYQMKFCFIPAHMYRDKTSVKPSK 703 (1020)
Q Consensus 624 k~iKTP~mtv~L~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~~~~~y~i~~~l~~~~~~~~~~~i~~~~ 703 (1020)
+++|.|.+..++... +++.... . +
T Consensus 923 r~pk~~a~ise~~G~----------------------------------------------v~~~~~~--~---~----- 946 (1156)
T PRK00566 923 RKPKGPAIIAEIDGT----------------------------------------------VSFGKET--K---G----- 946 (1156)
T ss_pred ccCCCceEEEecCCE----------------------------------------------EEecccc--C---C-----
Confidence 666655433333210 1110000 0 0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccchhhhhhhhhhcc
Q psy16767 704 IIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVN 783 (1020)
Q Consensus 704 i~~~~~~~f~~~~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~ 783 (1020)
.+ .+. . . + .+++ .
T Consensus 947 ---------------------~~---~i~---i--------~---~----------------~~~~-----~-------- 959 (1156)
T PRK00566 947 ---------------------KR---RIV---I--------T---P----------------DDGE-----E-------- 959 (1156)
T ss_pred ---------------------ce---EEE---E--------e---C----------------CCCc-----e--------
Confidence 00 000 0 0 0 0000 0
Q ss_pred ccccCCCCCcchHHhhhhcccccCCCcccccchhhcccchhHHHHHHhhccccceeeeccccCCceEEEEecccceeccC
Q psy16767 784 QEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLFLPSNLFEEK 863 (1020)
Q Consensus 784 ~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~i~~~~~d~~~~~~~~~~~lp~~~~~~~ 863 (1020)
.+| .... .. .+. + .
T Consensus 960 ----~~y--------------------------------------------------~vp~--~~--~~~-----v-~-- 973 (1156)
T PRK00566 960 ----REY--------------------------------------------------LIPK--GK--HLL-----V-Q-- 973 (1156)
T ss_pred ----EEE--------------------------------------------------EccC--CC--eee-----e-c--
Confidence 000 0000 00 000 0 0
Q ss_pred CceEE----EEEeccchhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccc
Q psy16767 864 ESKHL----LKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 939 (1020)
Q Consensus 864 ~~e~~----l~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~M 939 (1020)
++.++ ..|||. =|+++|++++||||++..|++||++|+..+|++||.+|+.+|++.|
T Consensus 974 ~gd~v~~G~~l~~g~-------------------~~~~~il~v~G~~~~~~~lv~eiq~vY~~QGv~I~dKHievIvrqM 1034 (1156)
T PRK00566 974 EGDHVEAGDKLTDGS-------------------IDPHDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQM 1034 (1156)
T ss_pred CCCEEccCCcccCCC-------------------CCHHHHHHhcCHHHHHHHHHHHHHHHHHhCCcccccceeehHHHHH
Confidence 01111 113332 2389999999999999999999999999999999999999999999
Q ss_pred eeee----------------------------------------eEEeeeccccccCcchhhhhcchhHHHHHHHHHhcC
Q psy16767 940 THSG----------------------------------------TYVAMNRNGIRLNPSFIQKMTFEMPLEKIRQASMQG 979 (1020)
Q Consensus 940 T~~G----------------------------------------~~~~~nR~G~~~~~spl~kaSFE~t~~~L~~AA~~g 979 (1020)
|.++ .+.||||.+++ ..|+|+.|||++|+++|.+||+.|
T Consensus 1035 ~~kv~i~~~gdt~~~~g~~v~~~~~~~~n~~~~~~g~~~~~~~~~llGItka~l~-t~SflsaASFQeTtkvLt~AAi~g 1113 (1156)
T PRK00566 1035 LRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPATGRPVLLGITKASLA-TESFLSAASFQETTRVLTEAAIKG 1113 (1156)
T ss_pred hCCeEEecCCCcCCCCCceeeHHHHHHHHHHHHHCCCCCCcccceeeeeeecccc-cCcccccccccchHHHHHHHHhcC
Confidence 9764 35788888887 489999999999999999999999
Q ss_pred CCccCCCcccceecCCccccCccceE
Q psy16767 980 REDSLRAPSARVMLGQECRQGTGLFQ 1005 (1020)
Q Consensus 980 ~~D~l~svSa~Ii~Gk~~~~GTG~fd 1005 (1020)
+.|+|+|+.++||+|+++|+|||...
T Consensus 1114 k~D~L~GlkENVIiG~liPaGTG~~~ 1139 (1156)
T PRK00566 1114 KVDPLRGLKENVIIGRLIPAGTGLAR 1139 (1156)
T ss_pred CCCcCCCcccceEecCcccCCCCcch
Confidence 99999999999999999999999853
No 6
>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=3.5e-103 Score=963.81 Aligned_cols=624 Identities=23% Similarity=0.351 Sum_probs=434.8
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeecccc--------cccChHHHHHHHHHH
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRD--------TFLTRAEYMNLVYQA 68 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d--------~fl~~~~~~~l~~~~ 68 (1020)
|||||||| |++|||||+.||++++||+||++|+|+++|+||+|+|+|+||.++ .|+++++++.. |+
T Consensus 443 FDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~~-~~- 520 (1140)
T TIGR02386 443 FDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRA-YD- 520 (1140)
T ss_pred CCcceeEeecCCCHHHHHHHHHHhCCcccEecCCCCCceEEeechhhheeeEeeeccccccCcCceeCCHHHHHHH-HH-
Confidence 99999999 999999999999999999999999999999999999999999985 79999998763 33
Q ss_pred hcccCcccccCCCcccc----CCCCC--CCcEEEEEEccccCCCCCccccccccccccccccccCccccCccccccCceE
Q psy16767 69 LCILNTEIRTLPPTIWK----PMPLW--TGKQVLSTVIINLTPKDKVIIRHGELLSGILDKKQFGSTQYGLVHAVWDTHV 142 (1020)
Q Consensus 69 ~~~~~~~i~l~~Pailk----p~~lw--TGKqv~s~~l~~~~P~~~~~in~~~~~~~k~~~~~~~~~~~~~~~~~~d~~v 142 (1020)
.+.+ +.|++++ ++++| +|||||+.++ |.+++++|. .
T Consensus 521 ----~~~i--~l~~~i~~~~~g~~~~tt~Gr~if~~il----P~~~~~~n~------------------------~---- 562 (1140)
T TIGR02386 521 ----NGKV--HLHALIGVRTSGEILETTVGRVIFNEIL----PEGFPYIND------------------------N---- 562 (1140)
T ss_pred ----cCCc--cCCCceEEeccccEEEccchHHHHHHHc----CCccccccc------------------------c----
Confidence 1222 3344443 34677 5888888777 987655443 0
Q ss_pred EEeccceeeeccCcccccCcchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHHHHHHH
Q psy16767 143 TIRHGELLSGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINK 222 (1020)
Q Consensus 143 ~I~~Gell~G~LdK~~lG~~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~~~i~~ 222 (1020)
.+|||+.+| +|||.+|+.||++.|+.|||++++|+++|++.+|||||++|+.+|++ +.+++++
T Consensus 563 ---------~~l~Kk~lg----~LI~~i~~~~G~~~t~~~LD~lk~Lgf~~at~~GfSigi~Dl~ip~~----K~~ii~~ 625 (1140)
T TIGR02386 563 ---------EPLSKKEIS----SLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDE----KYEILKE 625 (1140)
T ss_pred ---------cccchHHHH----HHHHHHHHHhChHHHHHHHHHHHHHHHHHHHhcCeeeeeccCCCCHH----HHHHHHH
Confidence 178999998 89999999999999999999999999999999999999999999986 5789999
Q ss_pred HHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhccC-chhHHHHHHHHHHHHHHHHHHHHhhccccCCCCC-CCCCChhHHH
Q psy16767 223 ARRLGTEAACNALGLPLDTDPEIISSQLQEAYAS-IPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIE-PFPANNLQFM 300 (1020)
Q Consensus 223 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~-~~~~N~~~~M 300 (1020)
|++++.++.++ ++.+.+. .+++.+ +..+++++++.+.+.++.. +.. ..|.||+++|
T Consensus 626 a~~~v~~i~~~----------------y~~G~lt~~er~~k-----vi~iw~~~~d~v~~~~~~~-l~~~~~~~N~i~mM 683 (1140)
T TIGR02386 626 ADKEVAKIQKF----------------YNKGLITDEERYRK-----VVSIWSETKDKVTDAMMKL-LKKDTYKFNPIFMM 683 (1140)
T ss_pred HHHHHHHHHHH----------------HHcCCCChHHHHHH-----HHHHHHHHHHHHHHHHHHh-cccccCCCCcHhhh
Confidence 98877655443 3333332 223333 3344556666666655432 211 2367999999
Q ss_pred HhhcCCcchhhHHHHHhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhh
Q psy16767 301 VESGAKGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLID 380 (1020)
Q Consensus 301 ~~SGAKGS~~N~~Qi~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiD 380 (1020)
+.||||||+.|++||+||+|||. -.+||++|+ | |.|||++||+|+|||||||||||||+|
T Consensus 684 a~SGARGS~~ni~QL~GmrGlma--------~p~Grii~~-------P-----I~ssF~eGLtp~EyF~st~GaRkGLiD 743 (1140)
T TIGR02386 684 ADSGARGNISQFRQLAGMRGLMA--------KPSGDIIEL-------P-----IKSSFREGLTVLEYFISTHGARKGLAD 743 (1140)
T ss_pred hhcccccCHHHHHHHHhCCCccc--------CCCCCcccc-------c-----hhhccccCCCHHHHhhhccchhccccc
Confidence 99999999999999999999974 245789986 2 999999999999999999999999999
Q ss_pred hccccCCcchhHHHHHhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhcccccccc-hhhhhhHHHHhhHHHHHhh
Q psy16767 381 TAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYLTDKQF-SFLEDNIKWICSYKVILNL 459 (1020)
Q Consensus 381 TAvKTa~sGYLqRrLvk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~~~~~~-~~~~~n~~~~~~~~~~~~~ 459 (1020)
||||||+|||||||||+++||++|.||-.-. ..|-.|+....+++ ..-. -+...-+ .+++++
T Consensus 744 TAlKTAdSGYLtRRLVdv~qDviV~~dDCgT-~~gi~v~~~~~~~~-~~i~--~l~~ri~GR~~~~d------------- 806 (1140)
T TIGR02386 744 TALKTADSGYLTRRLVDVAQDVVVREEDCGT-EEGIEVEAIVEGKD-EIIE--SLKDRIVGRYSAED------------- 806 (1140)
T ss_pred hheeecccceeeeehhhhhcceEEEeCCCCC-CCCEEEEEeecCCc-eEEe--ehhheeEEEEEhhh-------------
Confidence 9999999999999999999999999985442 23544544432221 1100 0000000 000000
Q ss_pred hccCchhHHHHHHHhhhcCCCCCcccCCCcchhHHHHHHHHHhhcHHHHHHHHHhccCCCCCCcccCCCCcccccchHHH
Q psy16767 460 LKKHPLSLALLLLLTFKSSGKPNFIFSPHRTKFTMDLLEQWYQLDDKARKKYRKKFKACPQPLISTFQPDAHFGSISENL 539 (1020)
Q Consensus 460 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 539 (1020)
+.++ .+++... ..-..++.+...++.+.. .....+. +|..
T Consensus 807 ------------------i~~~----~~~~~i~-----~~~~~i~~~~~~~i~~~~-i~~v~iR---S~lt--------- 846 (1140)
T TIGR02386 807 ------------------VYDP----DTGKLIA-----EANTLITEEIAEKIENSG-IEKVKVR---SVLT--------- 846 (1140)
T ss_pred ------------------eEeC----CCCcEEE-----eCCCCcCHHHHHHHHHcC-CCEEEec---CCee---------
Confidence 0000 0000000 000000111111111100 0000000 0100
Q ss_pred HHHHHHHhhccCcchhHHHHHHHHHHh--hhcccCCCCCcchhhhhcccCCccccccccccccCCcccc--ccccChhhH
Q psy16767 540 ADSVVKYTKGRTDASHVDKFYDMIFYK--NLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDM--NVTLGIPRL 615 (1020)
Q Consensus 540 ~~~l~~~~~~~~~~~~~~~~~~~~~~k--y~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~--nvTlGvPRL 615 (1020)
| .+...+|..|+.+ ....+|+.|||||+|||||||||+|||||+|||.+|+++. ++|+|+||+
T Consensus 847 ------------C-~s~~gvC~~CYG~~La~~~~V~~GeaVGiiAAQSIGEPGTQLTmRTFHtGGv~~~~~DIT~GlpRv 913 (1140)
T TIGR02386 847 ------------C-ESEHGVCQKCYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASGDITQGLPRV 913 (1140)
T ss_pred ------------e-CCCCCCccccCCCcccCCcEecccccceeEeeeecCCCcchhehhheeeccccccccccccCchhh
Confidence 1 1234466667655 3478999999999999999999999999999999999875 999999999
Q ss_pred HHHHHHhhcCCCCCeEEEEcCCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecCCCCCcceEEEEEEeccccccc
Q psy16767 616 REILMMATKAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMNYQMKFCFIPAHMYRD 695 (1020)
Q Consensus 616 kEIi~~ASk~iKTP~mtv~L~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~~~~~y~i~~~l~~~~~~~~ 695 (1020)
.|++ .| +++|.|.+..++... ++|..+..
T Consensus 914 ~elf-ea-r~p~~~a~iae~~G~----------------------------------------------v~~~~~~~--- 942 (1140)
T TIGR02386 914 KELF-EA-RTPKDKAVIAEVDGT----------------------------------------------VEIIEDIV--- 942 (1140)
T ss_pred hhhh-hc-ccCCCceEEEecCCE----------------------------------------------EEEeeccc---
Confidence 9999 56 666655443333210 11100000
Q ss_pred ccCCChhhHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccchhhh
Q psy16767 696 KTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDA 775 (1020)
Q Consensus 696 ~~~i~~~~i~~~~~~~f~~~~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ 775 (1020)
.+ .+ .+ .. . + ++++.
T Consensus 943 -~~--------------------------~~---~i---~i--------~---~----------------~~~~~----- 957 (1140)
T TIGR02386 943 -KN--------------------------KR---VV---VI--------K---D----------------ENDEE----- 957 (1140)
T ss_pred -CC--------------------------cE---EE---EE--------E---C----------------CCCce-----
Confidence 00 00 00 00 0 0 00000
Q ss_pred hhhhhhccccccCCCCCcchHHhhhhcccccCCCcccccchhhcccchhHHHHHHhhccccceeeeccccCCceEEEEec
Q psy16767 776 VQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLFL 855 (1020)
Q Consensus 776 ~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~i~~~~~d~~~~~~~~~~~l 855 (1020)
.+| .... .. .+.
T Consensus 958 ------------~~y--------------------------------------------------~ip~--~~--~l~-- 969 (1140)
T TIGR02386 958 ------------KKY--------------------------------------------------TIPF--GA--QLR-- 969 (1140)
T ss_pred ------------eEE--------------------------------------------------eccC--Cc--eEE--
Confidence 000 0000 00 000
Q ss_pred ccceeccCCceEE----EEEeccchhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcch
Q psy16767 856 PSNLFEEKESKHL----LKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRH 931 (1020)
Q Consensus 856 p~~~~~~~~~e~~----l~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rH 931 (1020)
++ ++.++ ..||| +-|+++|++++||||++..|++||++|+..+|++||.+|
T Consensus 970 ----v~--~gd~V~~G~~l~~g-------------------~~~~~~il~v~G~~a~~~~lv~evq~vY~~QGv~I~dKH 1024 (1140)
T TIGR02386 970 ----VK--DGDSVSAGDKLTEG-------------------SIDPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKH 1024 (1140)
T ss_pred ----ec--CCCEEccCCcccCC-------------------CCCHHHHHHhcCHHHHHHHHHHHHHHHHHhCCccccchh
Confidence 00 01111 11222 246899999999999999999999999999999999999
Q ss_pred hhhhcccceeeeeEE----------------------------------------eeeccccccCcchhhhhcchhHHHH
Q psy16767 932 LSLVADYMTHSGTYV----------------------------------------AMNRNGIRLNPSFIQKMTFEMPLEK 971 (1020)
Q Consensus 932 l~LlAD~MT~~G~~~----------------------------------------~~nR~G~~~~~spl~kaSFE~t~~~ 971 (1020)
+.+|++.||.++.+. |++|..++ ..|.|+.|||++|+++
T Consensus 1025 ievIvrqM~~kv~i~~~gdt~~l~g~~v~~~~~~~~n~~~~~~g~~~~~~~~~llGitkasl~-t~SflsaASFqeTtkv 1103 (1140)
T TIGR02386 1025 IEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIPQLLGITKASLN-TESFLSAASFQETTKV 1103 (1140)
T ss_pred HhHHHHHHhCcEEEEeCCCcCCCCCCeeeHHHHHHHHHHHHhCCCCCccceeeeeeeeehhcc-CCCcccccchhhHHHH
Confidence 999999999997555 45665654 4899999999999999
Q ss_pred HHHHHhcCCCccCCCcccceecCCccccCccc
Q psy16767 972 IRQASMQGREDSLRAPSARVMLGQECRQGTGL 1003 (1020)
Q Consensus 972 L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~ 1003 (1020)
|.+||+.|+.|+|+|+.++||+|+++|+|||.
T Consensus 1104 Lt~Aai~gk~D~L~GlkENVIiG~liPaGTG~ 1135 (1140)
T TIGR02386 1104 LTDAAIKGKVDYLLGLKENVIIGNLIPAGTGL 1135 (1140)
T ss_pred HHHHHhcCCCCCCCCcccceEecCcccCCCCc
Confidence 99999999999999999999999999999996
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=1.3e-103 Score=973.85 Aligned_cols=404 Identities=32% Similarity=0.477 Sum_probs=362.6
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeecccccccChHHHHHHHHHHhcccCccc
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCILNTEI 76 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d~fl~~~~~~~l~~~~~~~~~~~i 76 (1020)
|||||||+ |++|||||++||++++||+||++|+|++|++||+|+|+|+||.+|+||++++++++++++. + .+
T Consensus 454 FDGDeMn~h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~~d~f~~~~~~~~l~~~~~--~--~~ 529 (868)
T TIGR02390 454 FDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAG--Y--FG 529 (868)
T ss_pred cccceeeEecCCCHHHHHHHHHHhhchhceecCCCCCeeEEeehhhhhheeeeeeccccCCHHHHHHHHhcCC--c--cc
Confidence 99999999 9999999999999999999999999999999999999999999999999999999998732 2 24
Q ss_pred ccCCCccccCCCCCCCcEEEEEEccccCCCCCccccccccccc-cccccccCccccCccccccCceEEEeccceeeeccC
Q psy16767 77 RTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSG-ILDKKQFGSTQYGLVHAVWDTHVTIRHGELLSGILD 155 (1020)
Q Consensus 77 ~l~~Pailkp~~lwTGKqv~s~~l~~~~P~~~~~in~~~~~~~-k~~~~~~~~~~~~~~~~~~d~~v~I~~Gell~G~Ld 155 (1020)
.+|+|||+||++|||||||||++| |.+ +|+ ..+ ++++..|... ...+..|+.|+|+||||++|+||
T Consensus 530 ~~~~p~i~kp~~lwTGKqi~s~~l----p~~---~n~---~~~~~~~~~~~~~~---~~~~~~d~~v~i~~g~ll~G~ld 596 (868)
T TIGR02390 530 DPPEPAIEKPKEYWTGKQIFSAFL----PED---LNF---EGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVID 596 (868)
T ss_pred cCCCceecCCcccccHHHHHHHhc----CCC---Ccc---eecccccccccccc---cccCCCcceEEEecCeEEeeeec
Confidence 679999999999999999999998 875 566 554 5544433210 11234589999999999999999
Q ss_pred cccccCcchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHHHHHHHHHHHHHHHHHHHc
Q psy16767 156 KKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAACNAL 235 (1020)
Q Consensus 156 K~~lG~~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~~~i~~a~~~~~~~~~~~~ 235 (1020)
|+++|+++++|+|.+|++||+++|+.||+++++|+++||+.+|||||++|++++++..++++++|+++++.+.+++..+.
T Consensus 597 K~~lg~~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~ 676 (868)
T TIGR02390 597 KKAIGAEKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYR 676 (868)
T ss_pred HHHhccCcccHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhccEEeehhheeeCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988776655432
Q ss_pred CCCCCCCHHHHHHHHHHhcc---CchhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCChhHHHHhhcCCcchhhH
Q psy16767 236 GLPLDTDPEIISSQLQEAYA---SIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVNT 312 (1020)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~~~---~~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~N~ 312 (1020)
.+.+ ++.+..+.+|..+.+.|+++++.+++.+... ..|+|++++|+.||||||.+|+
T Consensus 677 ----------------~g~l~~~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~----l~~~N~~~~M~~sGsKGS~~Ni 736 (868)
T TIGR02390 677 ----------------NGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKY----LDPENHAVIMARTGARGSLLNI 736 (868)
T ss_pred ----------------cCCCccCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh----cCCCcchhhhhhccCCcccccH
Confidence 1111 3445567788888889999999888776542 5689999999999999999999
Q ss_pred HHHHhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhhhccccCCcchhH
Q psy16767 313 MQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQ 392 (1020)
Q Consensus 313 ~Qi~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYLq 392 (1020)
+||+||||||+++|+|||+|++|||||||.++|.+|+|+|||.|||++||+|+|||||||||||||||||||||+|||||
T Consensus 737 ~Qi~~~lGQQ~~~g~ri~~~~~~rtlp~f~~~d~~~~~~GfV~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYLq 816 (868)
T TIGR02390 737 TQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQ 816 (868)
T ss_pred HHHHhccCccccCCCcCccccccCCCCCCCCCCCCcccCceecccccCCCCHHHHHHHHhhhccccccccccccccchhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhcccccccch
Q psy16767 393 RCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYLTDKQFS 441 (1020)
Q Consensus 393 RrLvk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~~~~~~~ 441 (1020)
|||||+||||+|+||+||||++|+||||.||+||+||++.+++++.+++
T Consensus 817 RrLvk~lEdl~v~yD~tVR~~~g~iiQf~YG~dg~d~~~~~~~~~~~~~ 865 (868)
T TIGR02390 817 RRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVDPMKSDHGKPVDVK 865 (868)
T ss_pred HHHHHHHhheEEecCCeEEeCCCcEEEEeccCCCcCHHHhccCccccce
Confidence 9999999999999999999999999999999999999998876654443
No 8
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=2.1e-103 Score=974.83 Aligned_cols=411 Identities=32% Similarity=0.475 Sum_probs=366.9
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeecccccccChHHHHHHHHHHhcccCccc
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCILNTEI 76 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d~fl~~~~~~~l~~~~~~~~~~~i 76 (1020)
|||||||+ |++|||||++||++++||+||++|+|++|++||+|+|+|+||.+|+||++++++++++++. . ..+
T Consensus 458 FDGDeMn~h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~~d~f~~~~~~~~l~~~~~--~-~~~ 534 (882)
T PRK08566 458 FDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAG--I-DEL 534 (882)
T ss_pred ccCcEEEEecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeehHHHHHHHHHHhccccCCHHHHHHHHHhCC--c-ccc
Confidence 99999999 9999999999999999999999999999999999999999999999999999999999832 1 235
Q ss_pred ccCCCccccCCCCCCCcEEEEEEccccCCCCCccccccccccc-cccccccCccccCccccccCceEEEeccceeeeccC
Q psy16767 77 RTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSG-ILDKKQFGSTQYGLVHAVWDTHVTIRHGELLSGILD 155 (1020)
Q Consensus 77 ~l~~Pailkp~~lwTGKqv~s~~l~~~~P~~~~~in~~~~~~~-k~~~~~~~~~~~~~~~~~~d~~v~I~~Gell~G~Ld 155 (1020)
.+|+|||+||+++||||||||++| |.+ +|+ ..+ +++.+.|... ...+..|+.|+|+||||++|+||
T Consensus 535 ~~~~pai~~p~~lwTGKqi~s~~l----p~~---~~~---~~~~~~~~~~~~~~---~~~~~~d~~v~i~~gell~g~ld 601 (882)
T PRK08566 535 PEPEPAIENGKPYWTGKQIFSLFL----PKD---LNL---EFKAKICSGCDECK---KEDCEHDAYVVIKNGKLLEGVID 601 (882)
T ss_pred ccCCcccCCCcccccHHHHHHHHc----CCC---CCc---eeeccccccccccc---cccCCCCceEEEecCEEEecccc
Confidence 789999999999999999999998 765 565 555 5555555411 11233589999999999999999
Q ss_pred cccccCcchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHHHHHHHHHHHHHHHHHHHc
Q psy16767 156 KKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAACNAL 235 (1020)
Q Consensus 156 K~~lG~~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~~~i~~a~~~~~~~~~~~~ 235 (1020)
|++||+++++|||.+|++||+++|+.||+++++|+++||+.+|||||++|++++++..++++++|+++++.+.++++.+.
T Consensus 602 K~~lg~~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~ 681 (882)
T PRK08566 602 KKAIGAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYE 681 (882)
T ss_pred HHHhhcccchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCEEeehhhcccCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988776665433
Q ss_pred CCCCCCCHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCChhHHHHhhcCCcchhhHHHH
Q psy16767 236 GLPLDTDPEIISSQLQEAYASIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVNTMQI 315 (1020)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~N~~Qi 315 (1020)
.... .. .++.+..+.+|..+.+.++++++.+++.+... ..|+|++++|+.||||||++|++||
T Consensus 682 ~g~l------------~~-~~~~~~~~~~e~~i~~~l~~~r~~~~~~~~~~----l~~~N~~~~M~~SGsKGS~~N~~Qi 744 (882)
T PRK08566 682 NGEL------------EP-LPGRTLEETLEMKIMQVLGKARDEAGEIAEKY----LGLDNPAVIMARTGARGSMLNLTQM 744 (882)
T ss_pred cCCC------------cc-ccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh----cCCCCcceeeeccccccCHHHHHHH
Confidence 2100 00 13445567788888999999999888877643 5689999999999999999999999
Q ss_pred HhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhhhccccCCcchhHHHH
Q psy16767 316 SCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCL 395 (1020)
Q Consensus 316 ~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYLqRrL 395 (1020)
+||||||+++|+|||+|++|||||||.++|.+|+|+|||.|||++||+|+|||||||||||||||||||||+||||||||
T Consensus 745 ~~~lGqQ~~~g~ri~~~~~~rtLP~f~~~d~~~~~~GfV~~sF~~GL~p~EfffH~m~GReGliDTAvkTa~sGYlqRrL 824 (882)
T PRK08566 745 AACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRL 824 (882)
T ss_pred HhccCceecCCCcCccCccCccCCCCCCCCCCcccCceeeccccCCCCHHHHHHHHhhhcccccccceeeccCccchHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhcccccccchhhh
Q psy16767 396 VKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYLTDKQFSFLE 444 (1020)
Q Consensus 396 vk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~~~~~~~~~~ 444 (1020)
||+||||+|+||+||||++|+||||.||+||+||++++++++.+++.+.
T Consensus 825 vk~ledl~v~yD~tVR~s~g~iiQf~YG~dg~d~~~~~~~~~~~~~~~~ 873 (882)
T PRK08566 825 INALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDHGKPVDVDRII 873 (882)
T ss_pred HHHHhheEEeeCCceEcCCCcEEEEeccCCCcCHHHhcCCCcccHHHHH
Confidence 9999999999999999999999999999999999998877655555544
No 9
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=5.7e-95 Score=889.33 Aligned_cols=620 Identities=22% Similarity=0.320 Sum_probs=430.8
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeecc-cc-------cccChHHHHHHHHHH
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSL-RD-------TFLTRAEYMNLVYQA 68 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~-~d-------~fl~~~~~~~l~~~~ 68 (1020)
|||||||+ |++|||||+.||++++||+||++|+|+++|+||+|+|+|+||. ++ .|++.++++.+..+.
T Consensus 539 FDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~~~~e~~~a~~~~ 618 (1460)
T PRK14906 539 FDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDAR 618 (1460)
T ss_pred CcCceeeeecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeeeeeeeeeEEeeeccccccccCceeCCHHHHHHHHhcC
Confidence 99999999 9999999999999999999999999999999999999999996 33 688888877665541
Q ss_pred -hcccCcccccCCCc---------------cccCCCCCCCcEEEEEEccccCCCCCccccccccccccccccccCccccC
Q psy16767 69 -LCILNTEIRTLPPT---------------IWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSGILDKKQFGSTQYG 132 (1020)
Q Consensus 69 -~~~~~~~i~l~~Pa---------------ilkp~~lwTGKqv~s~~l~~~~P~~~~~in~~~~~~~k~~~~~~~~~~~~ 132 (1020)
..+.+..|.+..|. ..++...|+||+||+.+| |.++++
T Consensus 619 ~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~tt~Gr~Ifn~il----P~d~~f---------------------- 672 (1460)
T PRK14906 619 ADLDLQAKIVVRLSRDMTVRGSYGDLEETKAGERIETTVGRIIFNQVL----PEDYPY---------------------- 672 (1460)
T ss_pred CCccccccEEEecCcccccccccccccCCCCCceEECCCCEEEEeccc----CCCccc----------------------
Confidence 12333333333222 112345799999999887 876433
Q ss_pred ccccccCceEEEeccceeeeccCcccccCcchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHH
Q psy16767 133 LVHAVWDTHVTIRHGELLSGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQER 212 (1020)
Q Consensus 133 ~~~~~~d~~v~I~~Gell~G~LdK~~lG~~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~ 212 (1020)
++++++|+.+| +||+.+|+.||.+.|+.|||.+++++++|++.+|||||++|+.+|++
T Consensus 673 -----------------vN~~l~KK~Lg----~LI~~i~~~~G~~~t~~fLD~Ik~LGf~yaT~sG~SIgi~Di~ip~~- 730 (1460)
T PRK14906 673 -----------------LNYKMVKKDIG----RLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDD- 730 (1460)
T ss_pred -----------------ccceeeHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEEeecccccChH-
Confidence 34478999998 79999999999999999999999999999999999999999999886
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCC
Q psy16767 213 DRKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQEAYASIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPF 292 (1020)
Q Consensus 213 ~~~r~~~i~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~ 292 (1020)
+.+++++|++++.++.+ +++.+.+... ..+..+..+++++++++++.++.. ..
T Consensus 731 ---K~~iI~~A~~~V~ei~~----------------~y~~G~iT~~----Er~~kVi~iw~~a~d~v~~~~~~~----l~ 783 (1460)
T PRK14906 731 ---KPEILAEADEKVAAIDE----------------DYEDGFLSER----ERHKQVVDIWTEATEEVGEAMLAG----FD 783 (1460)
T ss_pred ---HHHHHHHHHHHHHHHHH----------------HHHcCCCcHH----HHHHHHHHHHHHHHHHHHHHHHHh----cc
Confidence 57899999887665443 3444444221 113445566778888888887753 45
Q ss_pred CCChhHHHHhhcCCcchhhHHHHHhhcccee-ecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhh
Q psy16767 293 PANNLQFMVESGAKGSTVNTMQISCLLGQIE-LEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHC 371 (1020)
Q Consensus 293 ~~N~~~~M~~SGAKGS~~N~~Qi~~~lGQQ~-l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~ 371 (1020)
+.||+++|+.||||||..|++||+||+|||. ..|++++. +|.|||++||+|.||||||
T Consensus 784 ~~N~i~mMa~SGARGS~~QI~QLaGmRGlma~p~G~iIe~---------------------PI~SnFrEGLt~~EyFiSt 842 (1460)
T PRK14906 784 EDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDL---------------------PIKANFREGLSVLEYFIST 842 (1460)
T ss_pred cCCCeEeeeeccCcccHHHHHHHHhcccceecCCCCcccc---------------------ccccccccCCCHHHHHHHc
Confidence 7999999999999999999999999999973 35554411 3999999999999999999
Q ss_pred cccccchhhhccccCCcchhHHHHHhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhcccccccchhhhhhHHHHh
Q psy16767 372 MAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYLTDKQFSFLEDNIKWIC 451 (1020)
Q Consensus 372 m~gReGLiDTAvKTa~sGYLqRrLvk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~~~~~~~~~~~n~~~~~ 451 (1020)
|||||||+|||||||+|||||||||+++||++ ||..||.. ..|+...... + ...+.+..
T Consensus 843 ~GaRKGL~DTALKTAdSGYLTRRLVdVaQDVi------V~e~DCgT------~~Gi~v~~~~--~---~~~l~~ri---- 901 (1460)
T PRK14906 843 HGARKGLVDTALRTADSGYLTRRLVDVAQDVI------VREEDCGT------DEGVTYPLVK--P---KGDVDTNL---- 901 (1460)
T ss_pred ccccchhhhhhhhccccchHHHHHHHhhhheE------EEeccCCC------CCCEEEEEee--c---ccchhhee----
Confidence 99999999999999999999999999766665 66677654 4555543210 0 00011100
Q ss_pred hHHHHHhhhccCchhHHHHHHHhhhc--CCCCCcccCCCcchhH-HHHHHHHHhhcHHH-HHHHHHhccCCCCCCcccCC
Q psy16767 452 SYKVILNLLKKHPLSLALLLLLTFKS--SGKPNFIFSPHRTKFT-MDLLEQWYQLDDKA-RKKYRKKFKACPQPLISTFQ 527 (1020)
Q Consensus 452 ~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 527 (1020)
. .++.. +.++ . ++.... ..+ ++... ..++.+. ......+ .+
T Consensus 902 -----~---------------GR~~~~di~~~----~-g~~i~~~~~~------I~~~~~~~~i~~~-gi~~v~i---RS 946 (1460)
T PRK14906 902 -----I---------------GRCLLEDVCDP----N-GEVLLSAGDY------IESMDDLKRLVEA-GVTKVQI---RT 946 (1460)
T ss_pred -----e---------------eEEEHhhhcCC----C-CCEEEeCCCe------eCcHHHHHHHHHC-CCCEEEE---eC
Confidence 0 00000 0000 0 000000 000 00000 0111110 0000000 00
Q ss_pred CCcccccchHHHHHHHHHHhhccCcchhHHHHHHHHHHhh--hcccCCCCCcchhhhhcccCCccccccccccccCCccc
Q psy16767 528 PDAHFGSISENLADSVVKYTKGRTDASHVDKFYDMIFYKN--LLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGD 605 (1020)
Q Consensus 528 ~~~~~~~~~e~~~~~l~~~~~~~~~~~~~~~~~~~~~~ky--~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~ 605 (1020)
|.. | .+...+|..|+.+- ...+|+.|||||+|||||||||+||+||+|||.+|+++
T Consensus 947 ~lt---------------------C-~s~~gvC~kCYG~dLatg~~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGv~~ 1004 (1460)
T PRK14906 947 LMT---------------------C-HAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVAG 1004 (1460)
T ss_pred Cee---------------------E-CCCCCChhhCcCCcccCCcEeccccceeeeeeeecCCCcceeeeeeeecccccc
Confidence 100 1 13345667776653 35889999999999999999999999999999999988
Q ss_pred cccccChhhHHHHHHHhhcCCCCCeEEEEcCCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecCCCCCcceEEEE
Q psy16767 606 MNVTLGIPRLREILMMATKAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMNYQMKF 685 (1020)
Q Consensus 606 ~nvTlGvPRLkEIi~~ASk~iKTP~mtv~L~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~~~~~y~i~~ 685 (1020)
..+|.|+||+.|++ -| +++|-|.+...+.. .+.+ .+++ ..+.+
T Consensus 1005 ~dit~GLpRv~eLf-Ea-r~pk~~a~i~e~~G--------------------------~v~i------~~~~-~~~~i-- 1047 (1460)
T PRK14906 1005 DDITQGLPRVAELF-EA-RKPKGEAVLAEISG--------------------------TLQI------TGDK-TEKTL-- 1047 (1460)
T ss_pred cccccCcchhhhhe-ee-ccCCCceeeeccCC--------------------------EEEe------ccCC-CceEE--
Confidence 89999999999999 55 55564433221111 0000 0000 00000
Q ss_pred EEecccccccccCCChhhHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCCCcCCC
Q psy16767 686 CFIPAHMYRDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVS 765 (1020)
Q Consensus 686 ~l~~~~~~~~~~~i~~~~i~~~~~~~f~~~~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 (1020)
.+.+..
T Consensus 1048 ~i~~~~-------------------------------------------------------------------------- 1053 (1460)
T PRK14906 1048 TIHDQD-------------------------------------------------------------------------- 1053 (1460)
T ss_pred EEECCC--------------------------------------------------------------------------
Confidence 000000
Q ss_pred CccccchhhhhhhhhhccccccCCCCCcchHHhhhhcccccCCCcccccchhhcccchhHHHHHHhhccccceeeecccc
Q psy16767 766 SDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKK 845 (1020)
Q Consensus 766 ~~~~~~~~d~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~i~~~~~d~~ 845 (1020)
++. .+|.- + .-+.+
T Consensus 1054 --~~~-----------------~~y~v-------------------------~-------~~~~~--------------- 1067 (1460)
T PRK14906 1054 --GNS-----------------REYVV-------------------------S-------ARVQF--------------- 1067 (1460)
T ss_pred --Cce-----------------eEEEc-------------------------c-------CCccc---------------
Confidence 000 00000 0 00000
Q ss_pred CCceEEEEecccceeccCCceEE----EEEeccchhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhh
Q psy16767 846 NHMWCKLLFLPSNLFEEKESKHL----LKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFA 921 (1020)
Q Consensus 846 ~~~~~~~~~lp~~~~~~~~~e~~----l~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~ 921 (1020)
+|.+ .++.++ ..|+| +=|.++++++.|++|+..+|++||++|+.
T Consensus 1068 ---------~~~v----~~gd~v~~G~~l~~G-------------------~~~p~~il~~~g~~~~~~ylv~eVQ~VYr 1115 (1460)
T PRK14906 1068 ---------MPGV----EDGVEVRVGQQITRG-------------------SVNPHDLLRLTDPNTTLRYIVSQVQDVYV 1115 (1460)
T ss_pred ---------cccc----CCCCEEccCCCccCC-------------------CCCHHHHHHhcCHHHHHHHHHHHHHHHHH
Confidence 0000 001110 11222 23588999999999999999999999999
Q ss_pred ccCcccCcchhhhhcccceeee----------------------------------------eEEeeeccccccCcchhh
Q psy16767 922 VYGIEVDPRHLSLVADYMTHSG----------------------------------------TYVAMNRNGIRLNPSFIQ 961 (1020)
Q Consensus 922 ~~g~~v~~rHl~LlAD~MT~~G----------------------------------------~~~~~nR~G~~~~~spl~ 961 (1020)
.+|+.||.+|+.+|+-.|+.+= .+.|||+..+. ..|-|.
T Consensus 1116 ~QGV~InDKHiEvIvRQMl~kV~I~d~Gdt~fl~Ge~vd~~~~~~~n~~~~~~g~~pa~~~p~llGITKasL~-t~SflS 1194 (1460)
T PRK14906 1116 SQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANNLILEGKQPPVGQPLLLGITKASLA-TDSWLS 1194 (1460)
T ss_pred hcCceeccccHHHHHHHHhceEEEecCCCcCCCCCCeeeHHHHHHHHHHHHHcCCCCceeeeEEeeeeecccc-cccccc
Confidence 9999999999999999999552 56666666666 479999
Q ss_pred hhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCccce
Q psy16767 962 KMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLF 1004 (1020)
Q Consensus 962 kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~f 1004 (1020)
-|||.+|.++|.+||+.|..|.|.|.-++||+|+++|.|||..
T Consensus 1195 aASFQeTtrVLt~AAi~gk~D~L~GLKENVIiG~lIPAGTG~~ 1237 (1460)
T PRK14906 1195 AASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGLS 1237 (1460)
T ss_pred cccccchHHHHHHHHhcCCCCcCCCCccceEecceecCCCCcc
Confidence 9999999999999999999999999999999999999999973
No 10
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=7.4e-91 Score=885.41 Aligned_cols=313 Identities=25% Similarity=0.335 Sum_probs=251.2
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeecccccccC--------hHHHHHHHHHH
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLT--------RAEYMNLVYQA 68 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d~fl~--------~~~~~~l~~~~ 68 (1020)
|||||||| |++|||||+.||++++||+||++|+||++|+||+|+|+|+||.++.|+. ..++......+
T Consensus 1850 FDGDqMnvHvPqS~eA~aEa~~LM~s~~nilsP~~G~Pi~~p~QD~vlG~y~LT~~~~~~~~~~~~F~~~~e~~~~~~~~ 1929 (2890)
T PRK09603 1850 FDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTK 1929 (2890)
T ss_pred CCCceeEEeecCCHHHHHHHHHHhcccceEEEcCCCceeEEeecceeeeeEEeeccccCCCCccceeCCHHHHHHHHHcC
Confidence 99999999 9999999999999999999999999999999999999999999986544 34433222211
Q ss_pred hcccCcccccCCCccccCCCCCC--CcEEEEEEccccCCCCCccccccccccccccccccCccccCccccccCceEEEec
Q psy16767 69 LCILNTEIRTLPPTIWKPMPLWT--GKQVLSTVIINLTPKDKVIIRHGELLSGILDKKQFGSTQYGLVHAVWDTHVTIRH 146 (1020)
Q Consensus 69 ~~~~~~~i~l~~Pailkp~~lwT--GKqv~s~~l~~~~P~~~~~in~~~~~~~k~~~~~~~~~~~~~~~~~~d~~v~I~~ 146 (1020)
.. .+..|.|++++|+.+|| |||||+.+| |+.. ++
T Consensus 1930 ~~----~~~~~i~~~~~p~~l~Tt~GK~ifs~il----P~~~---~~--------------------------------- 1965 (2890)
T PRK09603 1930 EL----DIHAKIRVLDQGNIIATSAGRMIIKSIL----PDFI---PT--------------------------------- 1965 (2890)
T ss_pred CC----ccCCcceeecCCcEEEcCccceeeeccC----cccc---cc---------------------------------
Confidence 11 12345566778999999 999999988 8642 11
Q ss_pred cceeeeccCcccccCcchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHHHHHHHHHHH
Q psy16767 147 GELLSGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRL 226 (1020)
Q Consensus 147 Gell~G~LdK~~lG~~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~~~i~~a~~~ 226 (1020)
.++.|.|||+.+| +|||.+|+.||++.|+.|||++++|+++|++.+|||||++|+.+|++ |.+++++|.++
T Consensus 1966 -~~~n~~ldKK~Lg----~LI~~i~~~yG~~~t~~fLD~lk~LGf~yat~~G~SIgI~Dl~ip~~----K~~iI~~A~~e 2036 (2890)
T PRK09603 1966 -DLWNRPMKKKDIG----VLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKD----KQKMVEKAKVE 2036 (2890)
T ss_pred -ccEeeeechHHHH----HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhCCEeeeeccCcccHH----HHHHHHHHHHH
Confidence 1234679999998 79999999999999999999999999999999999999999999986 67899998887
Q ss_pred HHHHHHHHcCCCCCCCHHHHHHHHHHhcc-CchhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCChhHHHHhhcC
Q psy16767 227 GTEAACNALGLPLDTDPEIISSQLQEAYA-SIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGA 305 (1020)
Q Consensus 227 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~N~~~~M~~SGA 305 (1020)
+.++ ..+++.+.+ ..+++.+.++.|. .+.+.+.+.+.+.+. ...+|.||+++|+.|||
T Consensus 2037 V~ei----------------~~~y~~G~it~~Er~~kvid~w~-~~~d~v~~~~~~~l~----~~~~~~N~i~mMa~SGA 2095 (2890)
T PRK09603 2037 VKKI----------------QQQYDQGLLTDQERYNKIIDTWT-EVNDKMSKEMMTAIA----KDKEGFNSIYMMADSGA 2095 (2890)
T ss_pred HHHH----------------HHHHHcCCCCccHHHHHHHHHHH-HHHHHHHHHHHHHhh----hcCCCCCcHHHHHhccc
Confidence 6544 334555655 4456667777653 444444444443331 12467899999999999
Q ss_pred CcchhhHHHHHhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhhhcccc
Q psy16767 306 KGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKT 385 (1020)
Q Consensus 306 KGS~~N~~Qi~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiDTAvKT 385 (1020)
|||..|++||+||+||+.. .+|+. .+. | |.|||++||+|+|||||||||||||+||||||
T Consensus 2096 RGS~~NI~QLaGmrGqMak--------p~G~i------ie~-P-----I~snFrEGLtp~EyFfst~GaRKGLiDTALKT 2155 (2890)
T PRK09603 2096 RGSAAQIRQLSAMRGLMTK--------PDGSI------IET-P-----IISNFKEGLNVLEYFNSTHGARKGLADTALKT 2155 (2890)
T ss_pred cccHHHHHHHHHcCCcEEC--------CCCCc------ccC-h-----hhcCcccCCCHHHHHHhccccccchhhhhhhc
Confidence 9999999999999999631 22332 222 3 89999999999999999999999999999999
Q ss_pred CCcchhHHHHHhhhcceEEeec
Q psy16767 386 SRSGYLQRCLVKHLEGLTVHYD 407 (1020)
Q Consensus 386 a~sGYLqRrLvk~lEdl~V~yd 407 (1020)
|+||||||||||++||++|..+
T Consensus 2156 AdSGYLTRRLVdvaQDviI~e~ 2177 (2890)
T PRK09603 2156 ANAGYLTRKLIDVSQNVKVVSD 2177 (2890)
T ss_pred cccchhhhhHHHhhcceEEEec
Confidence 9999999999998888876543
No 11
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=2.5e-91 Score=886.39 Aligned_cols=317 Identities=24% Similarity=0.315 Sum_probs=248.5
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeeccccccc----ChHHHHHHHHHHhccc
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFL----TRAEYMNLVYQALCIL 72 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d~fl----~~~~~~~l~~~~~~~~ 72 (1020)
|||||||+ |++|||||+.||++++||+||++|+|+++|+||+|+|+|+||.++.++ ...+++++++. +.
T Consensus 1894 FDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~ilG~y~LT~~~~~~~~~~~f~~~~~~~~a-~~-- 1970 (2836)
T PRK14844 1894 FDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQEPKEDDLPSFGAFCEVEHS-LS-- 1970 (2836)
T ss_pred CCCceeeeecCCcHHHHHHHHHHhCCcccEEecCCCceeEeehhhhhhhhhhhcccccccccccccCCHHHHHHH-HH--
Confidence 99999999 999999999999999999999999999999999999999999998754 44556665443 21
Q ss_pred CcccccCCCccccCCCCC---C------------CcEEEEEEccccCCCCCccccccccccccccccccCccccCccccc
Q psy16767 73 NTEIRTLPPTIWKPMPLW---T------------GKQVLSTVIINLTPKDKVIIRHGELLSGILDKKQFGSTQYGLVHAV 137 (1020)
Q Consensus 73 ~~~i~l~~Pailkp~~lw---T------------GKqv~s~~l~~~~P~~~~~in~~~~~~~k~~~~~~~~~~~~~~~~~ 137 (1020)
.+. ++.++.++|+.+| + ||+||+.+| |++. ++
T Consensus 1971 ~~~--~~i~~~i~~~~~~~~~~~~~~~~~~~tt~GR~if~~il----P~~~---~~------------------------ 2017 (2836)
T PRK14844 1971 DGT--LHIHSSIKYRMEYINSSGETHYKTICTTPGRLILWQIF----PKHE---NL------------------------ 2017 (2836)
T ss_pred cCC--cccCceEEeeeccccCCCCcccceEecccHHHHHHHHc----CCcc---cc------------------------
Confidence 222 3445667777777 3 444444333 5521 11
Q ss_pred cCceEEEeccceeeeccCcccccCcchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHH
Q psy16767 138 WDTHVTIRHGELLSGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRT 217 (1020)
Q Consensus 138 ~d~~v~I~~Gell~G~LdK~~lG~~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~ 217 (1020)
++++++|+++|+.++ +||+.+|+.||++.|+.|||++++|+++|++.+|||+|++|+.+|++ +.
T Consensus 2018 --------~~~~~n~~l~KK~l~----~II~~~~~~yG~~~t~~fLD~lk~LGf~yaT~~G~SIgi~Di~iP~~----K~ 2081 (2836)
T PRK14844 2018 --------GFDLINQVLTVKEIT----SIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPET----KA 2081 (2836)
T ss_pred --------CcceEeeeechhHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhccEEeeHhHcccCHH----HH
Confidence 346788999999996 89999999999999999999999999999999999999999999987 46
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhccC-chhHHHHHHHHHHHHHHHHHHHHhhccccCCCC---CCCC
Q psy16767 218 KIINKARRLGTEAACNALGLPLDTDPEIISSQLQEAYAS-IPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLI---EPFP 293 (1020)
Q Consensus 218 ~~i~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~---~~~~ 293 (1020)
+++++|.+++.++. .+++.+.+. ++++.+++ .+++++++++.+.++.. +. ...+
T Consensus 2082 ~iI~~a~~~v~~i~----------------~~y~~G~it~~Er~~kvi-----~iW~~~~d~v~~~~~~~-l~~~~~~~~ 2139 (2836)
T PRK14844 2082 THVDHARGEIKKFS----------------MQYQDGLITRSERYNKVI-----DEWSKCTDMIANDMLKA-ISIYDGNSK 2139 (2836)
T ss_pred HHHHHHHHHHHHHH----------------HHHHcCCCCHHHHHHHHH-----HHHHHHHHHHHHHHHHh-hhhccccCC
Confidence 78999888765443 344455552 33344443 44567777777766542 21 1236
Q ss_pred CChhHHHHhhcCCcchhhHHHHHhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcc
Q psy16767 294 ANNLQFMVESGAKGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMA 373 (1020)
Q Consensus 294 ~N~~~~M~~SGAKGS~~N~~Qi~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~ 373 (1020)
.||+++|+.||||||..|+.|++||+||+. . ++|.... .| |.|||++||+|.||||||||
T Consensus 2140 ~N~i~mMa~SGARGS~sQI~QLaGmRGLma-----k---p~G~iIe-------~P-----I~SNFrEGLsv~EyFiSt~G 2199 (2836)
T PRK14844 2140 YNSVYMMVNSGARGSTSQMKQLAGMRGLMT-----K---PSGEIIE-------TP-----IISNFREGLNVFEYFNSTHG 2199 (2836)
T ss_pred CCceeeeecccCccCHHHHHHHHhcceeee-----c---CCCCeee-------cc-----hhhhhccCCCHHHhhhhccc
Confidence 899999999999999999999999999852 2 2333321 23 99999999999999999999
Q ss_pred cccchhhhccccCCcchhHHHHHhhhcceEEeeceEEEeCCCcE
Q psy16767 374 GREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSL 417 (1020)
Q Consensus 374 gReGLiDTAvKTa~sGYLqRrLvk~lEdl~V~yd~tvr~~~~~i 417 (1020)
|||||+|||+|||+|||||||||+++||+ .||..||..
T Consensus 2200 aRKGL~DTALKTAdSGYLTRRLVDVaQDv------iI~e~DCgT 2237 (2836)
T PRK14844 2200 ARKGLADTALKTANSGYLTRRLVDVSQNC------IVTKHDCKT 2237 (2836)
T ss_pred cccchhhhhhhcccccchhhhhhhhhceE------EEEecccCC
Confidence 99999999999999999999999965555 566777654
No 12
>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=2.7e-83 Score=717.38 Aligned_cols=336 Identities=30% Similarity=0.444 Sum_probs=268.8
Q ss_pred HHHHHHHHHHhhhcccCCCCCcchhhhhcccCCccccccccccccCCccccccccChhhHHHHHHHhhcCCCCCeEEEEc
Q psy16767 556 VDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPF 635 (1020)
Q Consensus 556 ~~~~~~~~~~ky~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~ASk~iKTP~mtv~L 635 (1020)
.++|...|+.||.+++|+||||||+|||||||||+|||||||||||||++||||+|||||+||| ||+|+||||+|+++|
T Consensus 25 ~~~~l~~i~~ky~~alv~PGeaVG~IAAQSIGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEII-Na~k~i~TP~~ti~L 103 (367)
T TIGR02389 25 LDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIV-DARKTPSTPSMTIYL 103 (367)
T ss_pred HHHHHHHHHHHHHHhcCCCccccchhhhhhcCCccccccccccccccccccCccccchhHHHHh-hcccCCCCCeEEEEe
Confidence 4567778999999999999999999999999999999999999999999999999999999999 899999999999999
Q ss_pred CCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecCCCCCcceEEEEEEecccccccccCCChhhHHHHHHHHHHHH
Q psy16767 636 LPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMNYQMKFCFIPAHMYRDKTSVKPSKIIDHFERKFLKE 715 (1020)
Q Consensus 636 ~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~~~~~y~i~~~l~~~~~~~~~~~i~~~~i~~~~~~~f~~~ 715 (1020)
.++...+++.|+.++.+|++++|+|++.++++.. . .+.+++.|. .......+++++.|...+.+.+.
T Consensus 104 ~~~~~~~~~~a~~v~~~iE~t~l~dv~~~~~~~~----~-----~~~l~i~ld--~~~l~~~~i~~~~i~~~i~~~~~-- 170 (367)
T TIGR02389 104 EDEYEKDREKAEEVAKKIEATKLEDVAKDISIDL----A-----DMTVIIELD--EEQLKERGITVDDVEKAIKKAKL-- 170 (367)
T ss_pred cCcchhhHHHHHHHHHHhhheeHHHHHhhhheec----c-----CcEEEEEEC--HHHHHhcCCCHHHHHHHHHHhcc--
Confidence 9887766689999999999999999999887643 1 224666663 22334556777766655443210
Q ss_pred HHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccchhhhhhhhhhccccccCCCCCcch
Q psy16767 716 LEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPED 795 (1020)
Q Consensus 716 ~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~d~ 795 (1020)
. .... .++ +....+++ ... +.
T Consensus 171 ----------~---~~~~------------------------------~~~-------~~~~i~i~--~~~-------~~ 191 (367)
T TIGR02389 171 ----------G---KVIE------------------------------IDM-------DGNTITIK--PPK-------PS 191 (367)
T ss_pred ----------c---ccce------------------------------eec-------CCCEEEEE--ecC-------ch
Confidence 0 0000 000 00001111 100 00
Q ss_pred HHhhhhcccccCCCcccccchhhcccchhHHHHHHhhccccceeeeccccCCceEEEEe--ccc----ceeccCCceEEE
Q psy16767 796 EERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLF--LPS----NLFEEKESKHLL 869 (1020)
Q Consensus 796 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~i~~~~~d~~~~~~~~~~~--lp~----~~~~~~~~e~~l 869 (1020)
...++.+..... .+.+ +|+ ++ ...+++|+|
T Consensus 192 ----------------------------~~~l~~l~~~l~---------------~~~v~Gi~gI~r~~i-~~~~~~~~l 227 (367)
T TIGR02389 192 ----------------------------LKELRKLKEKIK---------------NLHIKGIKGIKRVVI-RKEGDEYVI 227 (367)
T ss_pred ----------------------------HHHHHHHHHHhh---------------hceEeCCCCceEEEE-ECCCCeEEE
Confidence 011222211000 1111 232 12 234568999
Q ss_pred EEeccchhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceeeeeEEeee
Q psy16767 870 KTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMN 949 (1020)
Q Consensus 870 ~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~G~~~~~n 949 (1020)
+|||+||.++|.++ .||++|++||||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|.+.|||
T Consensus 228 ~teG~nl~~v~~~~-~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~ 306 (367)
T TIGR02389 228 YTEGSNLKEVLKLE-GVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIG 306 (367)
T ss_pred EEeccCHHHHHcCC-CCccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhcCCceEEecc
Confidence 99999999999996 79999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccc-CcchhhhhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCccceEEeec
Q psy16767 950 RNGIRL-NPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLFQLRNR 1009 (1020)
Q Consensus 950 R~G~~~-~~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~fdll~~ 1009 (1020)
||||+. +.|||++||||+|+++|++||.+|+.|+|+|||+||+||+++|+|||+|||+++
T Consensus 307 R~Gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~ 367 (367)
T TIGR02389 307 RHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLVMD 367 (367)
T ss_pred ccccccCCCCHHHhcChHhHHHHHHHHhhcCCCCcCCChHHHhhcCCCcCCcCCeEEEeeC
Confidence 999976 599999999999999999999999999999999999999999999999999874
No 13
>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=2.8e-83 Score=707.31 Aligned_cols=304 Identities=48% Similarity=0.767 Sum_probs=245.5
Q ss_pred hhhcccCCCCCcchhhhhcccCCccccccccccccCCccccccccChhhHHHHHHHhhcCCCCCeEEEEcCCCCchhHHH
Q psy16767 566 KNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPFLPDMPKLEKK 645 (1020)
Q Consensus 566 ky~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~ASk~iKTP~mtv~L~~~~~~~~~~ 645 (1020)
||.+++|+||||||+|||||||||+||||||||||||+++|||||||||||||||+|||+||||+|++||.++... +.
T Consensus 1 ky~~slv~PGE~VG~iaAQSIGEPsTQMTLnTFH~AGv~~~nVTlGvPRL~EIi~~Ask~i~TP~m~v~l~~~~~~--~~ 78 (309)
T cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIKTPSMTLPLKNGKSA--ER 78 (309)
T ss_pred CchhccCCCCcccchhhhhccCCcccccccccccccCccccccccccccHHHHHhhhccCCCCCeEEEEecCchhH--HH
Confidence 6899999999999999999999999999999999999999999999999999999999999999999999987765 68
Q ss_pred HHHHHhhccceehhhhcceeEEEEEeecCCCCCcceEEEEEEecccccccccCCChhhHHHHHHHHHHHHHHHHHHHHHH
Q psy16767 646 ANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMNYQMKFCFIPAHMYRDKTSVKPSKIIDHFERKFLKELEVAIAKRAA 725 (1020)
Q Consensus 646 a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~~~~~y~i~~~l~~~~~~~~~~~i~~~~i~~~~~~~f~~~~~~~i~k~~~ 725 (1020)
|++++++|++++|+||++++++.+ |...+.+.|.+.+ .
T Consensus 79 a~~~~~~ie~~~l~dv~~~~~v~~----------------------------------i~~~~~~~~~~~~--------~ 116 (309)
T cd02735 79 AETLKKRLSRVTLSDVVEKVEVTE----------------------------------ILKTIERVFKKLL--------G 116 (309)
T ss_pred HHHHHhheeEeEHHHhhhhhehhH----------------------------------HHHHHHHHhhhhh--------C
Confidence 999999999999999998877521 3333433332211 0
Q ss_pred ccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccchhhhhhhhhhccccccCCCCCcchHHhhhhcccc
Q psy16767 726 QGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREED 805 (1020)
Q Consensus 726 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 805 (1020)
. ...+ +++... +.+.- .
T Consensus 117 ~-~~~~-----------------------------------------------~i~~~~------~~~~~--~------- 133 (309)
T cd02735 117 K-WCEV-----------------------------------------------TIKLPL------SSPKL--L------- 133 (309)
T ss_pred C-EEEE-----------------------------------------------EEEecC------CchhH--H-------
Confidence 0 0000 000000 00000 0
Q ss_pred cCCCcccccchhhcccchhHHHHHHh-----hccccceeeeccccCCceEEEEecccceeccCCceEEEEEeccchhhhh
Q psy16767 806 DNTSNIGERFKIEFRDSTNVFVKDVV-----NQHNIVHKYSYDKKNHMWCKLLFLPSNLFEEKESKHLLKTDGINVNFIS 880 (1020)
Q Consensus 806 ~~~~~~~~~~~~~~~~~~~~~i~~v~-----~~~~~i~~~~~d~~~~~~~~~~~lp~~~~~~~~~e~~l~teG~nl~~~~ 880 (1020)
.-..++... ...+.|.++....++ ..+..+|+|+|||+||.++|
T Consensus 134 -----------------~~~~~~~~l~~~~i~gi~gI~r~~i~~~~--------------~~~~~~~~l~teG~nl~~v~ 182 (309)
T cd02735 134 -----------------LLSIVEKLARKAVIREIPGITRCFVVEED--------------KGGKTKYLVITEGVNLAALW 182 (309)
T ss_pred -----------------HHHHHHHHhcccEEeCCCCccEEEEecCc--------------CCCceEEEEEeccccHHHHH
Confidence 000011111 011112222111100 11234799999999999999
Q ss_pred ccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceeeeeEEeeeccccccCcchh
Q psy16767 881 QYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLNPSFI 960 (1020)
Q Consensus 881 ~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~G~~~~~nR~G~~~~~spl 960 (1020)
.+.+.||++|++||||++|+++|||||||++|++||++||+.||++||+|||.||||+||++|.+.|+||+||+.+.|||
T Consensus 183 ~~~~~vd~~r~~sNdi~ei~~~lGIEAar~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~~~~~nr~gi~~~~S~l 262 (309)
T cd02735 183 KFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGMESSTSPL 262 (309)
T ss_pred hccCccccccceeCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCcEeecchhheccCCCHH
Confidence 99889999999999999999999999999999999999999999999999999999999999999999999997789999
Q ss_pred hhhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCccceEEe
Q psy16767 961 QKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLFQLR 1007 (1020)
Q Consensus 961 ~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~fdll 1007 (1020)
++||||+|+++|.+||.+|+.|+|+|||+||+||+++++|||+|||+
T Consensus 263 ~~asFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~fdll 309 (309)
T cd02735 263 QKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309 (309)
T ss_pred HhhhhhhHHHHHHHHhhcCCCCCCCChHHheeeCCccCccceeEEeC
Confidence 99999999999999999999999999999999999999999999986
No 14
>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=7.4e-82 Score=716.10 Aligned_cols=370 Identities=32% Similarity=0.463 Sum_probs=270.5
Q ss_pred HHHHHHHHHHhhhcccCCCCCcchhhhhcccCCccccccccccccCCccccccccChhhHHHHHHHhhcCCCCCeEEEEc
Q psy16767 556 VDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPF 635 (1020)
Q Consensus 556 ~~~~~~~~~~ky~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~ASk~iKTP~mtv~L 635 (1020)
.++|...|+.||.+++++||||||++||||||||+|||||||||||||++||||+|||||+||| ||+|+||||+|+|+|
T Consensus 8 ~~~~~~~~~~~~~~~~~~~ge~vg~~aaQSiGEP~TQmTLnTFH~AGVas~NVTlGVPRLkEII-nasK~ikTP~~tv~L 86 (410)
T cd02584 8 FDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEII-NVAKNIKTPSLTVYL 86 (410)
T ss_pred HHHHHHHHHHHHHHhhcCCCCCcchhhhhhcCCchhcccccccccccccccccccCccchHHHh-hcccCCCCCeEEEEe
Confidence 4567788999999999999999999999999999999999999999999999999999999999 899999999999999
Q ss_pred CCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecC-----C------------------CCCcceEEEEEEecccc
Q psy16767 636 LPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEIS-----P------------------EPHMNYQMKFCFIPAHM 692 (1020)
Q Consensus 636 ~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~-----~------------------~~~~~y~i~~~l~~~~~ 692 (1020)
.++...+++.|+.++.+|++++|+||+.++++.+.+... . +....|.++++|...
T Consensus 87 ~~~~~~d~~~A~~v~~~IE~t~l~dv~~~~~i~ydp~~~~~~i~~d~~~i~~~~~~~d~~~~~~~~~~~~lrl~ld~~-- 164 (410)
T cd02584 87 EPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEQDRLSPWLLRIELDRK-- 164 (410)
T ss_pred cCcccchHHHHHHHHhheeEeEHHHhhhheEEEecCcccceeecccHHHHHHhhccCcccccccccCCeeEEEEECHH--
Confidence 988666668999999999999999999999886532100 0 022456666666332
Q ss_pred cccccCCChhhHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccch
Q psy16767 693 YRDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDE 772 (1020)
Q Consensus 693 ~~~~~~i~~~~i~~~~~~~f~~~~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 772 (1020)
....+.++...|...+.+.+ .. .+..+ .++++.
T Consensus 165 ~~~~~~i~~~~i~~~i~~~~------------~~---~~~v~------------------------------~~~~~~-- 197 (410)
T cd02584 165 KMTDKKLSMEQIAKKIKEEF------------KD---DLNVI------------------------------FSDDNA-- 197 (410)
T ss_pred HHHHcCCCHHHHHHHHHHhc------------CC---CeEEE------------------------------EcCCCc--
Confidence 22345555554443332110 00 00000 000000
Q ss_pred hhhhhhhhhccccccCCCCCcchHHhhhhcccccCCCcccccchhhcccchhHHHHHH-hh--------ccccceeeecc
Q psy16767 773 EDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDV-VN--------QHNIVHKYSYD 843 (1020)
Q Consensus 773 ~d~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v-~~--------~~~~i~~~~~d 843 (1020)
+....+++... . .++..++.+ .+....+. .. ..+.|++....
T Consensus 198 -~~~~iri~~~~--~-~~~~~~~~~-------------------------~~~~l~~~~~~~l~~i~l~Gi~~I~r~~i~ 248 (410)
T cd02584 198 -EKLVIRIRIIN--D-DEEKEEDSE-------------------------DDVFLKKIESNMLSDMTLKGIEGIRKVFIR 248 (410)
T ss_pred -ceeEEEEEecC--c-cccccccch-------------------------hHHHHHHHHHhhCCCcEEeCCCCceEEEEE
Confidence 00011111110 0 000000000 00011111 01 11112221111
Q ss_pred ccCCceEEEEecccceeccCCceEEEEEeccchhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhcc
Q psy16767 844 KKNHMWCKLLFLPSNLFEEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVY 923 (1020)
Q Consensus 844 ~~~~~~~~~~~lp~~~~~~~~~e~~l~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~ 923 (1020)
.++..++... .+- ..+.++|+|+|||+||+++|.++ .||++|++||||++|+++|||||||++|++||++||+.|
T Consensus 249 ~~~~~~~~~~--~g~--~~~~~~~~l~teG~nl~~v~~~~-~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~ 323 (410)
T cd02584 249 EENKKKVDIE--TGE--FKKREEWVLETDGVNLREVLSHP-GVDPTRTTSNDIVEIFEVLGIEAARKALLKELRNVISFD 323 (410)
T ss_pred cCCceEecCC--CCc--ccCCcceEEEecCcCHHHHhCCC-CCccccCEeCCHHHHHHhcCHHHHHHHHHHHHHHHHHhc
Confidence 1100000000 000 01345799999999999999995 699999999999999999999999999999999999999
Q ss_pred CcccCcchhhhhcccceeeeeEEeeecccccc-CcchhhhhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCcc
Q psy16767 924 GIEVDPRHLSLVADYMTHSGTYVAMNRNGIRL-NPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTG 1002 (1020)
Q Consensus 924 g~~v~~rHl~LlAD~MT~~G~~~~~nR~G~~~-~~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG 1002 (1020)
|++||+|||+||||+||++|.++||||+||++ +.|||++||||+|+++|++||.+|+.|+|+|||+||+||+++|+|||
T Consensus 324 Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG 403 (410)
T cd02584 324 GSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTG 403 (410)
T ss_pred CCccCHHHHHHHHHHHhhceEEeeEeeeeeeccCCChhhhccchhHHHHHHHHHhcCCCCcCCCchHheeecCccccccc
Confidence 99999999999999999999999999999987 58999999999999999999999999999999999999999999999
Q ss_pred ceEEeec
Q psy16767 1003 LFQLRNR 1009 (1020)
Q Consensus 1003 ~fdll~~ 1009 (1020)
+|||++|
T Consensus 404 ~f~l~~d 410 (410)
T cd02584 404 CFDLLLD 410 (410)
T ss_pred eEEEEeC
Confidence 9999975
No 15
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=100.00 E-value=4.4e-81 Score=711.61 Aligned_cols=337 Identities=30% Similarity=0.414 Sum_probs=267.6
Q ss_pred HHHHHHHHHHhhhcccCCCCCcchhhhhcccCCccccccccccccCCccccccccChhhHHHHHHHhhcCCCCCeEEEEc
Q psy16767 556 VDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPF 635 (1020)
Q Consensus 556 ~~~~~~~~~~ky~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~ASk~iKTP~mtv~L 635 (1020)
.++|...|..+|.+++|+||||||+|||||||||+|||||||||||||+++|||+|||||+||| +|+|+||||+|+|+|
T Consensus 163 ~~~i~~ei~~~y~~~~v~pGE~VG~IAAQSIGEP~TQMTLnTFH~AGVas~NVTlGVPRLkEII-Na~K~isTP~mtiyL 241 (509)
T PRK14897 163 YEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIV-DARKKPSTPTMTIYL 241 (509)
T ss_pred HHHHHHHHHHHHHHhccCCCCCcchhhhhhhCCccccccccccccccccccccccCcchhHHHh-hcccCCCCceEEEEe
Confidence 4566777899999999999999999999999999999999999999999999999999999999 899999999999999
Q ss_pred CCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecCCCCCcceEEEEEEecccccccccCCChhhHHHHHHHHHHHH
Q psy16767 636 LPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMNYQMKFCFIPAHMYRDKTSVKPSKIIDHFERKFLKE 715 (1020)
Q Consensus 636 ~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~~~~~y~i~~~l~~~~~~~~~~~i~~~~i~~~~~~~f~~~ 715 (1020)
.++...+++.|+.++.+|++++|.||+..+... ..+.++++|. ......++++.+.|...+.+..
T Consensus 242 ~~~~~~d~e~A~~V~~~IE~ttL~dv~~~~~d~----------~~~~i~i~Ld--~~~l~~~~l~~~~I~~~I~~~~--- 306 (509)
T PRK14897 242 KKDYREDEEKVREVAKKIENTTLIDVADIITDI----------AEMSVVVELD--EEKMKERLIEYDDILAAISKLT--- 306 (509)
T ss_pred cCcccccHHHHHHHHhhheeeEHHHHHHHHHHh----------ccceEEEEEC--HHHHHHcCCCHHHHHHHHHhcc---
Confidence 987766668999999999999999998644211 1233666663 3334467777766665543210
Q ss_pred HHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccchhhhhhhhhhccccccCCCCCcch
Q psy16767 716 LEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPED 795 (1020)
Q Consensus 716 ~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~d~ 795 (1020)
. .. . . +++ + .++..... +.
T Consensus 307 ----------~----~~---~--------~--------------------~~~-----~----~I~i~~~~-------~~ 325 (509)
T PRK14897 307 ----------F----KT---V--------E--------------------IDD-----G----IIRLKPQQ-------PS 325 (509)
T ss_pred ----------c----eE---E--------e--------------------cCC-----C----EEEEEeCc-------hH
Confidence 0 00 0 0 000 0 01111100 00
Q ss_pred HHhhhhcccccCCCcccccchhhcccchhHHHHHHhhccccceeeeccccCCceEEEEe--ccc----ceec-cCCceEE
Q psy16767 796 EERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLF--LPS----NLFE-EKESKHL 868 (1020)
Q Consensus 796 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~i~~~~~d~~~~~~~~~~~--lp~----~~~~-~~~~e~~ 868 (1020)
...++.+..... .+.+ +|+ ++.. .++++|+
T Consensus 326 ----------------------------~~~L~~l~~~l~---------------~i~I~GipgI~r~~i~~~~~~~~~~ 362 (509)
T PRK14897 326 ----------------------------FKKLYLLAEKVK---------------SLTIKGIKGIKRAIARKENDERRWV 362 (509)
T ss_pred ----------------------------HHHHHHHHHHhh---------------ccEEeCCCCccEEEEecCCCCceeE
Confidence 011122111100 1111 232 2222 2334699
Q ss_pred EEEeccchhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceeeeeEEee
Q psy16767 869 LKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAM 948 (1020)
Q Consensus 869 l~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~G~~~~~ 948 (1020)
|+|||+||.++|.+ +.||++||+||||++|+++|||||||++|++||+.||+.||++||+|||+||||+||++|.+.||
T Consensus 363 L~TeG~NL~~vl~~-~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHL~LIAD~MT~~G~v~~i 441 (509)
T PRK14897 363 IYTQGSNLKDVLEI-DEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAI 441 (509)
T ss_pred EEeeccCHHHHhcC-CCcccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhCcCCccccc
Confidence 99999999999999 57999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccccc-CcchhhhhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCccceEEeeccccc
Q psy16767 949 NRNGIRL-NPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLFQLRNREKKK 1013 (1020)
Q Consensus 949 nR~G~~~-~~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~fdll~~~~~~ 1013 (1020)
|||||+. +.|||++||||+|++||++||++|+.|+|+|||+|||+|+++|+|||+|||+++..+.
T Consensus 442 ~R~Gi~~~~~SpL~rASFE~T~~~L~~AA~~Ge~D~L~GvsenII~G~~ipvGTG~fdL~~~~~~~ 507 (509)
T PRK14897 442 GRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYKGRKK 507 (509)
T ss_pred ccccccccCCCHHHhcchHhHHHHHHHHhhcCCCCcCCChHHhhhcCCccCCcCceEEEEecCCCC
Confidence 9999976 6999999999999999999999999999999999999999999999999999976543
No 16
>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=7.8e-81 Score=698.79 Aligned_cols=335 Identities=30% Similarity=0.473 Sum_probs=270.8
Q ss_pred HHHHHHHHHHhhhcccCCCCCcchhhhhcccCCccccccccccccCCccccccccChhhHHHHHHHhhcCCCCCeEEEEc
Q psy16767 556 VDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPF 635 (1020)
Q Consensus 556 ~~~~~~~~~~ky~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~ASk~iKTP~mtv~L 635 (1020)
.++|...++.+|.+++|+||||||++||||||||+|||||||||||||++||||+|||||+||| ||+|+||||+|+++|
T Consensus 21 ~~~~~~~~~~~~~~~~~~~Ge~vG~iaAQSiGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEII-na~K~i~TP~mti~L 99 (363)
T cd06528 21 AEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIV-DARKEPSTPTMTIYL 99 (363)
T ss_pred HHHHHHHHHHHHHHHhhccCccccceeeeecCccceecccccccccccccccCccccccHHHHh-hcccCCCCceEEEEe
Confidence 4567777899999999999999999999999999999999999999999999999999999999 899999999999999
Q ss_pred CCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecCCCCCcceEEEEEEecccccccccCCChhhHHHHHHHHHHHH
Q psy16767 636 LPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMNYQMKFCFIPAHMYRDKTSVKPSKIIDHFERKFLKE 715 (1020)
Q Consensus 636 ~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~~~~~y~i~~~l~~~~~~~~~~~i~~~~i~~~~~~~f~~~ 715 (1020)
.++...+++.|+.++.+|++++|+|++.++++.. ..|.++++|. ......++++++.|...+.+.+
T Consensus 100 ~~~~~~~~~~a~~v~~~iE~t~l~di~~~~~i~~---------~~~~l~i~ld--~~~l~~~~l~~~~i~~~i~~~~--- 165 (363)
T cd06528 100 EEEYKYDREKAEEVARKIEETTLENLAEDISIDL---------FNMRITIELD--EEMLEDRGITVDDVLKAIEKLK--- 165 (363)
T ss_pred cCcchhhHHHHHHHHHhhceeEHHHhhhheEEec---------cCcEEEEEEC--HHHHHHcCCCHHHHHHHHHHhc---
Confidence 9877666689999999999999999999998743 1355777773 3333466778777665543221
Q ss_pred HHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccchhhhhhhhhhccccccCCCCCcch
Q psy16767 716 LEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPED 795 (1020)
Q Consensus 716 ~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~d~ 795 (1020)
+ .. +.. + + +. ...... . + +.
T Consensus 166 ----------~--~~-------------~~~------------------~--~-----~~---~~~~~~-~-----~-~~ 185 (363)
T cd06528 166 ----------K--GK-------------VGE------------------E--G-----DV---TLIVLK-A-----E-EP 185 (363)
T ss_pred ----------C--Cc-------------ccc------------------c--C-----Cc---cEEEEc-C-----C-cc
Confidence 0 00 000 0 0 00 000000 0 0 00
Q ss_pred HHhhhhcccccCCCcccccchhhcccchhHHHHHHhhccccceeeeccccCCceEEEEe--ccc----ceeccCCceEEE
Q psy16767 796 EERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLF--LPS----NLFEEKESKHLL 869 (1020)
Q Consensus 796 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~i~~~~~d~~~~~~~~~~~--lp~----~~~~~~~~e~~l 869 (1020)
....++.+.... ..+.+ +|+ ++ ...+++|+|
T Consensus 186 ---------------------------~~~~l~~l~~~l---------------~~~~v~Gi~gI~r~~i-~~~~~~~~l 222 (363)
T cd06528 186 ---------------------------SIKELRKLAEKI---------------LNTKIKGIKGIKRVIV-RKEEDEYVI 222 (363)
T ss_pred ---------------------------hHHHHHHHHHhh---------------cccEEeCCCCceEEEE-ecCCceEEE
Confidence 011222222110 01112 333 12 233458999
Q ss_pred EEeccchhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceeeeeEEeee
Q psy16767 870 KTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMN 949 (1020)
Q Consensus 870 ~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~G~~~~~n 949 (1020)
+|||+||.++|.++ .||++|++||||++|+++|||||||++|++||++||+.||++||+|||.||||+||++|.+.|+|
T Consensus 223 ~teG~nl~~v~~~~-~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~ 301 (363)
T cd06528 223 YTEGSNLKAVLKVE-GVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIG 301 (363)
T ss_pred EecCcCHHHHhcCC-CCcccccccCCHHHHHHhCCHHHHHHHHHHHHHHHHHhcCCeecHHHHHHHHHHhccCCceeccc
Confidence 99999999999995 69999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccc-CcchhhhhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCccceEEeec
Q psy16767 950 RNGIRL-NPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLFQLRNR 1009 (1020)
Q Consensus 950 R~G~~~-~~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~fdll~~ 1009 (1020)
|+||++ +.|||++||||+|+++|++||.+|+.|+|.|||+||+||+++|+|||+|||+++
T Consensus 302 R~gi~~~~~S~L~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~d 362 (363)
T cd06528 302 RHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTMD 362 (363)
T ss_pred chhhcCCCCChhhhCchhhHHHHHHHHHhcCCCCcCCCcHHHeeeCCCCCCcCCeeEEEec
Confidence 999976 599999999999999999999999999999999999999999999999999986
No 17
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=100.00 E-value=1.4e-79 Score=693.19 Aligned_cols=336 Identities=29% Similarity=0.469 Sum_probs=272.5
Q ss_pred HHHHHHHHHHhhhcccCCCCCcchhhhhcccCCccccccccccccCCccccccccChhhHHHHHHHhhcCCCCCeEEEEc
Q psy16767 556 VDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPF 635 (1020)
Q Consensus 556 ~~~~~~~~~~ky~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~ASk~iKTP~mtv~L 635 (1020)
.++|...|+.||.+++++||||||++||||||||+|||||||||+||++++|||+|||||+||| ||+|+||||+|+++|
T Consensus 40 ~~~~~~~i~~~y~~~~v~pGe~VG~iaAQsIGEP~TQMTL~TFH~AGva~~nVTlGvPRlkEIi-na~K~~~TP~~tv~L 118 (383)
T PRK04309 40 VEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIV-DARKEPSTPMMTIYL 118 (383)
T ss_pred HHHHHHHHHHHHHHhhcCCCCccchhhhhhccchhhhcccccccccCccccCcccCchhHHHHH-hcccCCCCCeEEEEe
Confidence 4567778899999999999999999999999999999999999999999999999999999999 899999999999999
Q ss_pred CCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecCCCCCcceEEEEEEecccccccccCCChhhHHHHHHHHHHHH
Q psy16767 636 LPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMNYQMKFCFIPAHMYRDKTSVKPSKIIDHFERKFLKE 715 (1020)
Q Consensus 636 ~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~~~~~y~i~~~l~~~~~~~~~~~i~~~~i~~~~~~~f~~~ 715 (1020)
.++...+++.|+.++.+|++++|+|++.++.+.. + .+.+++.| +......+++++..|.+.+.+.+.
T Consensus 119 ~~~~~~d~~~a~~v~~~iE~t~L~~v~~~i~~~~------~---~~~l~i~l--d~~~i~~~~l~~~~I~~~i~~~~~-- 185 (383)
T PRK04309 119 KDEYAYDREKAEEVARKIEATTLENLAKDISVDL------A---NMTIIIEL--DEEMLEDRGLTVDDVKEAIEKKKG-- 185 (383)
T ss_pred cCcccccHHHHHHHHhheeeeEHhhhhhheEecc------C---CcEEEEEE--CHHHHHHcCCCHHHHHHHHHHhcC--
Confidence 9876666689999999999999999999888632 1 23466666 344455678887766665543210
Q ss_pred HHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccchhhhhhhhhhccccccCCCCCcch
Q psy16767 716 LEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPED 795 (1020)
Q Consensus 716 ~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~d~ 795 (1020)
.... +. + + ...++.+ . ++
T Consensus 186 -------------~~~~-----------~~---~------------------------~--~i~i~~~--~------~~- 203 (383)
T PRK04309 186 -------------GEVE-----------IE---G------------------------N--TLIISPK--E------PS- 203 (383)
T ss_pred -------------ccee-----------cc---C------------------------C--eEEEEec--C------ch-
Confidence 0000 00 0 0 0011110 0 00
Q ss_pred HHhhhhcccccCCCcccccchhhcccchhHHHHHHhhccccceeeeccccCCceEEEEe--ccc----ceeccCCceEEE
Q psy16767 796 EERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLF--LPS----NLFEEKESKHLL 869 (1020)
Q Consensus 796 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~i~~~~~d~~~~~~~~~~~--lp~----~~~~~~~~e~~l 869 (1020)
...++.+..... .+.+ +|+ ++ ...+++|+|
T Consensus 204 ----------------------------~~~l~~l~~~l~---------------~~~vkGi~gI~r~~i-~~~~~~~~l 239 (383)
T PRK04309 204 ----------------------------YRELRKLAEKIR---------------NIKIKGIKGIKRVII-RKEGDEYVI 239 (383)
T ss_pred ----------------------------HHHHHHHHHHhc---------------ccEEECCCCceEEEE-ecCCCeEEE
Confidence 011122211100 0111 222 12 234568999
Q ss_pred EEeccchhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceeeeeEEeee
Q psy16767 870 KTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMN 949 (1020)
Q Consensus 870 ~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~G~~~~~n 949 (1020)
+|||+||.++|.+ +.||++|++||||++|+++|||||||++|++||++||+.||++||+|||.||||+||++|.+.|+|
T Consensus 240 ~teG~nl~~v~~~-~~VD~~rt~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~ 318 (383)
T PRK04309 240 YTEGSNLKEVLKV-EGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIG 318 (383)
T ss_pred EEcccCHHHHhcC-CCEeeccccCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhccCceEEeee
Confidence 9999999999999 579999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccc-CcchhhhhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCccceEEeecccc
Q psy16767 950 RNGIRL-NPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLFQLRNREKK 1012 (1020)
Q Consensus 950 R~G~~~-~~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~fdll~~~~~ 1012 (1020)
||||++ +.|||++||||+|+++|++||.+|+.|+|+|||+||+||+++|+|||+|||+++.++
T Consensus 319 R~Gi~~~~~S~l~~aSFE~T~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~~~~ 382 (383)
T PRK04309 319 RHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPL 382 (383)
T ss_pred chhhcCCCCCHHHhCchhhHHHHHHHHHhcCCCCCCCCcHHHhhcCCCcCCCCceEEEEcCCCC
Confidence 999976 689999999999999999999999999999999999999999999999999998765
No 18
>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=3.6e-79 Score=669.35 Aligned_cols=299 Identities=32% Similarity=0.482 Sum_probs=241.3
Q ss_pred hhhcccCCCCCcchhhhhcccCCccccccccccccCCccccccccChhhHHHHHHHhhcCCCCCeEEEEcCCCCchhHHH
Q psy16767 566 KNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPFLPDMPKLEKK 645 (1020)
Q Consensus 566 ky~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~ASk~iKTP~mtv~L~~~~~~~~~~ 645 (1020)
||.+++|+||||||++||||||||+|||||||||+||++++|||+|||||+||| +|||+||||+|+++|.+..+ ++.
T Consensus 1 ky~~~~v~pGe~vG~iaaQsiGEp~TQmTL~TFH~aGv~~~nvtlGvPRlkEIi-nasK~~~TP~~ti~l~~~~~--~~~ 77 (300)
T cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEII-NASKNISTPIITAKLENDRD--EKS 77 (300)
T ss_pred CchhhccCCCccchhhhhhhcCCccccccccccccccccccccccCchHHHHHH-hcccCCCCCeEEEEecCccc--HHH
Confidence 689999999999999999999999999999999999999999999999999999 89999999999999998544 489
Q ss_pred HHHHHhhccceehhhhcceeEEEEEeecCCCCCcceEEEEEEecccccccccCCChhhHHHHHHHHHHHHHHHHHHHHHH
Q psy16767 646 ANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMNYQMKFCFIPAHMYRDKTSVKPSKIIDHFERKFLKELEVAIAKRAA 725 (1020)
Q Consensus 646 a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~~~~~y~i~~~l~~~~~~~~~~~i~~~~i~~~~~~~f~~~~~~~i~k~~~ 725 (1020)
|+.++.+|++++|+|++.++++.+ +|+. ..+.+++ +..+.+.+.+..+... + ....+++.+.
T Consensus 78 a~~v~~~ie~t~l~di~~~~~~~~----~p~~---~~~~i~~--d~~~i~~~~l~~~~~~------~---~~~~l~~~l~ 139 (300)
T cd02736 78 ARIVKGRIEKTYLGEVASYIEEVY----SPDD---CYILIKL--DKKIIEKLQLSKSNLY------F---LLQSLKRKLP 139 (300)
T ss_pred HHHHHHHHhhccHHHhhhheEEEE----cCCC---ceEEEEe--cHHHHHHhcCCcccHH------H---HHHHHHHHhc
Confidence 999999999999999999988744 3332 2233333 2222222222111000 0 0000000000
Q ss_pred ccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccchhhhhhhhhhccccccCCCCCcchHHhhhhcccc
Q psy16767 726 QGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREED 805 (1020)
Q Consensus 726 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 805 (1020)
.
T Consensus 140 ~------------------------------------------------------------------------------- 140 (300)
T cd02736 140 D------------------------------------------------------------------------------- 140 (300)
T ss_pred c-------------------------------------------------------------------------------
Confidence 0
Q ss_pred cCCCcccccchhhcccchhHHHHHHhhccccceeeeccccCCceEEEEecccceeccCCceEEEEEeccchhhhhccCCc
Q psy16767 806 DNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLFLPSNLFEEKESKHLLKTDGINVNFISQYRHL 885 (1020)
Q Consensus 806 ~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~i~~~~~d~~~~~~~~~~~lp~~~~~~~~~e~~l~teG~nl~~~~~~~~~ 885 (1020)
.+....+.|.++... ....+++|+|+|||+||.++|.++ .
T Consensus 141 -----------------------~~v~Gi~gI~r~~i~----------------~~~~~~~~~l~teG~nl~~v~~~~-~ 180 (300)
T cd02736 141 -----------------------VVVSGIPEVKRAVIN----------------KDKKKGKYKLLVEGYGLRAVMNTP-G 180 (300)
T ss_pred -----------------------ceEeCCCCceEEEEe----------------cCCCCCcEEEEEecccHHHHhcCC-c
Confidence 000000111111110 011235799999999999999995 7
Q ss_pred ccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceeeeeEEeeecccccc-Ccchhhhhc
Q psy16767 886 LDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRL-NPSFIQKMT 964 (1020)
Q Consensus 886 iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~G~~~~~nR~G~~~-~~spl~kaS 964 (1020)
||++|++||||++|+++|||||||++|++||++||+.||++||+|||.||||+||++|.++||||+||++ +.|||++||
T Consensus 181 Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~itR~gi~~~~~S~l~~aS 260 (300)
T cd02736 181 VIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLAS 260 (300)
T ss_pred EeccCCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhccCceeeeecccccccCCCHHHhcc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999986 689999999
Q ss_pred chhHHHHHHHHHhcCCCccCCCcccceecCCccccCccce
Q psy16767 965 FEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLF 1004 (1020)
Q Consensus 965 FE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~f 1004 (1020)
||+|+++|++||.+|+.|+|+|||+||+||+++|+|||+|
T Consensus 261 FE~t~~~L~~AA~~g~~D~l~gvse~ii~G~~~~~GTG~f 300 (300)
T cd02736 261 FEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300 (300)
T ss_pred hHhHHHHHHHHhhcCCCCcCCCcHHHeeeCCCcCCCCCCC
Confidence 9999999999999999999999999999999999999997
No 19
>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=3.8e-73 Score=626.64 Aligned_cols=277 Identities=50% Similarity=0.743 Sum_probs=221.3
Q ss_pred CCChhhHHHhhcccccchhhhccccCCcchhHHHHHhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhcccccccc
Q psy16767 361 GIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYLTDKQF 440 (1020)
Q Consensus 361 GL~p~EfFfH~m~gReGLiDTAvKTa~sGYLqRrLvk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~~~~~~ 440 (1020)
||+|.|||||||||||||||||||||+||||||||||+|||++|.||+|||++++.|+||.||+||
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 999999999999999999999999999999999999999999999999999999999999999877
Q ss_pred hhhhhhHHHHhhHHHHHhhhccCchhHHHHHHHhhhcCCCCCcccCCCcchhHHHHHHHHHhhcHHHHHHHHHhccCCCC
Q psy16767 441 SFLEDNIKWICSYKVILNLLKKHPLSLALLLLLTFKSSGKPNFIFSPHRTKFTMDLLEQWYQLDDKARKKYRKKFKACPQ 520 (1020)
Q Consensus 441 ~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 520 (1020)
T Consensus 67 -------------------------------------------------------------------------------- 66 (277)
T PF04998_consen 67 -------------------------------------------------------------------------------- 66 (277)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCcccCCCCcccccchHHHHHHHHHHhhccCcchhHHHHHHHHHHhhhcccCCCCCcchhhhhcccCCcccccccccccc
Q psy16767 521 PLISTFQPDAHFGSISENLADSVVKYTKGRTDASHVDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHF 600 (1020)
Q Consensus 521 ~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~~~~~~~~~~~~~~~~ky~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~ 600 (1020)
+|+||||||+|||||||||+|||||||||+
T Consensus 67 --------------------------------------------------~v~~Ge~VGiiaAQSIGEP~TQ~TL~TFH~ 96 (277)
T PF04998_consen 67 --------------------------------------------------LVEPGEAVGIIAAQSIGEPGTQMTLRTFHT 96 (277)
T ss_dssp --------------------------------------------------B--TTSBHHHHHHHHHHCHGCCSHHSCTSS
T ss_pred --------------------------------------------------ccCccccchhhhhchhcchhHHhhhccccc
Confidence 135899999999999999999999999999
Q ss_pred CCccccccccChhhHHHHHHHhhcCCCCCeEEEEcCCCCchhHHHHHHHHhhccceehhhhcceeEEEEEeecCCCCCcc
Q psy16767 601 AGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMN 680 (1020)
Q Consensus 601 AG~~~~nvTlGvPRLkEIi~~ASk~iKTP~mtv~L~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~~~~~ 680 (1020)
||++++|||+|+|||+||+ +++++++||+++++.........+.+..+......
T Consensus 97 aG~~~~~vt~giprl~eii-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------------- 150 (277)
T PF04998_consen 97 AGVASKNVTQGIPRLKEII-NASKKIKTPIITVYGKKKIISEKKKIKIIRKKIKI------------------------- 150 (277)
T ss_dssp SCSSTSSCSSSHHHHHHHH-TTCSSSSSEEEEECSCSSECSSSHHHHHHHHTCSS-------------------------
T ss_pred Cceeeecccccceeecccc-ccccccccceEEeecccceecccccceEEEEeeee-------------------------
Confidence 9999999999999999999 78999999999987765432211222222211111
Q ss_pred eEEEEEEecccccccccCCChhhHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCC
Q psy16767 681 YQMKFCFIPAHMYRDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALG 760 (1020)
Q Consensus 681 y~i~~~l~~~~~~~~~~~i~~~~i~~~~~~~f~~~~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 760 (1020)
.. ....... .
T Consensus 151 --------------------------------------------~~---~~~~~~~--------~--------------- 160 (277)
T PF04998_consen 151 --------------------------------------------IK---NGKKVKN--------G--------------- 160 (277)
T ss_dssp --------------------------------------------SC---STTCEHT--------T---------------
T ss_pred --------------------------------------------ee---cccceec--------c---------------
Confidence 00 0000000 0
Q ss_pred CcCCCCccccchhhhhhhhhhccccccCCCCCcchHHhhhhcccccCCCcccccchhhcccchhHHHHHHhhccccceee
Q psy16767 761 RVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKY 840 (1020)
Q Consensus 761 ~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~i~~~ 840 (1020)
.... . . .......
T Consensus 161 -----------------~~~~--------~-~-------------------------------~~~~~~~---------- 173 (277)
T PF04998_consen 161 -----------------DKIK--------K-G-------------------------------SIISKDI---------- 173 (277)
T ss_dssp -----------------CESS--------S-S-------------------------------CSEHHHH----------
T ss_pred -----------------eeee--------c-c-------------------------------eeeeecc----------
Confidence 0000 0 0 0000000
Q ss_pred eccccCCceEEEEecccceeccCCceEEEEEeccchhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhh
Q psy16767 841 SYDKKNHMWCKLLFLPSNLFEEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVF 920 (1020)
Q Consensus 841 ~~d~~~~~~~~~~~lp~~~~~~~~~e~~l~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~ 920 (1020)
......+|+++++|.||..+|.+++++|++|++||||++|+++|||||||++|++|+..||
T Consensus 174 -------------------~~~~~~~~~l~~~g~~l~~v~~~qgvid~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~ 234 (277)
T PF04998_consen 174 -------------------LEKKSKEYVLQTEGSNLQEVYSSQGVIDNDKHISNDIRQMLSKLGIEAARNSIIKELKNVF 234 (277)
T ss_dssp -------------------CEECCCCCEEECCSHHHHHHTCSTT-EETCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHH
T ss_pred -------------------ccchhHHHHHHHHhhhchhheecccccCCCEEEeceeEeeeeeEEEEECCCceeecCcEee
Confidence 0113467899999999999999998899999999999999999999999999999999999
Q ss_pred hccCcccCcchhhhhcccceeeeeEEeeeccccccCcchhhhh
Q psy16767 921 AVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLNPSFIQKM 963 (1020)
Q Consensus 921 ~~~g~~v~~rHl~LlAD~MT~~G~~~~~nR~G~~~~~spl~ka 963 (1020)
..||++||+|||.|+||+||++|.++||||+||+.+.+||.+|
T Consensus 235 ~~~g~~vn~rhl~llad~mt~~g~~~gitR~gl~~~~~S~~~~ 277 (277)
T PF04998_consen 235 ESYGIEVNKRHLSLLADYMTYKGVLLGITRHGLNSNKSSFLSM 277 (277)
T ss_dssp HHCTSCCCHHHHHHHHHHHCCCSS---CCTTTTSSSSSSHHH-
T ss_pred HHHHHHHHHHHHHhCCCcCeeeeEEEEEEHHHhccCCCCccCC
Confidence 9999999999999999999999999999999999987777765
No 20
>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=1.2e-68 Score=602.11 Aligned_cols=317 Identities=21% Similarity=0.279 Sum_probs=227.6
Q ss_pred CCcchhhhhcccCCccccccccccccCCccccccccChhhHHHHHHHh--hcCCCCCeEEEEcCC-------CCchhHHH
Q psy16767 575 GENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMA--TKAIKTPSMEIPFLP-------DMPKLEKK 645 (1020)
Q Consensus 575 Ge~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~A--Sk~iKTP~mtv~L~~-------~~~~~~~~ 645 (1020)
|||||+|||||||||||||||||||+||++ +|||||||| +. ++++|||+++|+|.. +... +++
T Consensus 1 GE~VG~LAAqSIgEPAtQmtLntfh~agvs------~vprLKEiL-n~~~~~~~ktps~~v~L~~~~~~~~~~~~~-~~~ 72 (381)
T cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESS------PLELLKEVL-ECRSKSKSKENDRRVILSLHLCKCDHGFEY-ERA 72 (381)
T ss_pred CCcchhHHHhhhcchHHHhhhccchhcCCc------cHHHHHHHh-cccccCCCCCCCEEEEEeccccccccchHH-HHH
Confidence 999999999999999999999999999995 499999999 66 678999999999975 3222 578
Q ss_pred HHHHHhhccceehhhhcceeEEEEEeecCCC----------------------------CCcceEEEEEEeccccccccc
Q psy16767 646 ANRLAKSMTRITMADVLEKVKIKEWLEISPE----------------------------PHMNYQMKFCFIPAHMYRDKT 697 (1020)
Q Consensus 646 a~~i~~~l~~v~L~dvi~~i~v~~~~~~~~~----------------------------~~~~y~i~~~l~~~~~~~~~~ 697 (1020)
|+++++.|++++|++++..+.|.|++..... +..+|.+++.+...
T Consensus 73 a~~Vq~~Le~~tL~~v~~~~~I~Ydp~~~~t~i~~d~~~~~~~~~~~~~~~~~~~~~~~~~spw~~r~~l~~~------- 145 (381)
T cd02737 73 ALEVKNHLERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKKAIFSTSLKITKFSPWVCHFHLDKE------- 145 (381)
T ss_pred HHHHHHHhhhccHHHhhheEEEEECCCcccccccccHHHHHhhhhhhhhcccccccccccCCcceEEEEEehh-------
Confidence 9999999999999999999988664321100 01112222222100
Q ss_pred CCChhhHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccchhhhhh
Q psy16767 698 SVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQ 777 (1020)
Q Consensus 698 ~i~~~~i~~~~~~~f~~~~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~ 777 (1020)
...+ .....+.. . ++ ++.+.+ .+ .....
T Consensus 146 -------------------------~~~~--~~~~ci~~--------~----~~-----------~~~~~~-~~-~~~~~ 173 (381)
T cd02737 146 -------------------------CQKL--SDGPCLTF--------S----VS-----------KEVSKS-SE-ELLDV 173 (381)
T ss_pred -------------------------HhcC--CCCceEEe--------e----cC-----------cccccc-hh-HHHHH
Confidence 0011 00000000 0 00 000000 00 00000
Q ss_pred hhhhccccccCCCCCcchHHhhhhcccccCCCcccccchhhcccchhHHHHHHh----hccccceeeec---cccCCceE
Q psy16767 778 SHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVV----NQHNIVHKYSY---DKKNHMWC 850 (1020)
Q Consensus 778 ~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~----~~~~~i~~~~~---d~~~~~~~ 850 (1020)
+. +..+..++ +-.+.|+...- +.....|.
T Consensus 174 --~~------------------------------------------~~i~~~lL~~~lkG~~~I~kv~i~~~~~~~~~~~ 209 (381)
T cd02737 174 --LR------------------------------------------DRIIPFLLETVIKGDERIKSVNILWEDSPSTSWV 209 (381)
T ss_pred --HH------------------------------------------HHHHHHHhheeecccCCeeEEEEEecCCCccccc
Confidence 00 00000011 01111111110 00000110
Q ss_pred EEEecccceeccCCceEEEEEe---------ccchhhhhc----cCCcccccccccccHHHHHHhhhHHHHHHHHHHHHH
Q psy16767 851 KLLFLPSNLFEEKESKHLLKTD---------GINVNFISQ----YRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVK 917 (1020)
Q Consensus 851 ~~~~lp~~~~~~~~~e~~l~te---------G~nl~~~~~----~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~ 917 (1020)
+ + ......+||+|+|+ |.++..++. ..+.||++|++||||++|+++|||||||++|++||+
T Consensus 210 ~-----~-~~~~~~~E~vLe~~~~~~~~~t~G~~~~~vl~~c~~~~~~ID~~rt~sNdI~ev~~~lGIEAAR~~ii~El~ 283 (381)
T cd02737 210 K-----S-VGKSSRGELVLEVTVEESCKKTRGNAWNVVMDACIPVMDLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLE 283 (381)
T ss_pred c-----c-ccccccceEEEEEEeccccccccchhHHHHHHhhhcccccCcCCCcEECCHHHHHHHHhHHHHHHHHHHHHH
Confidence 0 0 00235679999988 999999995 336899999999999999999999999999999999
Q ss_pred hhhhccCcccCcchhhhhcccceeeeeEEeeeccccccC------cchhhhhcchhHHHHHHHHHhcCCCccCCCcccce
Q psy16767 918 NVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLN------PSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARV 991 (1020)
Q Consensus 918 ~v~~~~g~~v~~rHl~LlAD~MT~~G~~~~~nR~G~~~~------~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~I 991 (1020)
+||+.||++||+|||.||||+||++|.++|||||||++. +|||+|||||+|+++|++||.+|+.|+|+|||++|
T Consensus 284 ~v~~~~G~~Vd~rHL~LlAD~MT~~G~~~~~nR~Gi~~~~~s~~~~spl~~asFE~t~~~l~~AA~~g~~D~l~gvs~~i 363 (381)
T cd02737 284 SAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDAC 363 (381)
T ss_pred HHHHhcCCcccHHHHHHHHHHhccCCceEEecchhhhhcccccccCCHHHHhhHHHHHHHHHHHHhccCCCCCCChHHhe
Confidence 999999999999999999999999999999999999962 49999999999999999999999999999999999
Q ss_pred ecCCccccCccc-eEEee
Q psy16767 992 MLGQECRQGTGL-FQLRN 1008 (1020)
Q Consensus 992 i~Gk~~~~GTG~-fdll~ 1008 (1020)
+|||++++|||+ |||+|
T Consensus 364 i~G~~~~vGTG~~fdll~ 381 (381)
T cd02737 364 AWGKEAPVGTGSKFEILW 381 (381)
T ss_pred eeCCcCCCcCCcceeeeC
Confidence 999999999998 99986
No 21
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=1.3e-63 Score=617.58 Aligned_cols=345 Identities=25% Similarity=0.356 Sum_probs=227.8
Q ss_pred eccCcccccCcchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHHHHHHHHHHHHHHHH
Q psy16767 152 GILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAA 231 (1020)
Q Consensus 152 G~LdK~~lG~~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~~~i~~a~~~~~~~~ 231 (1020)
-++||+.++ +||+.+|+.||+..|+.|||.+++|+++|++.+|||+|++|+.+|++ |.+++++|++++.++.
T Consensus 6 ~~idKk~l~----~LI~~~~~~yG~~~t~~~lD~lk~LGf~~aT~~G~SigidDl~ip~~----K~~li~~Ae~~v~~~~ 77 (1331)
T PRK02597 6 RVVDKKALK----NLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPA----KRDLLEQAEEEITATE 77 (1331)
T ss_pred ccccHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCcEEEeecccccCHH----HHHHHHHHHHHHHHHH
Confidence 378999997 89999999999999999999999999999999999999999999987 6789999998876544
Q ss_pred HHHcCCCCCCCHHHHHHHHHHhcc-CchhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCChhHHHHhhcCCcchh
Q psy16767 232 CNALGLPLDTDPEIISSQLQEAYA-SIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTV 310 (1020)
Q Consensus 232 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~ 310 (1020)
+ .+..+.+ ..+++.+.++.| +++.+.+++++.+. +...+|.||+++|+.||||||+.
T Consensus 78 ~----------------~y~~G~it~~Er~~kvi~~w-~~t~e~l~~~~~~~-----~~~~dp~N~v~mMa~SGARGN~s 135 (1331)
T PRK02597 78 E----------------RYRRGEITEVERFQKVIDTW-NETNERLKDEVVKN-----FRQNDPLNSVYMMAFSGARGNMS 135 (1331)
T ss_pred H----------------HHHcCCCchhHHHHHHHHHH-HHHHHHHHHHHHHH-----HhhcCCCCcHHHHhhccCCccHH
Confidence 3 2334434 234555555555 44444554444332 33467899999999999999777
Q ss_pred hHHHHHhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhhhccccCCcch
Q psy16767 311 NTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGY 390 (1020)
Q Consensus 311 N~~Qi~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGY 390 (1020)
|+.|++||+|++ +. .+|++. + .| |.|||++||+|.|||||||||||||+|||||||+|||
T Consensus 136 QI~QLvGmRGLm-----a~---p~G~ii------~-lP-----I~snFrEGLs~~EyFis~~GaRKGLvDTAlKTAdSGY 195 (1331)
T PRK02597 136 QVRQLVGMRGLM-----AN---PQGEII------D-LP-----IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGY 195 (1331)
T ss_pred HHHHHhcchhhc-----cC---CCCcEE------e-cc-----hhhhhhcCCCHHHhheeccccccchhhcceecccchh
Confidence 777766666653 22 235543 1 13 9999999999999999999999999999999999999
Q ss_pred hHHHHHhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhcccccccchhhhhhHHHHhhHHHHHhhhccCchhHHHH
Q psy16767 391 LQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYLTDKQFSFLEDNIKWICSYKVILNLLKKHPLSLALL 470 (1020)
Q Consensus 391 LqRrLvk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~ 470 (1020)
||||||+ |.+|..||..||.. ..|+......... ..+..+.+.. .
T Consensus 196 LTRRLVd------v~QDviVre~DCgT------~~gi~~~~~~~~~-~~i~~l~~rl---------~------------- 240 (1331)
T PRK02597 196 LTRRLVD------VSQDVIVREEDCGT------TRGIVVEAMDDGD-RVLIPLGDRL---------L------------- 240 (1331)
T ss_pred HHHHHHH------hhcceEEEecCCCC------CCCEEEEEEecCC-EEEeEehhee---------E-------------
Confidence 9999999 55555677777654 2344332211000 0000000000 0
Q ss_pred HHHhhhc--CCCCCcccCCCcchhHHHHHHHHHhhcHHHHHHHHHhccCCCCCCcccCCCCcccccchHHHHHHHHHHhh
Q psy16767 471 LLLTFKS--SGKPNFIFSPHRTKFTMDLLEQWYQLDDKARKKYRKKFKACPQPLISTFQPDAHFGSISENLADSVVKYTK 548 (1020)
Q Consensus 471 ~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~~~ 548 (1020)
.++.. +.++ . ++... ..-..++.+...++.+. .. .++. ..+|..
T Consensus 241 --GR~~~~~i~~~----~-~~~i~-----~~n~~i~~~~~~~i~~~-~~--~~v~-iRsplt------------------ 286 (1331)
T PRK02597 241 --GRVLAEDVVDP----E-GEVIA-----ERNTAIDPDLAKKIEKA-GV--EEVM-VRSPLT------------------ 286 (1331)
T ss_pred --EEEEhhHeeCC----C-CCEEE-----eCCCCcCHHHHHHHHHc-CC--CEEE-EECCEE------------------
Confidence 00000 0000 0 00000 00000000111111110 00 0000 000100
Q ss_pred ccCcchhHHHHHHHHHHhh--hcccCCCCCcchhhhhcccCCccccccccccccCCccccccc-------cChhhHHHHH
Q psy16767 549 GRTDASHVDKFYDMIFYKN--LLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVT-------LGIPRLREIL 619 (1020)
Q Consensus 549 ~~~~~~~~~~~~~~~~~ky--~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvT-------lGvPRLkEIi 619 (1020)
| -+..++|.+|+..- ...+|+.|||||+|||||||||+||+||+|||.+||....++ .|++|+.|-+
T Consensus 287 ---C-~s~~gvC~~CYG~~la~~~lv~lGeaVGiiAaQSIGEPGTQLTmRTFHtGGv~~~~~~~~i~~~~~G~i~~~~~~ 362 (1331)
T PRK02597 287 ---C-EAARSVCRKCYGWSLAHNHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSPFAGTVEFGKKL 362 (1331)
T ss_pred ---e-cCCCCchhhccCcchhcCcccchhhhhhhhhhccccCCcchhehhhhhhccccccccceeEEeccCeEEEEecCC
Confidence 1 13345777776653 468899999999999999999999999999999999887888 9999999944
No 22
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=100.00 E-value=2.4e-61 Score=597.05 Aligned_cols=303 Identities=27% Similarity=0.427 Sum_probs=239.4
Q ss_pred cccccccccccCCccccccccChhhHHHHHHHhhcCCCCCeEEEEcCCCCchhHHHHHHHHhhccceehhhhcceeEEEE
Q psy16767 590 STQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKE 669 (1020)
Q Consensus 590 ~TQmTLnTFH~AG~~~~nvTlGvPRLkEIi~~ASk~iKTP~mtv~L~~~~~~~~~~a~~i~~~l~~v~L~dvi~~i~v~~ 669 (1020)
.||||||||||||+++||||||||||+||| ||||+||||+|++||.++...+++.|+.++++|++++|+||++++++..
T Consensus 540 v~~~~LnTFH~AGv~~~nVTlGvPRL~EIi-nask~i~TP~m~i~l~~~~~~~~~~a~~v~~~ie~~~L~dv~~~~~~~~ 618 (858)
T PRK14898 540 VTHNTMRTFHYAGVAEINVTLGLPRMIEIV-DARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAIDL 618 (858)
T ss_pred eeccccceeeccCccccccccCCchHHHHh-cccCCCCCceEEEEECCCccchHHHHHHHHhheeeEEHHHHHHHhhhhc
Confidence 699999999999999999999999999999 8999999999999999877665689999999999999999999887532
Q ss_pred EeecCCCCCcceEEEEEEecccccccccCCChhhHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccCCCCcccC
Q psy16767 670 WLEISPEPHMNYQMKFCFIPAHMYRDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEG 749 (1020)
Q Consensus 670 ~~~~~~~~~~~y~i~~~l~~~~~~~~~~~i~~~~i~~~~~~~f~~~~~~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~ 749 (1020)
+ ... +++.| +..+..+++++++.|...+...+- ..... .
T Consensus 619 ~-------~~~--~~i~l--~~~~~~~~~l~~~~i~~~i~~~~~---------------~~~~~-----------~---- 657 (858)
T PRK14898 619 W-------TQS--IKVEL--DEETLADRGLTIESVEEAIEKKLG---------------VKIDR-----------K---- 657 (858)
T ss_pred c-------ccE--EEEEE--CHHHHHHcCCCHHHHHHHHHHhcc---------------ccccC-----------C----
Confidence 1 112 44445 556667889988877765543210 00000 0
Q ss_pred CccccccccCCCcCCCCccccchhhhhhhhhhccccccCCCCCcchHHhhhhcccccCCCcccccchhhcccchhHHHHH
Q psy16767 750 EGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFVKD 829 (1020)
Q Consensus 750 ~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 829 (1020)
.. ..+++ ... .. ...+.+
T Consensus 658 ------------------------~~-~~~~~--~~~------~~-----------------------------~~~~~~ 675 (858)
T PRK14898 658 ------------------------GT-VLYLK--PKT------PS-----------------------------YKALRK 675 (858)
T ss_pred ------------------------CC-EEEEE--ecC------ch-----------------------------HHHHHH
Confidence 00 00000 000 00 000111
Q ss_pred HhhccccceeeeccccCCceEEEEe--ccc----ceecc---CCceEEEEEeccchhhhhccCCcccccccccccHHHHH
Q psy16767 830 VVNQHNIVHKYSYDKKNHMWCKLLF--LPS----NLFEE---KESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMA 900 (1020)
Q Consensus 830 v~~~~~~i~~~~~d~~~~~~~~~~~--lp~----~~~~~---~~~e~~l~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~ 900 (1020)
+..... .+.+ +|+ ++.+. +.++|+|+|||+||.++|.++ .||++||+||||++|+
T Consensus 676 ~~~~l~---------------~~~i~gi~gI~~~~i~~~~~~~~~~~~l~teG~nl~~~~~~~-~vd~~~~~sN~i~~i~ 739 (858)
T PRK14898 676 RIPKIK---------------NIVLKGIPGIERVLVKKEEHENDEEYVLYTQGSNLREVFKIE-GVDTSRTTTNNIIEIQ 739 (858)
T ss_pred HHHHhc---------------CcEEECCCCccEEEEecCCCCCCceEEEEecCcCHHHHhcCC-CCcccccccCCHHHHH
Confidence 111000 0111 222 11111 235899999999999999996 7999999999999999
Q ss_pred HhhhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceeeeeEEeeecccccc-CcchhhhhcchhHHHHHHHHHhcC
Q psy16767 901 STYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRL-NPSFIQKMTFEMPLEKIRQASMQG 979 (1020)
Q Consensus 901 ~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~G~~~~~nR~G~~~-~~spl~kaSFE~t~~~L~~AA~~g 979 (1020)
++|||||||++|++||++||+.||++||+|||+||||+||++|.++||||+||+. +.|||++||||+|+++|++||.+|
T Consensus 740 ~~lGIEAar~~ii~Ei~~v~~~~gi~V~~rHl~liad~MT~~G~~~~~~r~gi~~~~~s~l~~asFe~t~~~l~~Aa~~g 819 (858)
T PRK14898 740 EVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHG 819 (858)
T ss_pred HhhCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHccCCcEEEeccCCccCCCCCHHHhcChHhHHHHHHHHhhcC
Confidence 9999999999999999999999999999999999999999999999999999976 589999999999999999999999
Q ss_pred CCccCCCcccceecCCccccCccceEEeecccc
Q psy16767 980 REDSLRAPSARVMLGQECRQGTGLFQLRNREKK 1012 (1020)
Q Consensus 980 ~~D~l~svSa~Ii~Gk~~~~GTG~fdll~~~~~ 1012 (1020)
+.|+|+|||+|||||+++++|||+|||+++.+.
T Consensus 820 ~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~ 852 (858)
T PRK14898 820 EVDKLKGVIENVIVGKPIKLGTGCVDLRIDREY 852 (858)
T ss_pred CCCcCCCchHHeeeCCccCCcCceEEEEecCcc
Confidence 999999999999999999999999999998754
No 23
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=100.00 E-value=2.7e-58 Score=561.32 Aligned_cols=380 Identities=28% Similarity=0.303 Sum_probs=296.5
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeecccccccChHHHHHHHHHHhcccCccc
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCILNTEI 76 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d~fl~~~~~~~l~~~~~~~~~~~i 76 (1020)
|||||||+ |.+|||||+.||++++||+||++|+||++++||+|+|.||||..|.|+++.+++++++. ......
T Consensus 405 FDGDeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~~~~~~~~~ei~l~---~~~~~~ 481 (808)
T COG0086 405 FDGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLK---DEYADD 481 (808)
T ss_pred cCchhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEeccEEEEEecccCCCCcceEEEec---cccccc
Confidence 99999999 99999999999999999999999999999999999999999999999999999888654 112233
Q ss_pred ccCCCccccCCCCCCCcEEEEEEccccCCCCCcccccccc-ccccccccccCccccCcccccc-CceEEEeccceeeecc
Q psy16767 77 RTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGEL-LSGILDKKQFGSTQYGLVHAVW-DTHVTIRHGELLSGIL 154 (1020)
Q Consensus 77 ~l~~Pailkp~~lwTGKqv~s~~l~~~~P~~~~~in~~~~-~~~k~~~~~~~~~~~~~~~~~~-d~~v~I~~Gell~G~L 154 (1020)
..++||+.+|..+|||||++++++ |... ..++... .++....+. .... |..+.|.||+++.|++
T Consensus 482 ~e~~~ai~~~~~~~~~k~i~~~i~----~~~~-~~~i~~t~~~~~~~~~~---------~~~~~d~~~~i~~~~l~~~~i 547 (808)
T COG0086 482 REKAEAIAKKIELTTGKVIVSTIS----PDLA-ELSIIVTTDGRRIFNRG---------LPEDKDVLVKIVNGKLIKGVI 547 (808)
T ss_pred hhhhHHHhcccceeeeeEEEEEee----ccCC-cceEEEecchhhhhhcc---------CCcccceeeEEeccccceeee
Confidence 567899999999999999999876 3321 0111000 110000000 0112 5789999999999999
Q ss_pred CcccccCcchhHHHHHHHHhCHHHHH-HHHHHHHHHHHHHhhhcc-eeeeeCccccChHHHHHHHHHHHHHHHHHHHHHH
Q psy16767 155 DKKQFGSTQYGLVHAVWDTHGAEHAI-SLLSCLAKLFTVYLQRVG-FTLGVRDILVRQERDRKRTKIINKARRLGTEAAC 232 (1020)
Q Consensus 155 dK~~lG~~~~~Lih~i~~~yG~~~a~-~~Ld~l~rl~~~~L~~~G-fSvgi~D~~~~~~~~~~r~~~i~~a~~~~~~~~~ 232 (1020)
||... .+|+.||+..+. .+++.+.+|...|+...| |+++++|..+ +...++.+++.+|...+.+++.
T Consensus 548 ~k~~~---------~i~~~~g~~~~~~~~~~~~dkl~~~~~~~~~~~~~~i~~~d~--~~~~~~~e~v~~ae~~v~~~i~ 616 (808)
T COG0086 548 DKKIV---------TIYREYGPEVASKALVKLLDKLKNLGIKGIGGFGIGIGRKDI--EAEDEKDEIVIEAEGSVLKLIL 616 (808)
T ss_pred hhhHH---------HHHHHhCchhhHHHHHHHHHHHHHhheeeeccceEEeecccc--cchHHHHHHHHHHHHHHHHHHH
Confidence 99765 789999998888 888888888888998877 8888888762 2333467899999888766655
Q ss_pred HHcCCCCCCCHHHHHHHHHHhcc-Cch--hHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCC-ChhHHHHhhcCCcc
Q psy16767 233 NALGLPLDTDPEIISSQLQEAYA-SIP--QFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPA-NNLQFMVESGAKGS 308 (1020)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~~-~~~--~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~-N~~~~M~~SGAKGS 308 (1020)
++- .+.+ ..+ .....++.....+++++..+..+.+. ....++ |++.+|..+||+|
T Consensus 617 ~~~----------------~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~----~~~g~~~~~i~~m~~~Gs~~- 675 (808)
T COG0086 617 QYE----------------EGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITL----EEQGLDFVDIRHMGLSGARM- 675 (808)
T ss_pred Hhh----------------cCCccccCCCCeEEEeehHHHHHHHHHHHHHHhhhH----HhcCCcchhHHHHhhhhhcc-
Confidence 432 2222 111 11222333444445555444333322 234444 5555555555555
Q ss_pred hhhHHHHHhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhhhccccCCc
Q psy16767 309 TVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRS 388 (1020)
Q Consensus 309 ~~N~~Qi~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~s 388 (1020)
|++||.+|+|||.|.|+|++.+ +||||.+.+.++.+.|||.+||++||+|.|||||+|+||+||||||+|||+|
T Consensus 676 --n~sq~~~~iG~~gv~g~r~~~~----~~~~Fe~~~~~~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa~s 749 (808)
T COG0086 676 --NISQIVQLIGQQGVMGEKISVL----ARAAFEVTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADS 749 (808)
T ss_pred --CHHHHHHHhhhheeeccCCCcc----cccccccccccceeeeeeecccCCCCCcceEEeecCccccchHHHhhhhccc
Confidence 9999999999999999999888 9999999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhccc
Q psy16767 389 GYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYL 435 (1020)
Q Consensus 389 GYLqRrLvk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~ 435 (1020)
||||||||+++|||+|.||++||+..+.++||.||+||.|+++..++
T Consensus 750 GYl~RrLv~~~qdl~v~~d~~~~~g~~~~~~~~~ged~~~~~~~~~~ 796 (808)
T COG0086 750 GYLTRRLVDVAQDLIVQEDDCVTDGIGVVIQFEYGEDGEDLTERILG 796 (808)
T ss_pred CcceEEeechhcceEEEecCeEeecCceEEEEecCccccCHHHHhcC
Confidence 99999999999999999999999977889999999999999876543
No 24
>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=2.2e-54 Score=531.66 Aligned_cols=210 Identities=23% Similarity=0.400 Sum_probs=161.2
Q ss_pred eccCcccccCcchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHHHHHHHHHHHHHHHH
Q psy16767 152 GILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAA 231 (1020)
Q Consensus 152 G~LdK~~lG~~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~~~i~~a~~~~~~~~ 231 (1020)
.++||+.++ +|||.+|++||++.|+.|||.+++|+++|++.+|||+|++|+.+|++ +.+++++|++.+.+..
T Consensus 5 ~~idKk~l~----~LI~~~~~~yG~~~t~~~lD~lk~Lgf~~aT~~G~SigidDl~ip~~----K~~li~~a~~~v~~~~ 76 (1227)
T TIGR02388 5 RVVDKKALK----NLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPA----KQDLLEAAEKEIRATE 76 (1227)
T ss_pred cccchHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEEeeccCCCCHH----HHHHHHHHHHHHHHHH
Confidence 378999996 89999999999999999999999999999999999999999999987 5789999988766544
Q ss_pred HHHcCCCCCCCHHHHHHHHHHhcc-CchhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCChhHHHHhhcCCcchh
Q psy16767 232 CNALGLPLDTDPEIISSQLQEAYA-SIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTV 310 (1020)
Q Consensus 232 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~ 310 (1020)
+ +++.+.+ ..+++.+.++.| +++.+.+++++.+ .+...+|.||+++|+.||||||+.
T Consensus 77 ~----------------~y~~G~it~~Er~~~ii~~w-~~t~e~~~~~~~~-----~~~~~d~~N~v~mMa~SGARGNis 134 (1227)
T TIGR02388 77 E----------------RYRRGEITEVERFQKVIDTW-NGTNEELKDEVVN-----NFRQTDPLNSVYMMAFSGARGNMS 134 (1227)
T ss_pred H----------------HHHcCCCcchhhHHHHHHHH-HHHHHHHHHHHHH-----hhhhcCCCCcHHHHhhccCcccHH
Confidence 3 3334444 234444444443 3444444444332 223467899999999999999666
Q ss_pred hHHHHHhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhhhccccCCcch
Q psy16767 311 NTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGY 390 (1020)
Q Consensus 311 N~~Qi~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGY 390 (1020)
|+.|++|++|++ +. ..|+..+ .| |.+||++||+|.|||||||||||||||||||||+|||
T Consensus 135 Qi~QLvGmrGlm-----a~---p~G~ii~-------lP-----I~snFreGLt~~EyF~sa~GaRkGLvDTAlKTAdSGY 194 (1227)
T TIGR02388 135 QVRQLVGMRGLM-----AN---PQGEIID-------LP-----IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGY 194 (1227)
T ss_pred HHHHHhcchhee-----cC---CCCcEee-------cc-----chhhhhcCCCHHHhheeccccccchhhcceeccccch
Confidence 666655555554 22 2233321 13 9999999999999999999999999999999999999
Q ss_pred hHHHHHhhhcceEEeeceEEEeCCCcE
Q psy16767 391 LQRCLVKHLEGLTVHYDMTVRDSDLSL 417 (1020)
Q Consensus 391 LqRrLvk~lEdl~V~yd~tvr~~~~~i 417 (1020)
||||||+++||++ ||..||..
T Consensus 195 LTRRLVdv~qDvi------V~~~DCgT 215 (1227)
T TIGR02388 195 LTRRLVDVSQDVI------VREEDCGT 215 (1227)
T ss_pred HHHHHHHhhceEE------EEEcCCCC
Confidence 9999999666665 66667654
No 25
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=100.00 E-value=7.2e-54 Score=537.16 Aligned_cols=345 Identities=24% Similarity=0.333 Sum_probs=226.0
Q ss_pred eeccCcccccCcchhHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhcceeeeeCccccChHHHHHHHHHHHHHHHHHHHH
Q psy16767 151 SGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEA 230 (1020)
Q Consensus 151 ~G~LdK~~lG~~~~~Lih~i~~~yG~~~a~~~Ld~l~rl~~~~L~~~GfSvgi~D~~~~~~~~~~r~~~i~~a~~~~~~~ 230 (1020)
+-++||+.++ +||+.+|+.||++.|+.|||.+++|+++|++.+|||+|++|+.+|++ +.+++++|++++.++
T Consensus 11 N~~~~k~~l~----~li~~~~~~~G~~~t~~~lD~lk~lgf~~at~~G~Sigi~Dl~ip~~----K~~li~~a~~~v~~~ 82 (1364)
T CHL00117 11 NKVIDKTALK----RLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPS----KGWLVQDAEQQSLIL 82 (1364)
T ss_pred eccccHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcceEEecCcccCCHH----HHHHHHHHHHHHHHH
Confidence 3479999997 89999999999999999999999999999999999999999999987 578999998876544
Q ss_pred HHHHcCCCCCCCHHHHHHHHHHhcc-CchhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCChhHHHHhhcCCcch
Q psy16767 231 ACNALGLPLDTDPEIISSQLQEAYA-SIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGST 309 (1020)
Q Consensus 231 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~ 309 (1020)
.+ +++.+.+ ..+++++.+|.| ..+.+.+++++.+ + +...+|.||+++|+.||||||
T Consensus 83 ~~----------------~y~~G~it~~er~~~~i~~w-~~~~~~l~~~~~~-~----~~~~d~~N~v~mMa~SGARGn- 139 (1364)
T CHL00117 83 EK----------------HYHYGNVHAVEKLRQSIEIW-YATSEYLKQEMNP-N----FRMTDPLNPVYMMSFSGARGN- 139 (1364)
T ss_pred HH----------------HHHcCCCCHHHHHHHHHHHH-HHHHHHHHHHHHH-h----hccCCCCCcHhhhhhccCccc-
Confidence 33 3444544 345677777776 3455556665433 2 233678999999999999995
Q ss_pred hhHHHHHhhccceeecCCCCCCCCCCCcccCCCCCCCCcccccccccccccCCChhhHHHhhcccccchhhhccccCCcc
Q psy16767 310 VNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSG 389 (1020)
Q Consensus 310 ~N~~Qi~~~lGQQ~l~G~Rip~~~~grtLp~f~~~d~~p~a~GfI~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~sG 389 (1020)
++||.+|+|++.+ | ..|+....+ .| |.+||++||+|.|||||||||||||+|||||||+||
T Consensus 140 --~sQi~qLvGmRGl-------m----a~p~G~iI~-~P-----I~snFreGLs~~EyFis~~GaRkGLvDTAlkTAdSG 200 (1364)
T CHL00117 140 --ASQVHQLVGMRGL-------M----SDPQGQIID-LP-----IQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAG 200 (1364)
T ss_pred --HHHHHHHhcccce-------e----eCCCCcEee-cc-----hhhhhhcCCCHHHhheeccccccchhhcceeccccc
Confidence 5555555554332 2 122222212 24 999999999999999999999999999999999999
Q ss_pred hhHHHHHhhhcceEEeeceEEEeCCCcEEEEEecCcccccchhcccccccchhhhhhHHHHhhHHHHHhhhccCchhHHH
Q psy16767 390 YLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTKRQYLTDKQFSFLEDNIKWICSYKVILNLLKKHPLSLAL 469 (1020)
Q Consensus 390 YLqRrLvk~lEdl~V~yd~tvr~~~~~iiqf~yg~dg~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~ 469 (1020)
|||||||+++|||+ ||..||.. ..|+...... .......+.+.
T Consensus 201 YLtRRLVdv~qdvi------V~~~dCgt------~~gi~~~~~~--~~~~~~~l~~r----------------------- 243 (1364)
T CHL00117 201 YLTRRLVEVVQHIV------VRETDCGT------TRGISVSPRN--GMMIERILIQT----------------------- 243 (1364)
T ss_pred chhhHHHhhhccEE------EEeccCCC------CCCEEEEEec--CCeEEeEecce-----------------------
Confidence 99999999766665 66777654 4455543211 00000000000
Q ss_pred HHHHhhhcCCCCCcccCCCcchhHHHHHHHHHhhcHHHHHHHHHhccCCCCCCcccCCCCcccccchHHHHHHHHHHhhc
Q psy16767 470 LLLLTFKSSGKPNFIFSPHRTKFTMDLLEQWYQLDDKARKKYRKKFKACPQPLISTFQPDAHFGSISENLADSVVKYTKG 549 (1020)
Q Consensus 470 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~~~~ 549 (1020)
.+..+.+ ....++++..+ ..-..++.+...++... .. .++. ..+|-
T Consensus 244 ----l~GRv~~-~di~~~~~~i~-----~~n~~I~~~~~~~i~~~-~~--~~v~-iRSpl-------------------- 289 (1364)
T CHL00117 244 ----LIGRVLA-DDIYIGSRCIA-----TRNQDIGIGLANRFITF-RA--QPIS-IRSPL-------------------- 289 (1364)
T ss_pred ----eEEEEEh-hhEEeCCEEEE-----eCCCCcCHHHHHHHHHc-CC--CEEE-EeCCc--------------------
Confidence 0000000 00000000000 00000000111111110 00 0000 00011
Q ss_pred cCcchhHHHHHHHHHHh--hhcccCCCCCcchhhhhcccCCccccccccccccCCcccccccc-------ChhhHHHH
Q psy16767 550 RTDASHVDKFYDMIFYK--NLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTL-------GIPRLREI 618 (1020)
Q Consensus 550 ~~~~~~~~~~~~~~~~k--y~~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG~~~~nvTl-------GvPRLkEI 618 (1020)
.|. +...+|.+|+.+ -...+|+.|||||+|||||||||+||+||+|||.+|+++..++. |+.++.+-
T Consensus 290 -tC~-~~~~vC~~CYG~~la~~~lV~~GeaVGiiAaQSIGEPGTQLTmRTFH~GGv~t~~~~~~i~a~~~G~i~~~~~ 365 (1364)
T CHL00117 290 -TCR-STSWICQLCYGWSLAHGDLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVFTGGTAEQVRAPFNGKIKFNED 365 (1364)
T ss_pred -ccc-cHHHHHHHHhCcccccCcccChhhhhhhhhhhccCCCchhhhhhhhhhcccccccceeeEEeccCeEEEEecc
Confidence 011 345677777654 34688999999999999999999999999999999997755554 88888883
No 26
>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=100.00 E-value=2.3e-45 Score=366.92 Aligned_cols=109 Identities=39% Similarity=0.605 Sum_probs=106.4
Q ss_pred cHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceeeeeEEeeecccccc-CcchhhhhcchhHHHHHH
Q psy16767 895 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRL-NPSFIQKMTFEMPLEKIR 973 (1020)
Q Consensus 895 di~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~G~~~~~nR~G~~~-~~spl~kaSFE~t~~~L~ 973 (1020)
||++|+++|||||||++|++||++||+.||++||+|||.||||+||++|.+.|+||+||+. +.|||++||||+|+++|.
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 7789999999999999999999999999999999999999999999999999999999975 699999999999999999
Q ss_pred HHHhcCCCccCCCcccceecCCccccCccc
Q psy16767 974 QASMQGREDSLRAPSARVMLGQECRQGTGL 1003 (1020)
Q Consensus 974 ~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~ 1003 (1020)
+||.+|+.|+|+|||++|+||+++++|||+
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 999999999999999999999999999996
No 27
>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=100.00 E-value=1.9e-41 Score=350.86 Aligned_cols=100 Identities=25% Similarity=0.527 Sum_probs=94.1
Q ss_pred hhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceeeeeEE------------------------------------
Q psy16767 903 YGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYV------------------------------------ 946 (1020)
Q Consensus 903 ~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~G~~~------------------------------------ 946 (1020)
+||||||..|++||++||+.||++||+|||.||||+||+++.+.
T Consensus 65 ~Giea~r~~iv~EIq~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~~~~~~~~~~y~ 144 (204)
T cd02655 65 LGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYE 144 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHHHhCCCCccccc
Confidence 89999999999999999999999999999999999999996643
Q ss_pred ----eeeccccccCcchhhhhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCccc
Q psy16767 947 ----AMNRNGIRLNPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGL 1003 (1020)
Q Consensus 947 ----~~nR~G~~~~~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~ 1003 (1020)
|+||.++. +.|+|++||||+|+++|.+||+.|+.|.|+|+++|||+|+++|+|||+
T Consensus 145 p~llGItk~~l~-~~Sfls~ASFqeT~kvL~~AAi~gk~D~L~GlkeNVI~G~liPaGTG~ 204 (204)
T cd02655 145 PVLLGITKASLN-TESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204 (204)
T ss_pred ceeeeeeecccc-CCCccccCChHHHHHHHHHHHhcCCCCCCCCchhheEECCccCCCCCC
Confidence 66666666 489999999999999999999999999999999999999999999995
No 28
>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=99.97 E-value=2.2e-32 Score=278.02 Aligned_cols=157 Identities=37% Similarity=0.598 Sum_probs=130.6
Q ss_pred ccccCCCCCCccccccceeeeeeeecccccccChHHHHHHHHHHhcccCcccccCCCccccCCCCCCCcEEEEEEccccC
Q psy16767 25 QYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCILNTEIRTLPPTIWKPMPLWTGKQVLSTVIINLT 104 (1020)
Q Consensus 25 ~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d~fl~~~~~~~l~~~~~~~~~~~i~l~~Pailkp~~lwTGKqv~s~~l~~~~ 104 (1020)
||+||++|+||++|+||+|+|+|+||++++|++++|++++++++.... .....+.|+|++|+++|||||++|.+|
T Consensus 1 NilSP~~G~Pii~~~QD~vlG~y~LT~~~~f~~~~e~~~~~~~~~~~~-~~~~~~~~~I~~~~~~~tgk~~~s~il---- 75 (158)
T PF04983_consen 1 NILSPANGKPIIGPTQDMVLGAYYLTSEDTFLSRDEAQQALMNGLIDD-KKIVLLHPAILKPKELWTGKQTFSRIL---- 75 (158)
T ss_dssp GSEETTTTEESSS--SHHHHHHHHHSSTTTEESHHHHHHHHHCSST-----CHCSSSSBSSSSSCEECHHHHHTTS----
T ss_pred CccCCCCCCceEEeccceEeEEEEEEecccccchHHHHHHHHcccccc-cceeccchhhhccccceeeccHHHHhc----
Confidence 799999999999999999999999999999999999999999742211 123678999999999999999999988
Q ss_pred CCCCccccccccccccccccccCccccCccccccCceEEEeccceeeeccCccccc-CcchhHHHHHHHHhCHHHHHHHH
Q psy16767 105 PKDKVIIRHGELLSGILDKKQFGSTQYGLVHAVWDTHVTIRHGELLSGILDKKQFG-STQYGLVHAVWDTHGAEHAISLL 183 (1020)
Q Consensus 105 P~~~~~in~~~~~~~k~~~~~~~~~~~~~~~~~~d~~v~I~~Gell~G~LdK~~lG-~~~~~Lih~i~~~yG~~~a~~~L 183 (1020)
|++ +++ ... +....++.++|++|+++.|++||+++| .+.++|+|.||++||+++|++||
T Consensus 76 ~~~---i~~---~~~--------------~~~~~~~~~~i~~g~~l~g~l~k~~lgk~~~~~li~~i~~~yG~~~~~~~l 135 (158)
T PF04983_consen 76 PNE---INP---EGF--------------SNDPDDGYVVINNGELLSGVLDKKTLGKKSLGSLIHQIYREYGPEATVQFL 135 (158)
T ss_dssp HTT---HHE---EES--------------TSCHSSHSEEECTSSEEEC--SHHHHSCSHTTCHHHHHHHHSHHHHHHHHH
T ss_pred ccc---ccc---ccc--------------cccccccceeecCCccchhheehheecccchhhHHHHHHHHHCHHHHHHHH
Confidence 654 444 110 000026789999999999999999999 67889999999999999999999
Q ss_pred HHHHHHHHHHhhhcceeeeeCcc
Q psy16767 184 SCLAKLFTVYLQRVGFTLGVRDI 206 (1020)
Q Consensus 184 d~l~rl~~~~L~~~GfSvgi~D~ 206 (1020)
|++|+++++|++.+|||||++|+
T Consensus 136 d~i~~lg~~~~t~~GfSvgi~D~ 158 (158)
T PF04983_consen 136 DAIKRLGFRYLTRSGFSVGIDDM 158 (158)
T ss_dssp HHHHHHHHHHHHHHTBB-SGGGC
T ss_pred HHHHHHHHHHHHHcCeeEecccC
Confidence 99999999999999999999997
No 29
>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=99.85 E-value=1e-21 Score=186.79 Aligned_cols=94 Identities=38% Similarity=0.581 Sum_probs=76.5
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCChhHHHHhhcCCcchhhHHHHHhhccceeecCCCCCCCCCCC
Q psy16767 257 IPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVNTMQISCLLGQIELEGKRPAMMVSGR 336 (1020)
Q Consensus 257 ~~~~~~~ld~~~~~~l~~~~~~i~~~~~~~~~~~~~~~N~~~~M~~SGAKGS~~N~~Qi~~~lGQQ~l~G~Rip~~~~gr 336 (1020)
.....+.++..+++.++.+++.+.+.+... ...+|++++|+.||||||++|++||+||+|||.++|+|||.+++||
T Consensus 15 ~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~----~~~~N~l~~M~~SGaKGs~~ni~Qi~g~lGqq~~~g~ri~~~~~~R 90 (108)
T PF05000_consen 15 GKTYEETFEQKINKILNKVRDEIGKIIKKN----LPFNNSLLIMINSGAKGSMSNISQISGCLGQQSVEGKRIPRGFSGR 90 (108)
T ss_dssp TCHHHHHHHHHHHHHHHHCCHHHHHHHHHC----STTTSHHHHHHHSSSS--HHHHHHHHST-EEEEETTSES--SSTTC
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHh----CCCCCcHHhhhhccCCCCHHHHHHHHHHHHHhhccccccccCCCCC
Confidence 445666777888888888888888777643 2237999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCCccccccc
Q psy16767 337 TLPSFLPYEVSPRAGGFV 354 (1020)
Q Consensus 337 tLp~f~~~d~~p~a~GfI 354 (1020)
|||||.+++..|+++|||
T Consensus 91 tlp~f~~~~~~~~~~GFI 108 (108)
T PF05000_consen 91 TLPHFKPFDESPESRGFI 108 (108)
T ss_dssp SSTTS-SS-SSTTTTTEE
T ss_pred cCCCcCCCCCCcccCCCC
Confidence 999999999999999998
No 30
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=99.68 E-value=1.8e-18 Score=212.82 Aligned_cols=325 Identities=21% Similarity=0.227 Sum_probs=228.1
Q ss_pred cccCCCCCcchhhhhcccCCccccccccccccCC--ccccccccChhhHHHHHHHhhcCCCCCeEEEEcCCCCchhHHHH
Q psy16767 569 LSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAG--RGDMNVTLGIPRLREILMMATKAIKTPSMEIPFLPDMPKLEKKA 646 (1020)
Q Consensus 569 ~slv~pGe~VG~iAAQSIGEP~TQmTLnTFH~AG--~~~~nvTlGvPRLkEIi~~ASk~iKTP~mtv~L~~~~~~~~~~a 646 (1020)
..++.|++++|..+|||+++|.||||+.|||+|| ++..++|.|.|||-++. .| +-.+||.|++++........+.+
T Consensus 408 DeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~-d~-~~~~~~~~ei~l~~~~~~~~e~~ 485 (808)
T COG0086 408 DEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIV-DA-KLPSTPVGEIYLKDEYADDREKA 485 (808)
T ss_pred hhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEeccEEEEEe-cc-cCCCCcceEEEeccccccchhhh
Confidence 4678899999999999999999999999999999 99999999999999988 66 88999999999874444334789
Q ss_pred HHHHhhccceehhhhcceeEEEE---EeecCCCCCcceEEEEEEecccccccccCCChh-hHHHHHHH-----HHHHHHH
Q psy16767 647 NRLAKSMTRITMADVLEKVKIKE---WLEISPEPHMNYQMKFCFIPAHMYRDKTSVKPS-KIIDHFER-----KFLKELE 717 (1020)
Q Consensus 647 ~~i~~~l~~v~L~dvi~~i~v~~---~~~~~~~~~~~y~i~~~l~~~~~~~~~~~i~~~-~i~~~~~~-----~f~~~~~ 717 (1020)
..+.+.+..++.+++++.+.... .+....+ .+......+..+ ++...+.. .......
T Consensus 486 ~ai~~~~~~~~~k~i~~~i~~~~~~~~i~~t~~--------------~~~~~~~~~~~~~d~~~~i~~~~l~~~~i~k~~ 551 (808)
T COG0086 486 EAIAKKIELTTGKVIVSTISPDLAELSIIVTTD--------------GRRIFNRGLPEDKDVLVKIVNGKLIKGVIDKKI 551 (808)
T ss_pred HHHhcccceeeeeEEEEEeeccCCcceEEEecc--------------hhhhhhccCCcccceeeEEeccccceeeehhhH
Confidence 99999999999999988655432 1222211 000000000000 00000000 0000000
Q ss_pred HHHHHHHHccccccccccccccccCCCCcccCCccccccccCCCcCCCCccccchhhhhhhhhhccccccCCCCCcchHH
Q psy16767 718 VAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEE 797 (1020)
Q Consensus 718 ~~i~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~d~~~ 797 (1020)
..+.+. +.. ... .. ..
T Consensus 552 ~~i~~~-------~g~---------~~~----------------------------~~---~~----------------- 567 (808)
T COG0086 552 VTIYRE-------YGP---------EVA----------------------------SK---AL----------------- 567 (808)
T ss_pred HHHHHH-------hCc---------hhh----------------------------HH---HH-----------------
Confidence 000000 000 000 00 00
Q ss_pred hhhhcccccCCCcccccchhhcccchhHHHHHHhhccccceeeeccccCCceEEEEe-cccceeccCCceEEEEEeccch
Q psy16767 798 RMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLF-LPSNLFEEKESKHLLKTDGINV 876 (1020)
Q Consensus 798 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~i~~~~~d~~~~~~~~~~~-lp~~~~~~~~~e~~l~teG~nl 876 (1020)
-....+++.. .+.... -+...+ ...+.......+|+..++|.++
T Consensus 568 --------------------------~~~~dkl~~~--~~~~~~-------~~~~~i~~~d~~~~~~~~e~v~~ae~~v~ 612 (808)
T COG0086 568 --------------------------VKLLDKLKNL--GIKGIG-------GFGIGIGRKDIEAEDEKDEIVIEAEGSVL 612 (808)
T ss_pred --------------------------HHHHHHHHHh--heeeec-------cceEEeecccccchHHHHHHHHHHHHHHH
Confidence 0000000000 000000 000000 0000001123457778889999
Q ss_pred hhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcc-cCcchhhhhcccceeeeeEEeeecccccc
Q psy16767 877 NFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIE-VDPRHLSLVADYMTHSGTYVAMNRNGIRL 955 (1020)
Q Consensus 877 ~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~-v~~rHl~LlAD~MT~~G~~~~~nR~G~~~ 955 (1020)
..+.++. ..|.+++.+||+.++..++|+||+++++++++..+....|.. ++.+|+.+.+|.|+.++....+-|+|+..
T Consensus 613 ~~i~~~~-~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~n~sq~~~~iG~~gv~g 691 (808)
T COG0086 613 KLILQYE-EGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGVMG 691 (808)
T ss_pred HHHHHhh-cCCccccCCCCeEEEeehHHHHHHHHHHHHHHhhhHHhcCCcchhHHHHhhhhhccCHHHHHHHhhhheeec
Confidence 9999996 479999999999999999999999999999999999999999 99999999999999999999999999987
Q ss_pred -CcchhhhhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCccceEEeecc
Q psy16767 956 -NPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLFQLRNRE 1010 (1020)
Q Consensus 956 -~~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~fdll~~~ 1010 (1020)
..|++++++||.+..+ ..|+.+++.+.+.|++.++++|++...|||+.|.-+..
T Consensus 692 ~r~~~~~~~~Fe~~~~~-~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KT 746 (808)
T COG0086 692 EKISVLARAAFEVTVKH-LEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKT 746 (808)
T ss_pred cCCCccccccccccccc-ceeeeeeecccCCCCCcceEEeecCccccchHHHhhhh
Confidence 4899999999999999 99999999999999999999999999999999986653
No 31
>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=99.63 E-value=3.2e-16 Score=195.51 Aligned_cols=111 Identities=23% Similarity=0.507 Sum_probs=100.8
Q ss_pred cccHHHHHHhh----------------hHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceee-------------e
Q psy16767 893 VNDIHYMASTY----------------GIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS-------------G 943 (1020)
Q Consensus 893 sNdi~~i~~~~----------------GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~-------------G 943 (1020)
+.+.|+++.+| |+|+++..|++||++|++.+|+.|+.|||.+|+|.||.+ |
T Consensus 1057 ~~~ph~iL~~~~~~~~~~~g~~~aa~~s~~~~q~~lv~eiq~vy~~QGv~I~~kHieiIvrqMtskV~i~~~G~t~~lpG 1136 (1227)
T TIGR02388 1057 PINPHDILDVFFSYYKDQDGLYEAAQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPG 1136 (1227)
T ss_pred CCCHHHHHhhhhhhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHhcceEeehhhHHHHHHHHhceEEEeeCCCcccCCc
Confidence 35678888884 999999999999999999999999999999999999999 7
Q ss_pred eE---------------------------EeeeccccccCcchhhhhcchhHHHHHHHHHhcCCCccCCCcccceecCCc
Q psy16767 944 TY---------------------------VAMNRNGIRLNPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQE 996 (1020)
Q Consensus 944 ~~---------------------------~~~nR~G~~~~~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~ 996 (1020)
++ .||||+.++ ..|+|++|||++|+++|.+||+.|+.|.|+|+.++||+|++
T Consensus 1137 eli~~~~~~~~n~~l~~~~~~~~~y~pvLlGITkasL~-t~Sfis~ASFqeTtrvL~~Aai~g~~D~l~glkENvI~G~l 1215 (1227)
T TIGR02388 1137 ELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLN-TDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRL 1215 (1227)
T ss_pred ceeeHHHHHHHHHHHHhcCCCccccceeEeeeeecccc-ccchhhhccHHHHHHHHHHHHHcCCcccccCchhheeecCc
Confidence 74 555555554 38999999999999999999999999999999999999999
Q ss_pred cccCccce
Q psy16767 997 CRQGTGLF 1004 (1020)
Q Consensus 997 ~~~GTG~f 1004 (1020)
+|+|||..
T Consensus 1216 iP~GTG~~ 1223 (1227)
T TIGR02388 1216 IPAGTGFS 1223 (1227)
T ss_pred cccCCCcc
Confidence 99999973
No 32
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=99.59 E-value=8.5e-16 Score=195.30 Aligned_cols=108 Identities=23% Similarity=0.485 Sum_probs=98.0
Q ss_pred hhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceee--------------eeE-----------------------
Q psy16767 903 YGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS--------------GTY----------------------- 945 (1020)
Q Consensus 903 ~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~--------------G~~----------------------- 945 (1020)
+.|||+|..|++||++|++.+|+.|+.|||.+|++.||.+ |++
T Consensus 1181 lS~~~~~~~lv~eiq~vy~~qGv~i~~kHieiivrqmt~kv~i~~~g~~~v~~pge~i~~~~~~~~~~~~~~~~~~~~~l 1260 (1364)
T CHL00117 1181 LSIAQSQISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSNVFLPGELIGLLRAERINRALEEAICYRPIL 1260 (1364)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCcEeehhhhhhhHHHhhCeEEEeecCccCccCCcceeeHHHHHHHhHHhhcCcceeeee
Confidence 3499999999999999999999999999999999999995 563
Q ss_pred EeeeccccccCcchhhhhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCccceEEeeccc
Q psy16767 946 VAMNRNGIRLNPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLFQLRNREK 1011 (1020)
Q Consensus 946 ~~~nR~G~~~~~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~fdll~~~~ 1011 (1020)
+|+||++++ ..|+|++|||++|+++|.+||+.|+.|.|+|+.++||+|+++|+|||...+.....
T Consensus 1261 lGitkasl~-t~Sfis~aSFqeT~rvL~~aai~g~~D~l~glkenvi~g~~ip~GTG~~~~~~~~~ 1325 (1364)
T CHL00117 1261 LGITKASLN-TQSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVHRSK 1325 (1364)
T ss_pred eeeeehhcc-ccchhhhcchHHHHHHHHHHHHcCCcccccCchhheeecCcccCCCCchhhhhhhh
Confidence 466666666 48999999999999999999999999999999999999999999999988776543
No 33
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=99.48 E-value=1.6e-14 Score=171.33 Aligned_cols=54 Identities=30% Similarity=0.295 Sum_probs=52.6
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeeccccc
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDT 54 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d~ 54 (1020)
|||||||| |++|||||+.||++.+|++||++|+|+++|+||+|+|+|+||.++.
T Consensus 490 FDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~ 547 (663)
T CHL00018 490 FDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNR 547 (663)
T ss_pred ccCcEEEEecCCCHHHHHHHHHHhcCccceeEcCCCceeEeechhhhhhhheecccCC
Confidence 99999999 9999999999999999999999999999999999999999998764
No 34
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=99.47 E-value=2.1e-14 Score=168.61 Aligned_cols=54 Identities=31% Similarity=0.350 Sum_probs=52.6
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeeccccc
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDT 54 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d~ 54 (1020)
|||||||| |++|||||+.||++++|++||++|+|+++++||+|+|+|+||.++.
T Consensus 469 FDGDeMnvHvPqS~~A~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~LT~~~~ 526 (627)
T PRK02625 469 FDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENP 526 (627)
T ss_pred cCCCeEEEecCCCHHHHHHHHHHhcCccceEEcCCCceeEeechhhhhheeeeeccCc
Confidence 99999999 9999999999999999999999999999999999999999999863
No 35
>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=99.47 E-value=2e-14 Score=168.65 Aligned_cols=53 Identities=30% Similarity=0.326 Sum_probs=52.1
Q ss_pred CCcccccc----CHHHHHHHHHHhcccCccccCCCCCCccccccceeeeeeeecccc
Q psy16767 1 MDGWTQNA----SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRD 53 (1020)
Q Consensus 1 FDGDEMnv----s~~AraEa~~Lm~~~~~ilsP~~G~Pi~gl~QD~vlg~~lLT~~d 53 (1020)
|||||||| |++|||||+.||++++|++||++|+|+++|+||+|+|+|+||.++
T Consensus 462 FDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llg~y~LT~~~ 518 (619)
T TIGR02387 462 FDGDQMAVHVPLSLEAQTEARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALN 518 (619)
T ss_pred CCCceeeeecCCCHHHHHHHHHHhhchhcEEecCCCceeEeechhhhhhhheeeccc
Confidence 99999999 999999999999999999999999999999999999999999875
No 36
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=98.63 E-value=1.9e-08 Score=126.83 Aligned_cols=41 Identities=46% Similarity=0.646 Sum_probs=36.5
Q ss_pred HHHHHHHHHhhhcccCCCCCcchhhhhcccCCccccccccc
Q psy16767 557 DKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNT 597 (1020)
Q Consensus 557 ~~~~~~~~~ky~~slv~pGe~VG~iAAQSIGEP~TQmTLnT 597 (1020)
+++...|+.+|.+++++||||||++||||||||+|||||.-
T Consensus 39 d~Il~~I~~~y~~a~vepge~vG~~aaqsi~~~~~~~~~~~ 79 (858)
T PRK14898 39 EEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSLPY 79 (858)
T ss_pred HHHHHHHHHHHhhCCCCCCceeeeeeehhcCCCCccccCCC
Confidence 44555678999999999999999999999999999998853
No 37
>PRK10738 hypothetical protein; Provisional
Probab=35.24 E-value=39 Score=33.64 Aligned_cols=59 Identities=17% Similarity=0.197 Sum_probs=44.6
Q ss_pred cCCChhhHHHhhcccccchhhhccccCCcchhHHHHHhhhcceEEeeceEEEeCCCcE---EEEEecCcc
Q psy16767 360 TGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSL---IQVLYGEDG 426 (1020)
Q Consensus 360 ~GL~p~EfFfH~m~gReGLiDTAvKTa~sGYLqRrLvk~lEdl~V~yd~tvr~~~~~i---iqf~yg~dg 426 (1020)
.|.+|.|+|..++||=.|+.=.. ||+|+-++ ++++.|.=++.-++....+ |.+.|-=+|
T Consensus 32 ~g~~P~EllL~aLg~Ct~i~v~~-------~l~k~~~~-~~~~~v~v~~~r~~~~p~~f~~I~~~~~~~g 93 (134)
T PRK10738 32 KAPSPMEMVLMAAGGCSAIDVVS-------ILQKGRQD-VVDCEVKLTSERREEAPRLFTHINLHFIVTG 93 (134)
T ss_pred CCCCHHHHHHHHHcCchHHHHHH-------HHHHCCCC-cccEEEEEEEEEcccCCCcccEEEEEEEEEC
Confidence 79999999999999998874333 88888654 8999998888766544444 677775444
No 38
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only]
Probab=25.38 E-value=93 Score=31.92 Aligned_cols=39 Identities=23% Similarity=0.300 Sum_probs=31.2
Q ss_pred EEEEEeccchhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHh
Q psy16767 867 HLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKN 918 (1020)
Q Consensus 867 ~~l~teG~nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~ 918 (1020)
-+|.++|.|+-..|+. ...+.+..|.|+||..||..|..
T Consensus 4 ~iLLVDGYNmIgaWp~-------------Lk~lkd~~~LE~AR~~LIe~l~~ 42 (173)
T COG3688 4 RILLVDGYNMIGAWPE-------------LKQLKDRNGLEAARDKLIEALAE 42 (173)
T ss_pred eEEEeccchhccccHH-------------HHHHHhhccHHHHHHHHHHHHHH
Confidence 3688899998777765 34677888999999999988754
No 39
>KOG0260|consensus
Probab=23.66 E-value=3.3 Score=53.15 Aligned_cols=134 Identities=13% Similarity=0.061 Sum_probs=108.1
Q ss_pred chhhhhccCCcccccccccccHHHHHHhhhHHHHHHHHHHHHHhhhhccCcccCcchhhhhcccceeeeeEEeeeccccc
Q psy16767 875 NVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIR 954 (1020)
Q Consensus 875 nl~~~~~~~~~iD~~r~~sNdi~~i~~~~GIEAar~~i~~ei~~v~~~~g~~v~~rHl~LlAD~MT~~G~~~~~nR~G~~ 954 (1020)
+++-++.|-.+.||.+...-.+.--...++|++.|..+.-=....-...| .+.+-||.|.+|.-...|+...++-.|..
T Consensus 1124 ~v~~~le~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~e~pd~D~~-~ispwlLrlelDr~~m~dk~ltm~~ia~~ 1202 (1605)
T KOG0260|consen 1124 LVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYYEMPDEDVG-RISPWLLRLELDRASMTDKKLTMEQIAEK 1202 (1605)
T ss_pred HHhhhcccccHHhhhccCcceecCCCcceeeccchhhHHhhhcCcccchh-hcChHHHHhhhhhhhcccccccHHHHHHH
Confidence 56677788788888887766666677899999998876533332222224 78899999999999999999999877754
Q ss_pred c------CcchhhhhcchhHHHHHHHHHhcCCCccCCCcccceecCCccccCccc-eEEeec
Q psy16767 955 L------NPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGL-FQLRNR 1009 (1020)
Q Consensus 955 ~------~~spl~kaSFE~t~~~L~~AA~~g~~D~l~svSa~Ii~Gk~~~~GTG~-fdll~~ 1009 (1020)
. ...++...-|-+.+-+..++|..++.|.+..--+..+||+.+-.|++- |.|+..
T Consensus 1203 i~~~f~~d~~~i~~ddna~klv~r~ri~~~~e~D~~l~~Ie~~ml~~~~l~G~~~i~kV~m~ 1264 (1605)
T KOG0260|consen 1203 INRGFGSDLACIFSDDNAEKLVLRLRIAKEEEDDVFLKCIEANMLGDMTLRGIPDIFKVYMS 1264 (1605)
T ss_pred HHhhccCCCceeecccCCcceEEEEEecCccchhHHHHHHHHhhhhhcccCCccccceEEEe
Confidence 2 356888888888888889999999999999999999999999999998 888764
No 40
>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=22.21 E-value=52 Score=32.92 Aligned_cols=52 Identities=13% Similarity=0.151 Sum_probs=30.5
Q ss_pred eehhhhcceeEEEEEeecC-----------------------CCCCcceEEEEEEecccccccccCCChhhHHHHHH
Q psy16767 656 ITMADVLEKVKIKEWLEIS-----------------------PEPHMNYQMKFCFIPAHMYRDKTSVKPSKIIDHFE 709 (1020)
Q Consensus 656 v~L~dvi~~i~v~~~~~~~-----------------------~~~~~~y~i~~~l~~~~~~~~~~~i~~~~i~~~~~ 709 (1020)
+||++|+....|.|.+... +....+|.++++|...... ..++++.+|...+.
T Consensus 1 TtL~~vt~~teIyYDPdp~~Tvi~eD~e~V~~y~e~pd~~~~~~~~spWlLRieLdr~~m~--dk~l~m~~I~~~I~ 75 (135)
T PF04990_consen 1 TTLRDVTASTEIYYDPDPRNTVIEEDREFVESYFEIPDEDDDPSRLSPWLLRIELDRKKMI--DKKLTMEDIAEKIK 75 (135)
T ss_dssp ECCHCHECEEEEEE-SSTTSSSSSTTHCHHHHCCCTT-SSTT-SSBESEEEEEEE-CCCCC--CTT--HHHHCCCHH
T ss_pred CcHHHhhhheeEEECCCCCCCcchhhHHHHHHHHhCCCcccCcccCCCeEEEEEEcHHHHH--hcCCCHHHHHHHHH
Confidence 5788888888887642211 1146799999999654433 55667766655443
Done!