Query 000525
Match_columns 1443
No_of_seqs 403 out of 2226
Neff 6.7
Searched_HMMs 46136
Date Mon Apr 1 18:00:48 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000525.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000525hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0261 RNA polymerase III, la 100.0 2E-265 4E-270 2312.8 46.7 1143 13-1280 9-1380(1386)
2 PRK14977 bifunctional DNA-dire 100.0 4E-249 9E-254 2394.4 88.3 1104 12-1265 4-1319(1321)
3 KOG0260 RNA polymerase II, lar 100.0 2E-243 4E-248 2163.8 64.6 1165 1-1271 1-1428(1605)
4 KOG0262 RNA polymerase I, larg 100.0 6E-228 1E-232 2038.2 61.2 1168 14-1264 10-1637(1640)
5 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 2E-188 4E-193 1793.7 61.2 778 15-875 2-864 (868)
6 PRK08566 DNA-directed RNA poly 100.0 6E-188 1E-192 1794.4 63.8 782 11-875 3-869 (882)
7 TIGR02386 rpoC_TIGR DNA-direct 100.0 3E-156 7E-161 1482.4 53.5 939 19-1256 1-1135(1140)
8 PRK00566 DNA-directed RNA poly 100.0 4E-154 9E-159 1464.2 55.1 938 16-1258 6-1139(1156)
9 PRK14906 DNA-directed RNA poly 100.0 2E-139 4E-144 1323.9 51.9 774 216-1256 310-1236(1460)
10 PRK14844 bifunctional DNA-dire 100.0 8E-139 2E-143 1361.1 47.0 903 215-1255 1663-2783(2836)
11 PRK09603 bifunctional DNA-dire 100.0 3E-137 7E-142 1351.2 46.3 523 215-840 1620-2177(2890)
12 COG0086 RpoC DNA-directed RNA 100.0 4E-125 8E-130 1188.5 25.4 718 17-861 4-788 (808)
13 PRK02625 rpoC1 DNA-directed RN 100.0 3.8E-77 8.3E-82 714.0 26.0 271 215-510 239-526 (627)
14 smart00663 RPOLA_N RNA polymer 100.0 8.1E-77 1.8E-81 673.9 21.2 274 219-503 1-295 (295)
15 TIGR02387 rpoC1_cyan DNA-direc 100.0 2.4E-76 5.2E-81 706.3 23.6 269 215-509 232-518 (619)
16 CHL00018 rpoC1 RNA polymerase 100.0 2.2E-74 4.8E-79 697.1 25.0 271 215-510 258-547 (663)
17 cd02737 RNAP_IV_NRPD1_C Larges 100.0 1.3E-71 2.8E-76 649.4 24.7 345 870-1261 1-381 (381)
18 cd02584 RNAP_II_Rpb1_C Largest 100.0 2.9E-64 6.4E-69 593.7 28.3 354 864-1262 21-410 (410)
19 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 1.2E-64 2.6E-69 588.3 24.4 324 864-1262 38-367 (367)
20 cd06528 RNAP_A'' A'' subunit o 100.0 8.5E-64 1.8E-68 582.4 24.4 323 864-1262 34-362 (363)
21 PRK04309 DNA-directed RNA poly 100.0 7.9E-63 1.7E-67 578.0 26.6 359 824-1265 18-382 (383)
22 PRK14897 unknown domain/DNA-di 100.0 1.3E-62 2.8E-67 580.4 22.8 325 864-1265 176-506 (509)
23 cd02736 RNAP_III_Rpc1_C Larges 100.0 5.3E-61 1.1E-65 546.0 20.3 290 865-1257 5-300 (300)
24 cd02735 RNAP_I_Rpa1_C Largest 100.0 8.4E-58 1.8E-62 524.1 19.8 299 864-1260 4-309 (309)
25 PF00623 RNA_pol_Rpb1_2: RNA p 100.0 4E-57 8.6E-62 475.3 5.2 159 319-478 1-166 (166)
26 TIGR02388 rpoC2_cyan DNA-direc 100.0 7.2E-51 1.6E-55 518.1 19.7 199 576-840 7-211 (1227)
27 PRK02597 rpoC2 DNA-directed RN 100.0 4.2E-50 9.1E-55 515.1 26.0 198 576-840 8-212 (1331)
28 PF04998 RNA_pol_Rpb1_5: RNA p 100.0 1E-51 2.2E-56 475.4 3.5 263 796-1204 1-272 (277)
29 PRK14898 DNA-directed RNA poly 100.0 1.8E-47 4E-52 491.6 23.3 306 885-1264 540-851 (858)
30 CHL00117 rpoC2 RNA polymerase 100.0 2E-45 4.4E-50 477.6 22.2 198 576-839 14-217 (1364)
31 PF04997 RNA_pol_Rpb1_1: RNA p 100.0 8.5E-44 1.8E-48 419.1 11.1 229 15-265 2-271 (337)
32 cd00630 RNAP_largest_subunit_C 100.0 2.1E-31 4.6E-36 276.9 7.8 109 1141-1255 49-157 (158)
33 PF04983 RNA_pol_Rpb1_3: RNA p 100.0 1E-28 2.2E-33 261.5 8.3 145 481-627 1-158 (158)
34 PF11523 DUF3223: Protein of u 99.9 5.1E-29 1.1E-33 228.4 2.6 75 1344-1418 1-76 (76)
35 cd02655 RNAP_beta'_C Largest s 99.9 2.6E-24 5.6E-29 232.0 9.0 113 1140-1255 54-203 (204)
36 KOG0260 RNA polymerase II, lar 99.6 2.6E-17 5.6E-22 203.3 0.4 532 870-1426 881-1424(1605)
37 PF05000 RNA_pol_Rpb1_4: RNA p 99.6 1.7E-15 3.7E-20 150.1 5.3 78 704-789 31-108 (108)
38 COG0086 RpoC DNA-directed RNA 99.2 1.6E-13 3.5E-18 175.9 -6.9 359 828-1264 377-747 (808)
39 PF04990 RNA_pol_Rpb1_7: RNA p 97.6 5.9E-05 1.3E-09 77.7 4.8 56 950-1005 1-78 (135)
40 cd02655 RNAP_beta'_C Largest s 97.3 4.1E-05 8.8E-10 83.9 -0.4 47 866-912 2-53 (204)
41 cd00630 RNAP_largest_subunit_C 96.3 0.00098 2.1E-08 70.6 -0.1 42 870-911 1-48 (158)
42 PRK14898 DNA-directed RNA poly 91.5 0.057 1.2E-06 72.0 0.1 39 851-892 41-79 (858)
43 PF05183 RdRP: RNA dependent R 49.6 11 0.00025 48.7 2.9 55 404-461 364-429 (579)
44 PF05094 LEF-9: Late expressio 29.3 74 0.0016 38.8 4.9 66 411-477 212-280 (487)
45 PF14754 IFR3_antag: Papain-li 28.0 12 0.00026 39.0 -1.6 30 53-82 36-68 (249)
46 PRK08270 anaerobic ribonucleos 25.7 50 0.0011 43.5 3.0 47 71-129 587-647 (656)
47 PHA03396 lef-9 late expression 23.7 1E+02 0.0023 37.8 4.8 66 411-477 215-283 (493)
48 TIGR00595 priA primosomal prot 22.4 55 0.0012 41.8 2.5 57 46-129 205-261 (505)
No 1
>KOG0261 consensus RNA polymerase III, large subunit [Transcription]
Probab=100.00 E-value=1.9e-265 Score=2312.82 Aligned_cols=1143 Identities=24% Similarity=0.361 Sum_probs=953.7
Q ss_pred CceeeeeEEEEcCChHHHHhccceEEec-------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccceeecC
Q 000525 13 PSGILTGISLGISTDTEKEKLSVMEIGA-------------VSEVTNPRLGLPNPTNECSSCGAKDRKACEGHFGFIKFP 79 (1443)
Q Consensus 13 ~~~~I~~I~F~~~S~eEI~~~Sv~~I~~-------------~~Gl~D~rLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~ 79 (1443)
-..+|++|+||++|++||++.++++|.+ ++|++|||||++++...|+|||+ ++.+|+|||||++|+
T Consensus 9 ~~kki~~i~F~~~s~~ei~~~a~v~v~~~~LY~~~~~~~P~~~G~LD~rMGvs~K~~~C~TCg~-~la~C~GHfGy~~L~ 87 (1386)
T KOG0261|consen 9 IPKKIKHIQFSILSPEEIRQQAEVEVSSKDLYDISTQRAPLPNGPLDPRMGVSNKKDKCATCGE-GLADCIGHFGYLKLA 87 (1386)
T ss_pred ccceeeeEeeccCCHHHHHhcceEEeeccchhhhhcccCCCcCCCcCcccCCCCCCCccchhcc-chhhcccccceEeec
Confidence 4678999999999999999999999975 37999999999999999999995 899999999999999
Q ss_pred ccccccccHHHHHHHHhccccccccccCcchhh----------------------hccccccccccccccccC-CCCCCc
Q 000525 80 FTILHPYFLSDIAKLLNSICPKCKTIRKERQKG----------------------AGSSRKEQPRVCKYCVRN-PAQWYP 136 (1443)
Q Consensus 80 ~PVfHpgf~~~i~kIL~~iC~~C~rlll~~~~k----------------------~l~~~~~~~~~C~~C~~~-~~~~~p 136 (1443)
+||||+|||+.++.||||||++|++++++...+ ++...|++...|.+|++. |.
T Consensus 88 LPVFhiGyfk~ti~iLq~ICK~Cs~ilL~~~~k~~fl~~lr~p~~~~l~k~~l~kri~~~CkK~~~C~hCg~~NG~---- 163 (1386)
T KOG0261|consen 88 LPVFHIGYFKATIQILQCICKNCSSILLSEEDKRQFLKKLRNPGLDNLRKKALLKRIVAKCKKVNTCSHCGALNGT---- 163 (1386)
T ss_pred ceeeeehhHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHhhCCCCChHHHHHHHHHHHHHhhccccccccCCcCce----
Confidence 999999999999999999999999999985321 112357788999999873 21
Q ss_pred ccccccccccccCccceeehhhhhhhccCCCCccc---cccccCccccccccccCCCccccCHHHHHHHhccCChhhHhh
Q 000525 137 RMRFKLSSKDLSGKTAIIVEIDEKLSKKNKKLPDD---YWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPSIREE 213 (1443)
Q Consensus 137 ~i~~~~~~~~~~~k~~ii~e~~~~~~~k~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~LsP~eV~~iLkkI~~ed~~~ 213 (1443)
++ + ...-.+|+|+.....++ ...+... .|......+.+.+.......+.|+|..|+++|++|++.|+++
T Consensus 164 -VK-K-----~~~~lkIiHd~~~~~~k-~~~~~~~~~~~~~~~~~~n~e~~~~~~~~~~~LnPl~vLnLFk~i~~~D~eL 235 (1386)
T KOG0261|consen 164 -VK-K-----AAALLKIIHDRFKLVKK-SDPLVTNERGEFKTAISHNKELEGHLSSCCEELNPLVVLNLFKQIKEDDCEL 235 (1386)
T ss_pred -ee-c-----cccceeEeeehhhcccc-ccchhhhhHHHHHHHhhcCcchHhHHHHHHhhcChHHHHHHHhhCCccccce
Confidence 11 0 00113566664322211 1111001 111112233344444555667899999999999999999998
Q ss_pred cc-----CCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhh---------CCcHHHHHHHHHHHH
Q 000525 214 FI-----LSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYR---------GRDIELSHLVQDCLK 279 (1443)
Q Consensus 214 ~~-----~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~---------~~~~~~~~~~~~~~~ 279 (1443)
+. .+|+.+|++++||||.|+|||+++++.. | ..|||+|.++..|+-.| ++..+++...++.+|
T Consensus 236 Lg~~~~~~~P~~Li~t~~~vPP~cIRPSV~~~~k~-g--tnEDDlT~KltEIi~tn~vik~~~~~g~~~~~imE~Wd~lQ 312 (1386)
T KOG0261|consen 236 LGMDSEEGRPENLIITRVPVPPVCIRPSVMSEDKA-G--TNEDDLTMKLTEIILTNDVIKKHLSKGTPINLIMEDWDFLQ 312 (1386)
T ss_pred eeeccCcCCchheEEEeccCCccccccceeecCCC-C--CCccchhhhhhhhhhHHHHHHHHhhcCCCchhhhhhhHHHH
Confidence 52 4899999999999999999999886521 1 35699999999998654 233333334444444
Q ss_pred Hh---hhhcccccCCc-------hhHhhhc-cCCcccCcCCcchhhccccCCCCCCCCceeEeCCCCCccccccccHHHH
Q 000525 280 IS---KLHLDKSSRKD-------SAEVRQK-KNIDISNSSGLRWIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVA 348 (1443)
Q Consensus 280 ~~---~~~~d~~~~~~-------~~~~~q~-~~~~~~~~~G~r~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a 348 (1443)
.. .+|++.++.+. .++..|| |||.+ |||+||+||||||||||||||||||+|||||||..+|
T Consensus 313 l~~AlyINSEl~g~~~~~~p~kp~RGf~QRLKGKqG-------RFRgNLSGKRVDFSGRTVISPDPNL~IdeVgVP~rvA 385 (1386)
T KOG0261|consen 313 LQVALYINSELPGIPINMAPKKPTRGFVQRLKGKQG-------RFRGNLSGKRVDFSGRTVISPDPNLRIDEVGVPIRVA 385 (1386)
T ss_pred HHHHHhhcccCCCCCCCCCCCCchHHHHHHhcccCC-------ceeccccCceeeccCceeeCCCCCcceeeccchHHHH
Confidence 42 25666554332 2677888 77765 7999999999999999999999999999999999999
Q ss_pred hhcCcceeechhhHHHhhhhh-cccccccCcceEeeC--CeEE------EecccccccCCCEEeceeccCceEEEeCCCC
Q 000525 349 ERLQISERLNSWNWERLSVCI-SFRLLEKGELYVCRK--GGLV------RIRRIDALELGDIIYRPLTDGDIVLINRPPS 419 (1443)
Q Consensus 349 ~~Lt~pe~Vt~~Ni~~l~~~~-~~~~~~~g~~~i~~~--g~~~------~~~~~~~l~~g~iV~Rhl~dgD~vl~NRqPs 419 (1443)
+.|||||+||.+|+++||+++ |++-+++||+|+.+. |... +-+.|.+|++||+|||||.|||+||||||||
T Consensus 386 kiLTfpE~Vt~~Ni~klr~lV~NGP~vhPGANyv~~r~~~~kr~L~yg~R~kiA~eLk~GdvVERHL~DgDvVLFNRQPS 465 (1386)
T KOG0261|consen 386 KILTFPERVTRANIRKLRQLVRNGPNVHPGANYVVQRGEGFKRFLKYGNRDKIADELKIGDVVERHLMDGDVVLFNRQPS 465 (1386)
T ss_pred HHhcchhhccHHHHHHHHHHHhcCCCCCCCcchhhhcccchhhHhhcCcHHHHHHhhccchHHHhhcccCCEEEEcCCch
Confidence 999999999999999999985 677889999998632 2111 1234678999999999999999999999999
Q ss_pred CCccccccccEEEecCCceEEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHH
Q 000525 420 IHPHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSL 499 (1443)
Q Consensus 420 LHk~Simah~v~v~p~~~t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l 499 (1443)
|||||||+|+|||+||. |||||.|+|+||||||||||||+||||++||||||.+||++++|+++|+||+|+++++||||
T Consensus 466 LHkmSIM~H~akV~p~R-TfRFNEcvCtPYNADFDGDEMNlHvPQTEEAraEA~~LMgvknNlvTPr~GEpiiAAtQDFi 544 (1386)
T KOG0261|consen 466 LHKMSIMSHRAKVMPWR-TFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIAATQDFI 544 (1386)
T ss_pred HHHHHHHHHHhhcccCc-eeeccccccCCcCCCCCcccccccCCchHHHHHHHHHHhccccccccCCCCCceeehhhhhh
Confidence 99999999999999986 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccCccccCHHHHHHHHhhC-C----CccCCCceecccCCccchHHHHHhhcCCCCCc-------------c---
Q 000525 500 TAAHLLMEDSVLLSHLQMQQLQMFC-P----HRFLSPDIFKISKDSVWSGKQLFSMLLPPDFE-------------Y--- 558 (1443)
Q Consensus 500 ~g~~llt~~d~fl~~~~~~~l~~~~-~----~~l~~pai~Kp~~~~lwTGKql~s~~lp~~~~-------------~--- 558 (1443)
+|+||||.||+||+|+++.||+.+. + ..+|||||+|| ..||||||+||.++.++.+ |
T Consensus 545 Tg~YLlt~KDtF~dRa~~~ql~s~~~d~~~~i~lppPaI~KP--~~LwTGKQ~fsvlirpn~~s~v~~Nl~~k~k~~~~~ 622 (1386)
T KOG0261|consen 545 TGGYLLTHKDTFLDRAEFSQLCSYMSDAMTHIDLPPPAILKP--VELWTGKQLFSVLIRPNDDSPVRVNLDAKNKNFSLV 622 (1386)
T ss_pred hcceeeecccccccHHHHHHHHHHHhccccccCCCChhhcCc--eeeeccCEEEEEEeccCCCCceEEeeccccceeecc
Confidence 9999999999999999999998652 2 27999999999 7999999999999976531 2
Q ss_pred -------ccCCCcEEEeCCeeccc-cCcccccC-CCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCccc
Q 000525 559 -------TFPSKDVYISGGKLISA-EGSSWLRD-YEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDLY 628 (1443)
Q Consensus 559 -------~~~~~~v~i~~gell~~-~~k~~lg~-~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~~ 628 (1443)
+.+|+.|.|+|+||++| +||++||+ ++.+||+.|.++||.. |++.|+++.+++.+||..+||||||+|+.
T Consensus 623 ~~k~~~mc~nDg~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lgnrGFSIGi~DVq 702 (1386)
T KOG0261|consen 623 KGKSFEMCPNDGYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGIDDVQ 702 (1386)
T ss_pred cCCCcccCCCCCeEEEecchhhhcccccccccCCCccceEeeehhhcchHHHHHHHHHHHHhhhhhccccccccccCCCC
Confidence 11257899999999986 89999998 6889999999999985 88999999999999999999999999999
Q ss_pred cccccchHHHHHHHHHhhHHHHHhhhhhhhhHHHhHHhhhhccCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHH
Q 000525 629 LASHSCSRKILMDEIFYGLREAQDTCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFW 708 (1443)
Q Consensus 629 ~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~ 708 (1443)
+.+...+.|+. -++.+++.|+ +.+..|..|+++-+++++ +..++|..+...|+. +++
T Consensus 703 Pg~~L~~~k~~------lv~~gY~kc~------~~I~e~~kG~L~~qpg~~---~eetLEa~I~~~Ls~--------IRe 759 (1386)
T KOG0261|consen 703 PGEILSQEKEE------LVNRGYAKCD------EKIEEYNKGKLQLQPGCN---EEETLEAEILSELST--------IRE 759 (1386)
T ss_pred ccHHHHHHHHH------HHHhHHHHHH------HHHHHHhccccccCCCCC---HHHHHHHHHHHHHHH--------HHH
Confidence 98765433332 3566777675 234557788888787764 456788877776654 578
Q ss_pred HHHHHHHhhCCCCCcceeeeccCCccchhhHhHhhhcccccccCCCCccccCccccccccccCCCCCCccccCCcccccc
Q 000525 709 DIQNLAYKYGSKDNSLLAMFKAGSKGNLLKLVQHSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAV 788 (1443)
Q Consensus 709 ~~~~~~~~~~~~~N~~~~M~~sGSKGS~~Nl~Qi~~~lGqQ~~~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~Gf 788 (1443)
++|++|...+.+.|++++|+.||||||.+|++||+||||||.+.|. |+|.+|..|+||||+..+..|.| +||
T Consensus 760 ~~G~~C~~eL~~~NsPliMa~CGSKGS~INiSQMvACVGQQ~ISG~---RvPdGf~dRsLPHF~r~Sk~P~a-----KGF 831 (1386)
T KOG0261|consen 760 EAGKICIRELHPRNSPLIMALCGSKGSKINISQMVACVGQQIISGH---RVPDGFEDRSLPHFERHSKTPAA-----KGF 831 (1386)
T ss_pred HHHHHHHHhcCcccChHHHHHhcCCCCcccHHHHHHHhhhhhhcCC---cCCCccccccCccccccCCCccc-----cch
Confidence 8999999999999999999999999999999999999999999995 99999999999999998888876 499
Q ss_pred ccccccCCCChhhHHHhcccCCCccccccc--CCCCcchHHHHHHHhheEeeecceEEccCCceEEEEEeccCCCCC---
Q 000525 789 VENSFLTGLNPLECFIHSVTSRDSSFSDNA--DLPGTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGTST--- 863 (1443)
Q Consensus 789 V~~sf~~GL~P~EfFfH~m~gReGliDtav--a~sGYLqRrLvk~lEdl~v~YD~tVR~s~G~~iiq~~yg~~g~~~--- 863 (1443)
|.||||+||+|.|||||+|+|||||||||| |+||||||||||+||||.++||||||||.| +||||+||+||.+.
T Consensus 832 V~NSFySGLTptEFfFHtm~GREGLVDTAVKTAETGYMqRRLmK~LEDL~~~YDgTVR~s~~-~vvqF~YG~DglDPa~m 910 (1386)
T KOG0261|consen 832 VANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKSLEDLSVQYDGTVRNSNG-DVVQFTYGGDGLDPAMM 910 (1386)
T ss_pred hhhhcccCCCchhhheeecccccchhhhhhhhhhhhhHHHHHHHHHHHHHHhhcCceecCCC-cEEEEeecCCCCChhhh
Confidence 999999999999999999999999999998 999999999999999999999999999999 59999999999540
Q ss_pred --------------------------------------------------------------------------------
Q 000525 864 -------------------------------------------------------------------------------- 863 (1443)
Q Consensus 864 -------------------------------------------------------------------------------- 863 (1443)
T Consensus 911 Eg~~~pv~f~r~~~~~~~~~~~~~~~~l~~~el~e~~~~~l~~~f~~~~~~F~~~~~~~i~~~~~~~~~~~~~~~d~~~~ 990 (1386)
T KOG0261|consen 911 EGKDQPVNFNRVFDHAKAIFPHRHDPPLSSEELDETLEEELLRKFTEKGDPFVHELREFIASLSKKIKKLQDKYGDECGP 990 (1386)
T ss_pred cCCCCchhHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcccccCC
Confidence
Q ss_pred ------------------------------CCcccCCceeccccccchhHHHHhcc---ccccc---cccccccccchhh
Q 000525 864 ------------------------------PTGEIGDQPVGSLSACAISEAAYSAL---DQPIS---LLETSPLLNLKNV 907 (1443)
Q Consensus 864 ------------------------------~~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~---~l~t~gl~rLkEI 907 (1443)
.+.++||.+||++||||||||+|||+ +|+++ .+.|.|+||++||
T Consensus 991 ~~~~~~~~~~~~~t~kql~~f~~~~~~ky~~a~~EpGTavGAi~aQSIGEPGTQMTLKTFHFAGVASMNiTlGVPRIkEI 1070 (1386)
T KOG0261|consen 991 KFCPDLLYQISRLTEKQLEKFVERCLDKYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEI 1070 (1386)
T ss_pred ccCccceeeeeeccHHHHHHHHHHHHHHHHhhhcCCcchhhhhhcccCCCCCceeeeeeeeecceeeeeeccCcchHHHH
Confidence 02368999999999999999999996 67665 3578999999999
Q ss_pred hccCCCCCCCccEeeeehhhhccccccCchhhHHHHHhhhcccchhhhhceEEEEEcCCCCcccccCceEEEEEeeHHHH
Q 000525 908 LECGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIM 987 (1443)
Q Consensus 908 l~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e~~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp~v~~~~Ldke~l 987 (1443)
+||++.++||..+..+- ++ .++..|+.||.+||+++|+|++++++.+|.|++++. .+.+|.+.|
T Consensus 1071 INAsk~ISTPIItA~L~--n~------~d~~~Ar~VKgRiEKt~L~dv~~yieeV~~p~~~fl--------~i~vd~~~I 1134 (1386)
T KOG0261|consen 1071 INASKTISTPIITAELE--NP------HDERSARVVKGRIEKTTLGDVCSYIEEVYGPDSCFL--------LIRVDLKRI 1134 (1386)
T ss_pred HhhhcccCccceeeeec--Cc------hhHHHHHHHhhhhhhhhHHHHHHHHHHHhCCcceEE--------EEEecHhHH
Confidence 99999998887777663 22 145789999999999999999999999999999864 889999999
Q ss_pred HHcCCC--HHHHHHHHHHhhhhhhhhhcccCCceeeecCccccccccccCCCceEEEEEeecccccc-hhhHHHHHHHhc
Q 000525 988 KRTGLK--EHSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMIVENFKRT-SIDLETIQMWVM 1064 (1443)
Q Consensus 988 ~~~~L~--i~~I~~~i~~~~~~~~~~l~~~~~~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~~~-~~~l~~l~~~ii 1064 (1443)
...+|. +++|..+|.+.. ..+....++.+..+ .. +.+++....+.+ ++.|+.|+.
T Consensus 1135 ~~l~L~i~~~~I~~sI~~s~-----~~k~~~~~v~v~~~------------~~--~~v~~~~~~~~S~~~~lq~lk~--- 1192 (1386)
T KOG0261|consen 1135 SLLQLEITIESIAYSILKSP-----KRKVKPNDVRVVGE------------TT--LRVTPVSDTKSSVYYNLQRLKR--- 1192 (1386)
T ss_pred hhhhccccHHHHHHHHhcCC-----ccccCCcceEEecc------------ee--EEEeecccccchhhhhHHHHHh---
Confidence 988776 588888877653 23333344555322 22 333333333333 678999887
Q ss_pred cccccceeeccccceEEEEeecccccccCCCCCCCceEEEEEeeccccccchhHHHHhhhhccccccccccccCCCcHHH
Q 000525 1065 PFLLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRS 1144 (1443)
Q Consensus 1065 p~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt~sn~I~e 1144 (1443)
.|.+++|+|+|.|.|++|+..++ ...++|++| |. + |.+||. ++||+.+||++||+.|
T Consensus 1193 -~L~~Vvv~gip~vnr~vi~~de~--------~~~y~L~vE--G~------g-----Lr~Vm~-t~GV~g~~TtsNnv~E 1249 (1386)
T KOG0261|consen 1193 -SLPNVVVKGIPEVNRAVINIDEK--------RGLYKLLVE--GT------G-----LRAVMN-TDGVKGRRTTSNNVLE 1249 (1386)
T ss_pred -hCCceEEecCcchhhhheeeccc--------CCceEEEEe--cc------c-----hHHHhc-cCCccccccccCceEE
Confidence 66699999999999999996442 233566655 33 3 566677 9999999999999999
Q ss_pred HHHHHcHHHHHHHHHHHHHHHhcccCCccCHHHHHHHHhhccceeeEeecchhhhhhhhccCCCcchhhhccccccHHHH
Q 000525 1145 FCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASF 1224 (1443)
Q Consensus 1145 i~~~lGIEAar~~ii~el~~~~~~~G~~V~~rHl~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asFe~t~~~l 1224 (1443)
|++||||||||.+||+||.+||+.||++||+||+|||||.||++|||+||||+|+++|++ |+|++||||+|+|||
T Consensus 1250 v~~vLGIEAAR~~II~EI~ytM~~HGmsiD~RHiMLLaDvMTyrGEVlGITRfGl~KM~~-----SVL~lASFEkT~DhL 1324 (1386)
T KOG0261|consen 1250 VEKVLGIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEVLGITRFGLAKMKD-----SVLMLASFEKTADHL 1324 (1386)
T ss_pred eehhhchHHHHHHHHHHHHHHHHhcCcccCHHHHHHHHHHhhhcceeeeeeehhhHHHHH-----HHHHHHhhhhhhHHH
Confidence 999999999999999999999999999999999999999999999999999999999999 899999999999999
Q ss_pred HHHHhhCCCcCCCCccceeccCCCCCccCccceEEEEccCCC-CCCcccccccCccc
Q 000525 1225 IKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHFDIIYSGEGR-TLSKPVDVYNLLST 1280 (1443)
Q Consensus 1225 ~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~f~ll~~~~~~-~~~~~~~~y~~l~~ 1280 (1443)
|+||.+|.+|.+.|||||||+|.|+++|| |.|+|+++.+.. .+.++.-+++-|+.
T Consensus 1325 F~AA~~~k~D~I~GVSEcIIlG~pm~iGT-G~fkl~~~~~~~~~~~~~~~if~~~~~ 1380 (1386)
T KOG0261|consen 1325 FDAAAYGKKDAIEGVSECIILGIPMCIGT-GIFKLLQRTDDKKVLKPKPPIFSSLNL 1380 (1386)
T ss_pred HHHHHhcCcccccchhhheecccceeccc-cHHHHHHhcCCcccCCCCCCccccccc
Confidence 99999999999999999999999999999 999999985542 22333455554443
No 2
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=4e-249 Score=2394.43 Aligned_cols=1104 Identities=24% Similarity=0.363 Sum_probs=905.9
Q ss_pred CCceeeeeEEEEcCChHHHHhccceEEecC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccceeecCc
Q 000525 12 VPSGILTGISLGISTDTEKEKLSVMEIGAV-----------SEVTNPRLGLPNPTNECSSCGAKDRKACEGHFGFIKFPF 80 (1443)
Q Consensus 12 ~~~~~I~~I~F~~~S~eEI~~~Sv~~I~~~-----------~Gl~D~rLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~ 80 (1443)
.+.++|.+|+||+||+|||+++||++|+++ |||||||||++++...|+|||+ +..+||||||||||++
T Consensus 4 ~~~~~I~~I~Fg~~S~eeIrk~Sv~~It~~~~~d~~g~P~~gGl~DprlG~~d~~~~C~TCg~-~~~~CpGHFGHIELa~ 82 (1321)
T PRK14977 4 LAVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGN-LAANCPGHFGHIELAE 82 (1321)
T ss_pred CccceeceEEEecCCHHHHHHhCeEEEecccccCCCCCcCCCCCCccccCCCCCCCCCCCCCC-CCCcCCCeeEEEEccC
Confidence 467889999999999999999999999863 8999999999999999999995 7999999999999999
Q ss_pred cccccccHHHHHHHHhccccccccccCcchhh----hc---------------c------------cccccccccccccc
Q 000525 81 TILHPYFLSDIAKLLNSICPKCKTIRKERQKG----AG---------------S------------SRKEQPRVCKYCVR 129 (1443)
Q Consensus 81 PVfHpgf~~~i~kIL~~iC~~C~rlll~~~~k----~l---------------~------------~~~~~~~~C~~C~~ 129 (1443)
|||||+||+.+++||+|+|++|||+++++... .+ . ..+++.+.|++|++
T Consensus 83 PVfHpgf~k~i~~iLr~iC~~C~rlll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~C~~C~~ 162 (1321)
T PRK14977 83 PVIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDEIIEEVRDQVKVYAKKAKECPHCGA 162 (1321)
T ss_pred CceecccHHHHHHHHHHHHHHhchhhcCcccHHHHHHHHHHhhhcccchhhhhhHHHHHHHHhhhhhhhccCCcCCCCCC
Confidence 99999999999999999999999999875310 00 0 01344568999986
Q ss_pred CCCCCCcccccccccccccCccceeehhhhhhhccCCCCccccccccCccccccccccCCCccccCHHHHHHHhccCChh
Q 000525 130 NPAQWYPRMRFKLSSKDLSGKTAIIVEIDEKLSKKNKKLPDDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPS 209 (1443)
Q Consensus 130 ~~~~~~p~i~~~~~~~~~~~k~~ii~e~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LsP~eV~~iLkkI~~e 209 (1443)
. .|.+++. +.. .++. . .+ ...+.|+|++|+++|++|+++
T Consensus 163 ~----~~~i~~~--------~~~------------------~~~~---~--~~------~~~~~l~p~~v~~if~~i~~~ 201 (1321)
T PRK14977 163 P----QHELEFE--------EPT------------------IFIE---K--TE------IEEHRLLPIEIRDIFEKIIDD 201 (1321)
T ss_pred C----CCeEEEe--------ece------------------eeee---c--cc------ccCcccCHHHHHHHHHhcCHH
Confidence 3 2333210 000 0000 0 00 123579999999999999999
Q ss_pred hHhhc-----cCCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHH---------HHHHHH
Q 000525 210 IREEF-----ILSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIE---------LSHLVQ 275 (1443)
Q Consensus 210 d~~~~-----~~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~---------~~~~~~ 275 (1443)
|+.++ ..+||||||++|||||+++||++.+++ + ..+|||||.+|..|+..|...+. .....+
T Consensus 202 d~~llg~~~~~~~p~~~il~~lpVpP~~~RP~v~~~~---~-~~~eddlt~~l~~Ii~~N~~l~~~~~~g~~~~~~~~~~ 277 (1321)
T PRK14977 202 DLELIGFDPKKARPEWAVLQAFLVPPLTARPSIILET---G-ERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEV 277 (1321)
T ss_pred HHHHhCCCCCCCCcceEEEeccccCCCCCcCcEEeCC---C-cccCCcHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHH
Confidence 99874 368999999999999999999998753 2 46899999999999987654322 222333
Q ss_pred HHHHHhh-hhcccccCCch-----------hHhhhc-cCCcccCcCCcchhhccccCCCCCCCCceeEeCCCCCcccccc
Q 000525 276 DCLKISK-LHLDKSSRKDS-----------AEVRQK-KNIDISNSSGLRWIKDVVLGKRNDDCFRMVVTGDPNIKLKEIG 342 (1443)
Q Consensus 276 ~~~~~~~-~~~d~~~~~~~-----------~~~~q~-~~~~~~~~~G~r~~R~nl~GKRv~~s~RsVI~pdp~l~~~evg 342 (1443)
+.||... .+.|+...+.+ .++.|+ +||.+ |||+|||||||||||||||||||||++||||
T Consensus 278 ~~LQ~~v~~~~dn~~~~~~~~~~~~~~rp~k~i~qrLkgKeG-------rfR~nlmGKRVdfSaRtVIspDP~L~i~EVG 350 (1321)
T PRK14977 278 DHLQYHTSTFFDNATAGIPQAHHKGSGRPLKSLFQRLKGKEG-------RFRGNLIGKRVDFSARTVISPDPMIDIDEVG 350 (1321)
T ss_pred HHHHHHHHHHhcccccCCCccccccCCCchhHHHHHhccccc-------cccccccccccccccceeEeCCCCccccccc
Confidence 3444322 34454432211 234444 34433 8999999999999999999999999999999
Q ss_pred ccHHHHhhcCcceeechhhHHHhhhhhc-ccccccCcceEe-eCCeEEEec------------ccccccCCCEEeceecc
Q 000525 343 IPCQVAERLQISERLNSWNWERLSVCIS-FRLLEKGELYVC-RKGGLVRIR------------RIDALELGDIIYRPLTD 408 (1443)
Q Consensus 343 vP~~~a~~Lt~pe~Vt~~Ni~~l~~~~~-~~~~~~g~~~i~-~~g~~~~~~------------~~~~l~~g~iV~Rhl~d 408 (1443)
||..||++|||||+||+||+++||+++. ....++||++|. .+|+.+.++ .+.+|++||+|||||+|
T Consensus 351 vP~~iA~~LT~Pe~Vt~~Ni~~l~~lv~nG~~~~pGA~~i~~~~g~~~~l~~~~~~~~~~~~~~a~~L~~g~iV~Rhl~d 430 (1321)
T PRK14977 351 VPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGANAIRKGDGTKIRLDFLEDKGKDALREAAEQLEIGDIVERHLAD 430 (1321)
T ss_pred CHHHHHHhCCCCEEEchhhHHHHHHHHHcCCcccCCcceEEcCCCceeeehhhhhccchhHHHHHHhcccCcEEEEEeec
Confidence 9999999999999999999999999864 455788999875 567655553 23578999999999999
Q ss_pred CceEEEeCCCCCCccccccccEEEecCCceEEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCC
Q 000525 409 GDIVLINRPPSIHPHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSG 488 (1443)
Q Consensus 409 gD~vl~NRqPsLHk~Simah~v~v~p~~~t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g 488 (1443)
||+|||||||||||||||||+|||+|+ +||||||+||+||||||||||||+|||||++|||||.+||++++||+||++|
T Consensus 431 GD~VL~NRQPSLHk~Simah~vkvl~~-kT~Rln~~vC~pyNADFDGDEMNlHvPQS~eArAEa~~Lm~v~~niisP~~G 509 (1321)
T PRK14977 431 GDIVIFNRQPSLHKLSILAHRVKVLPG-ATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTG 509 (1321)
T ss_pred CcEEEeccCCccccccceEEEEEEecC-ceEEecccccCcccCCcccceeeeecCCCHHHHHHHHHHHhhhhcEecCCCC
Confidence 999999999999999999999999998 6999999999999999999999999999999999999999999999999999
Q ss_pred CcccccchhHHHHHHhhccCccccCHHHHHHHHhhCCC--ccCCCcee-cccCCccchHHHHHhhcCCCCCcccc-----
Q 000525 489 RNLLSLGQDSLTAAHLLMEDSVLLSHLQMQQLQMFCPH--RFLSPDIF-KISKDSVWSGKQLFSMLLPPDFEYTF----- 560 (1443)
Q Consensus 489 ~pl~gl~QD~l~g~~llt~~d~fl~~~~~~~l~~~~~~--~l~~pai~-Kp~~~~lwTGKql~s~~lp~~~~~~~----- 560 (1443)
+|++|++||+|+|+|+||.+|+||++++|+||+++... .+|+|||+ || .+|||||||||++||+++||..
T Consensus 510 ~Pi~gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~~~~~~~lp~PaI~~kp--~~lwTGKQi~s~iLp~~~n~~~~~~~~ 587 (1321)
T PRK14977 510 GPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGITDPLPEPAIKTKD--GPAWTGKQLFSLFLPKDFNFEGIAKWS 587 (1321)
T ss_pred CeeEEeehhhhhhhhhhccCcccCCHHHHHHHHHhCCCccccCCCceecCC--CCeeeHHHHHHHHcCCCCCceeccccc
Confidence 99999999999999999999999999999999998654 48999999 88 7999999999999999888752
Q ss_pred -------------CCCcEEEeCCeeccc-cCcccccC---CCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhccccee
Q 000525 561 -------------PSKDVYISGGKLISA-EGSSWLRD---YEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTV 622 (1443)
Q Consensus 561 -------------~~~~v~i~~gell~~-~~k~~lg~---~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSi 622 (1443)
.++.|+|+||||++| +||+++|+ +++||+|.++++||++ |++||+++|+|+++||+++||||
T Consensus 588 ~~~~~~~~~~~~~~d~~v~I~~geLl~G~ldK~~~G~~~~~~~~Lih~i~~~yG~~~a~~fL~~l~~l~~~~L~~~GFSi 667 (1321)
T PRK14977 588 AGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSN 667 (1321)
T ss_pred ccccccccccCCCCcceEEeecCeEEeeecchHhhccccCCCCcHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEE
Confidence 134699999999987 89999998 7899999999999997 78999999999999999999999
Q ss_pred ecCccccccccchHHHHHHHHHhhHHHHHhhhhhhhhHHHhHH-----hhhhccCCcccccccccchhhHHHHHHHHHHH
Q 000525 623 SLSDLYLASHSCSRKILMDEIFYGLREAQDTCNFQQLMVDSHM-----NFLMSAKDSESTRSLQGEHLSYEKQRSAALSQ 697 (1443)
Q Consensus 623 gi~D~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~ 697 (1443)
|++|++++++. ++++.+.+ .++++.+. ++. +.+. ....+..+-.+++. ...++|.++...
T Consensus 668 gi~D~~~~~~~--~~~i~~~i----~~~~~~v~--~l~-~~~~~~~~i~~~~~~~~~~~G~~---~~~~~e~~i~~~--- 732 (1321)
T PRK14977 668 GPGDLIIPDEA--KQEIEDDI----QGMKDEVS--DLI-DQRKITRKITIYKGKEELLRGMK---EEEALEADIVNE--- 732 (1321)
T ss_pred eeCcEecCHHH--HHHHHHHH----HHHHHHHH--HHH-HHHhhhccccccccchhcCCCCc---HHHHHHHHHHHH---
Confidence 99999998764 23333322 23322211 111 1110 00011111112211 223445444443
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCcceeeeccCCccchhhHhHhhhcccccccCCCC-----ccccCccccccccccCC
Q 000525 698 ASVDAFKHVFWDIQNLAYKYGSKDNSLLAMFKAGSKGNLLKLVQHSLCLGLQHSLAPL-----SFRFPHELSCAAWNRLR 772 (1443)
Q Consensus 698 ~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~sGSKGS~~Nl~Qi~~~lGqQ~~~g~~-----~~r~p~~~~~~~l~~~~ 772 (1443)
|+++++++++.+.++++++|++++|+.||||||++|++||+||||||+++|++ +.|+|.++++|+||+|+
T Consensus 733 -----l~~~r~~~~~~~~~~l~~~N~l~~Mv~SGAKGS~~Ni~Qi~~~lGQQ~ve~~~~~~~~G~Ri~~~~~~RtLPhF~ 807 (1321)
T PRK14977 733 -----LDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGRLHEGYKDRALSHFQ 807 (1321)
T ss_pred -----HHHHHHHHHHHHHHhcCCCCcHHHHhhcccccCHHHHHHHHhccccccccccccccCCCCCCcCCCCCCcCCCCC
Confidence 44556788899999999999999999999999999999999999999999433 24899999999999999
Q ss_pred CCCCccccCCccccccccccccCCCChhhHHHhcccCCCccccccc--CCCCcchHHHHHHHhheEeeecceEEccCCce
Q 000525 773 AGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNA--DLPGTLTRRLMFFMRDLCTAYDGTVRNAYGNQ 850 (1443)
Q Consensus 773 ~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m~gReGliDtav--a~sGYLqRrLvk~lEdl~v~YD~tVR~s~G~~ 850 (1443)
+++..|++ +|||.|||++||+|+|||||||||||||||||| |+||||||||||+||||+|+|||||||++|+
T Consensus 808 ~~d~~p~a-----~GfV~nsFl~GL~P~EfFFHaM~GREGLiDTAVKTA~SGYLQRrLvk~lEDl~v~YD~TVR~s~g~- 881 (1321)
T PRK14977 808 EGDDNPDA-----HGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGH- 881 (1321)
T ss_pred CCCCCccc-----ccchhhhhcCCCCHHHHHHHhhcccccccccccccCcCchhHHHHHHHhcceEEecCCeEEeCCCC-
Confidence 98877765 599999999999999999999999999999998 9999999999999999999999999999995
Q ss_pred EEEEEeccCCCCC-------------------------------------------------------------------
Q 000525 851 IVQFSYNIEGTST------------------------------------------------------------------- 863 (1443)
Q Consensus 851 iiq~~yg~~g~~~------------------------------------------------------------------- 863 (1443)
||||.|||||.+.
T Consensus 882 iiQF~YGeDG~d~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 961 (1321)
T PRK14977 882 IIQFKFGEDGIDPQKLDHGEAFNLERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNANLPKLLADAIHGAELKEDELEA 961 (1321)
T ss_pred EEEEeecCCCcCHHHhccCCcccHHHHHHHhhhhccccCCCHHHHHHHHHHHHHhhhhhhHHHHHHHHHHcCCCHHHHHH
Confidence 9999999999430
Q ss_pred ----------CCcccCCceeccccccchhHHHHhcc---cccccc---ccccccccchhhhccCCCCCCCccEeeeehhh
Q 000525 864 ----------PTGEIGDQPVGSLSACAISEAAYSAL---DQPISL---LETSPLLNLKNVLECGSKKSNADQTMSLFLSN 927 (1443)
Q Consensus 864 ----------~~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~~---l~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~ 927 (1443)
.+.+.|||+||++||||||||+|||| +|.+++ +.|+|+|||+||+++++++ ++|+|+++|.+
T Consensus 962 ~~~~~~~~~~~~~~~pGe~VG~iaAQSiGEP~TQmTLnTFH~AGv~~~nvt~GvpRl~Eii~a~k~~--~tp~m~~~l~~ 1039 (1321)
T PRK14977 962 ICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKP--STPTMDIYLDD 1039 (1321)
T ss_pred HHHHHHHHHHhcccCCcccchhhhhhhccCceeeecccccccccccccCcccCccchHHhhhcccCC--CCCeEEEEeCC
Confidence 02356999999999999999999996 666653 5689999999999998854 46899999976
Q ss_pred hccccccCchhhHHHHHhhhcccchhhhhceEEEEEcCCCCcccccCceEEEEEeeHHHHHHcCCCHHHHHHHHHHhhhh
Q 000525 928 KLGKRRHGFEYGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKA 1007 (1443)
Q Consensus 928 ~~~k~~~~~e~~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~ 1007 (1443)
... .+++.|+.|+.+||+++|++++.++.+.|+|.. .++.+|++.+++++|+++.|.+.+.....
T Consensus 1040 ~~~----~~~~~a~~v~~~ie~~~l~~~~~~~~i~~~~~~----------~~i~~d~~~i~~~~i~~~~i~~~i~~~~~- 1104 (1321)
T PRK14977 1040 ECK----EDIEKAIEIARNLKELKVRALIADSAIDNANEI----------KLIKPDKRALENGCIPMERFAEIEAALAK- 1104 (1321)
T ss_pred ccc----chHHHHHHHHhheeeeEHHHhhhheEeeccCCc----------eEEecCHHHHHhcCCCHHHHHHHHHHhhc-
Confidence 543 234679999999999999999999999987652 36789999999999999887776554321
Q ss_pred hhhhhcccCCceeeecCccccccccccCCCceEEEEEeecccc--cchhhHHHHHHHhccccccceeeccccceEEEEee
Q 000525 1008 ARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMIVENFK--RTSIDLETIQMWVMPFLLKTVVKGFREIKKVDILW 1085 (1443)
Q Consensus 1008 ~~~~l~~~~~~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~--~~~~~l~~l~~~iip~ll~~vVkG~~~I~rv~I~~ 1085 (1443)
.+.+.+... ++ .+.+.+.+... .....|+.+++ .|++++|+|+|+|+||+|..
T Consensus 1105 --------~~~~~~~~~-----------~~--~i~~~~~~~~~~~~~~~~l~~l~~----~l~~~~i~Gi~~I~r~~i~~ 1159 (1321)
T PRK14977 1105 --------GKKFEMELE-----------DD--LIILDLVEAADRDKPLATLIAIRN----KILDKPVKGVPDIERAWVEL 1159 (1321)
T ss_pred --------CCceEEeec-----------CC--EEEEecCcccccchHHHHHHHHHH----hcCCcEEecCCCceEEEEEe
Confidence 011222111 12 22232222111 12345666666 67799999999999998864
Q ss_pred cccccccCCCCCCCceEEEEEeeccccccchhHHHHhhhhccccccccccccCCCcHHHHHHHHcHHHHHHHHHHHHHHH
Q 000525 1086 KDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESA 1165 (1443)
Q Consensus 1086 ~d~~~~~~~~~~~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt~sn~I~ei~~~lGIEAar~~ii~el~~~ 1165 (1443)
.++ .+.+||+|+|+|++ +.++|. +++|||+||+||||+||+++|||||||++|++||++|
T Consensus 1160 ~~~--------~~~~e~~l~teG~n-----------l~~vl~-~~~Vd~~rt~sN~i~ei~~~lGIEAaR~~ii~Ei~~v 1219 (1321)
T PRK14977 1160 VEK--------DGRDEWIIQTSGSN-----------LAAVLE-MKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASI 1219 (1321)
T ss_pred ecc--------CCCeeEEEEecCcC-----------HHHHhC-CCCCcccccEECCHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 221 23468999999987 677777 9999999999999999999999999999999999999
Q ss_pred hcccCCccCHHHHHHHHhhccceeeEeecc------hhhhhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCc
Q 000525 1166 ISDTGKNILPEHLLIVANTLSATGEFVGLN------AKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGS 1239 (1443)
Q Consensus 1166 ~~~~G~~V~~rHl~LlAd~MT~~G~~~gi~------r~G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gv 1239 (1443)
|++||++||+|||+||||+||++|++.++| |||+.+++. |||++||||+|+++|++||.+|+.|+|.||
T Consensus 1220 ~~~~G~~V~~rHi~LlaD~MT~~G~~~~i~~~~~~~R~Gi~~~~~-----s~l~~asFE~t~~~L~~AA~~g~~D~l~gv 1294 (1321)
T PRK14977 1220 LEDQGLEVDNRYIMLVADIMCSRGTIEAIGLQAAGVRHGFAGEKD-----SPLAKAAFEITTHTIAHAALGGEIEKIKGI 1294 (1321)
T ss_pred HHHcCCccCHHHHHHHHHHHccCceEEeccccccccccccccCCC-----CHHHhcCHHHHHHHHHHHHHhcCcCccCCh
Confidence 999999999999999999999999999999 999998765 999999999999999999999999999999
Q ss_pred cceeccCCCCCccCccceEEEEccCC
Q 000525 1240 VDALGWGKVPSVGTGGHFDIIYSGEG 1265 (1443)
Q Consensus 1240 s~~ii~Gk~~~~GTgg~f~ll~~~~~ 1265 (1443)
|||||||+++|+|| |.|+|+++..+
T Consensus 1295 senii~G~~~~~GT-G~~~Ll~~~~~ 1319 (1321)
T PRK14977 1295 LDALIMGQNIPIGS-GKVDLLMDFSG 1319 (1321)
T ss_pred HHhhhcCCCccCcc-ceEEEEecccc
Confidence 99999999999999 99999998654
No 3
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=100.00 E-value=1.7e-243 Score=2163.76 Aligned_cols=1165 Identities=25% Similarity=0.405 Sum_probs=972.4
Q ss_pred CCchhhccCCCCCceeeeeEEEEcCChHHHHhccceEEecC----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 000525 1 MDNEFCEEGLEVPSGILTGISLGISTDTEKEKLSVMEIGAV----------SEVTNPRLGLPNPTNECSSCGAKDRKACE 70 (1443)
Q Consensus 1 ~~~~~~~~~~~~~~~~I~~I~F~~~S~eEI~~~Sv~~I~~~----------~Gl~D~rLG~~~~~~~C~TCg~~~~~~Cp 70 (1443)
|+++ +++ +++|.++|++|+||++||+||++|||.+|..| |||.|||||++++...|.||++ ++.+||
T Consensus 1 m~~~-~~~-~~~pl~~v~~vqFgi~spdeir~mSV~~i~~~e~~e~~~pk~ggl~D~RlG~idr~~~CqTC~g-~~~~Cp 77 (1605)
T KOG0260|consen 1 MGDD-CEF-SQAPLRTVKSVQFGILSPDEIRRMSVAEIEFPETMEGGRPKLGGLMDPRLGTIDRDSLCQTCGG-NMFECP 77 (1605)
T ss_pred CCCC-ccc-ccCcceeeeEEEeeccChhhhhcceeEEeecccccccCCCCcCCccccccCCCCccchhhhhcc-ccccCC
Confidence 6666 444 68999999999999999999999999998653 8999999999999999999997 899999
Q ss_pred CccceeecCccccccccHHHHHHHHhccccccccccCcchhhhccccccccccccccccCCCCCCcccccccccccccCc
Q 000525 71 GHFGFIKFPFTILHPYFLSDIAKLLNSICPKCKTIRKERQKGAGSSRKEQPRVCKYCVRNPAQWYPRMRFKLSSKDLSGK 150 (1443)
Q Consensus 71 GHFGhIeL~~PVfHpgf~~~i~kIL~~iC~~C~rlll~~~~k~l~~~~~~~~~C~~C~~~~~~~~p~i~~~~~~~~~~~k 150 (1443)
|||||||||+|||||||++++++||+|+|++|+++++++..... .....|.+|.. +++.+.+.+...+.+..
T Consensus 78 GHFGhieLAkPvfH~gFl~kv~kiL~cVC~~C~ki~~~~~~~~~----~~~~~~~~~~k----~rl~~v~~vck~k~~ce 149 (1605)
T KOG0260|consen 78 GHFGHIELAKPVFHPGFLKKVKKILRCVCFYCSKILKDKFNPKE----DQILRKRYCSK----GRLLMVLDVCKGKVVCE 149 (1605)
T ss_pred cccceeeeccccccHHHHHHHHHHHHHhhhcchheeecccCcch----hhhhhhhcCCc----chHHHHHHhhccceeee
Confidence 99999999999999999999999999999999999987532111 11234555522 23344433322222222
Q ss_pred cceeeh--hhhhhhccCCCC---ccccccccCccccccccccCCCccccCHHHHHHHhccCChhhHhh-----ccCCCCc
Q 000525 151 TAIIVE--IDEKLSKKNKKL---PDDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPSIREE-----FILSKDA 220 (1443)
Q Consensus 151 ~~ii~e--~~~~~~~k~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~LsP~eV~~iLkkI~~ed~~~-----~~~rPE~ 220 (1443)
..+..+ .+++|+.+++.+ ..++|.+++... + ...+.+..|++++|+++|++|+++++.. .++||||
T Consensus 150 ~g~~~e~~g~sgcg~kqP~i~r~gl~l~a~~k~~~--e--~~~e~k~~ls~e~V~~i~k~Isded~~~lg~~~~~arpew 225 (1605)
T KOG0260|consen 150 GGIDVESDGRSGCGLKQPSIRRLGLDLWAFWKQGD--E--DSQESKRKLSAERVLEIFKRISDEDIDQLGFKPKIARPEW 225 (1605)
T ss_pred ccccccccccccccccCCceeccCchhhhhhhccC--c--cCCcccccCcHHHHHHHHHhhchhhhhhhcCCCCcCCCce
Confidence 222333 445677777643 456788887521 1 1123567899999999999999999865 3799999
Q ss_pred ceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHH------HHHHHHHHHHhh----hhcccccC
Q 000525 221 PFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIEL------SHLVQDCLKISK----LHLDKSSR 290 (1443)
Q Consensus 221 ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~------~~~~~~~~~~~~----~~~d~~~~ 290 (1443)
||||+|||||+.+||++++++. ...+||+|++|.+|++.|...+.. .+.+.++.+..+ .+.||...
T Consensus 226 mIlTvLPVPP~~vrP~iv~~~s----~rg~DdlthkLadIiK~n~~l~r~e~~ga~~H~i~e~~~LlqfhVat~~Dn~~p 301 (1605)
T KOG0260|consen 226 MILTVLPVPPPAVRPEIVMQGS----ARGEDDLTHKLADIIKKNIGLKRNEENGAPAHIIEEYEQLLQFHVATYVDNDIP 301 (1605)
T ss_pred eEEEEecCCCCcccceeeeccc----ccCcchhHHHHHHHHHHHHHHhhhhhcCCchhhHHHHHhHhhhhhhheeccccc
Confidence 9999999999999999988643 346799999999999875432211 123333333322 45666655
Q ss_pred CchhHhhhccCCcccC----cCCc-chhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCcceeechhhHHHh
Q 000525 291 KDSAEVRQKKNIDISN----SSGL-RWIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERL 365 (1443)
Q Consensus 291 ~~~~~~~q~~~~~~~~----~~G~-r~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~pe~Vt~~Ni~~l 365 (1443)
.++ ...|++|+..++ ++|+ .|+|+|||||||||||||||||||||++||||||..||++|||||+||+|||++|
T Consensus 302 gqp-~a~qksGrplkSi~arlKgkegriRgnLmGKRvDFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~NidrL 380 (1605)
T KOG0260|consen 302 GQP-QADQKSGRPLKSISARLKGKEGRIRGNLMGKRVDFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNIDRL 380 (1605)
T ss_pred CCc-ccccccCCcccchhhhhccccchhhhcccccccCcceeeeecCCCCcchhcccCcHHHHhhccCcceeccccHHHH
Confidence 554 467887776553 3344 2899999999999999999999999999999999999999999999999999999
Q ss_pred hhhhccc-ccccCcceE-eeCCeEEEecccc-----cccCCCEEeceeccCceEEEeCCCCCCccccccccEEEecCCce
Q 000525 366 SVCISFR-LLEKGELYV-CRKGGLVRIRRID-----ALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPISSV 438 (1443)
Q Consensus 366 ~~~~~~~-~~~~g~~~i-~~~g~~~~~~~~~-----~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v~p~~~t 438 (1443)
++++... .-.+||.|+ +++|.++.++... +|+.||+|||||+|||+|||||||||||||||||||||+|+. |
T Consensus 381 qeLV~~g~~~~pgakyiird~G~Ridlr~~~~~~d~~Lq~G~kVeRhl~DGD~VlfNRqPSlHKmSmmahrVrVlp~s-T 459 (1605)
T KOG0260|consen 381 QELVRRGLLEHPGAKYIIRDNGDRIDLRYHKRAGDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPYS-T 459 (1605)
T ss_pred HHHhhCCCCCCCCcceeeecCCcEEEEeecCCccccccccccEEEEeeccCCEEEEcCCCcHHHhhhhhcEEEEccCc-e
Confidence 9987543 456788875 6789888876544 899999999999999999999999999999999999999996 9
Q ss_pred EEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHHhhccCccccCHHHHH
Q 000525 439 VTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDSVLLSHLQMQ 518 (1443)
Q Consensus 439 ~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~llt~~d~fl~~~~~~ 518 (1443)
||||++||+||||||||||||+|||||++||||+.||+++++||+|||+|+|++|++||+|+|++++|.+|+||+|++++
T Consensus 460 frLNlsvtsPynADFDGDemnlhvPQS~etkAEl~EL~~vpkQiispQsnkpvmgivQDTLta~R~~t~Rd~Fl~r~~vm 539 (1605)
T KOG0260|consen 460 FRLNLSVTSPYNADFDGDEMNLHVPQSLETKAELEELAMVPKQIISPQSNKPVMGIVQDTLTAVRKMTKRDVFLNRAQVM 539 (1605)
T ss_pred EEeCeeecCCccCCCCCceeecccCcchhHHHHHHHHhhhhhhhcCCcCCCcceeeehhhHHHHHHHhhHhhhhcHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhC-CC--ccC-CCceecccCCccchHHHHHhhcCCCCCccccC---------------CCcEEEeCCeeccc-cCc
Q 000525 519 QLQMFC-PH--RFL-SPDIFKISKDSVWSGKQLFSMLLPPDFEYTFP---------------SKDVYISGGKLISA-EGS 578 (1443)
Q Consensus 519 ~l~~~~-~~--~l~-~pai~Kp~~~~lwTGKql~s~~lp~~~~~~~~---------------~~~v~i~~gell~~-~~k 578 (1443)
||+||+ +. ..| .|||+|| ++|||||||||+++|+++|+..+ ++.++|.+|+|+.+ ++|
T Consensus 540 nLlm~~p~~d~~~Pa~pai~Kp--~PlWTGkQifsliiP~~in~~r~~s~h~d~~~~~~~p~dt~~lie~g~l~~g~l~K 617 (1605)
T KOG0260|consen 540 NLLMYVPDWDGPPPAKPAILKP--KPLWTGKQIFSLIIPGGINYIRDHSTHPDSEDELISPGDTRVLIEGGELLIGVLCK 617 (1605)
T ss_pred HHHhhccccCCCCCCCcccCCC--CcccchhhheeeecCCCcceecccccCcCCCcccccCCCceEEEeCCceEEEEeec
Confidence 999998 44 445 6799999 89999999999999999987532 34699999999975 899
Q ss_pred ccccCCCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCccccccccchHHHHHHHHHhhHHHHHhhhhhh
Q 000525 579 SWLRDYEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTCNFQ 657 (1443)
Q Consensus 579 ~~lg~~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~ 657 (1443)
+.+|++.++|+|+++.+.|++ |+.|.+.+|+|.+.||...|||+||+|.+..+ +.+.+|++.+.+|++.. .
T Consensus 618 kt~G~s~g~lvh~i~~e~Gp~~~~~f~~~iQ~lin~wll~~gfsigIgDtiad~------~t~~~iq~~I~~ak~dv--~ 689 (1605)
T KOG0260|consen 618 KTVGSSAGGLVHVIFLEKGPKIARGFFDSIQTLINSWLLREGFSIGIGDTIADA------ATMCVIQNTIKEAKRDV--L 689 (1605)
T ss_pred cccccccCceEEEeehhhCHHHHHHHHHHHHHHHHHHHHhcCccccccccccCH------HHHHHHHHHHHHHHHHH--H
Confidence 999999999999999999997 78999999999999999999999999998653 34566677777776642 2
Q ss_pred hhHHHhHHhhhhccCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCcceeeeccCCccchh
Q 000525 658 QLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKYGSKDNSLLAMFKAGSKGNLL 737 (1443)
Q Consensus 658 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~sGSKGS~~ 737 (1443)
..+.++..+- ++..++.+ .+.++|++++.+|++| +++.+..+++++...||+.+|+.+|||||.+
T Consensus 690 ~vi~~a~~~~----L~~~pg~t---lretfe~~v~~vlndA--------rd~~gssA~~sl~esNn~k~Mv~aGSKGs~i 754 (1605)
T KOG0260|consen 690 AVIREAQNNE----LEPTPGRT---LRETFENKVNRVLNDA--------RDKSGSSAQKSLSESNNFKTMVVAGSKGSFI 754 (1605)
T ss_pred HHHHHHhhcc----ccCCcchh---HHHHHHHHHHHHHHHH--------HHhhhhHHHhhhhhcccHHHHHhhcCCCcce
Confidence 2222322221 22233322 4678999988888765 5778999999999999999999999999999
Q ss_pred hHhHhhhcccccccCCCCccccCccccccccccCCCCCCccccCCccccccccccccCCCChhhHHHhcccCCCcccccc
Q 000525 738 KLVQHSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDN 817 (1443)
Q Consensus 738 Nl~Qi~~~lGqQ~~~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m~gReGliDta 817 (1443)
||+|+++|+|||+++|+ |+|.+|..|+||+|..++.+|.+ ||||+|||++||+|+|||||||||||||||||
T Consensus 755 nisQ~saCVGqQnVEgk---rIpFGF~~Rtlphf~kDdysPes-----rGfVENSyL~GLtP~EfFfHamggREglidta 826 (1605)
T KOG0260|consen 755 NISQVSACVGQQNVEGK---RIPFGFPKRTLPHFSKDDYSPES-----RGFVENSYLTGLTPQEFFFHAMGGREGLIDTA 826 (1605)
T ss_pred ehhhhhhhhcccccccc---ccccCCCcccccccccCCCCccc-----cceeecccccCCCHHHHHHHHhcccchhhhhh
Confidence 99999999999999995 77777788999999888876654 69999999999999999999999999999999
Q ss_pred c--CCCCcchHHHHHHHhheEeeecceEEccCCceEEEEEeccCCCCC--------------------------------
Q 000525 818 A--DLPGTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGTST-------------------------------- 863 (1443)
Q Consensus 818 v--a~sGYLqRrLvk~lEdl~v~YD~tVR~s~G~~iiq~~yg~~g~~~-------------------------------- 863 (1443)
+ |+||||||||||+|||++|+|||||||+.| +||||.||+||.+-
T Consensus 827 vktaEtGyiqRRL~kameDimv~yDgTVRNs~g-qviQf~YGeDG~d~~~vE~q~~~~l~~~~a~f~~~~~~d~ld~~~~ 905 (1605)
T KOG0260|consen 827 VKTAETGYIQRRLMKAMEDIMVAYDGTVRNSLG-QVIQFKYGEDGLDGHPVEFQNGETLGSLNACFESEFAYDALDEPIS 905 (1605)
T ss_pred hcccccchHHHHHHHHHHHHHhhcCcceecccc-eeEEEEeccCccccceeeccccccccchHHHHHhhhhhhhhcCccc
Confidence 8 999999999999999999999999999999 69999999999320
Q ss_pred --------------------------------------------------------------------------------
Q 000525 864 -------------------------------------------------------------------------------- 863 (1443)
Q Consensus 864 -------------------------------------------------------------------------------- 863 (1443)
T Consensus 906 ~~~~~~~~e~~~~~~l~~lle~e~~~l~~dr~~l~~i~~~g~~k~~lp~n~~r~I~Na~~~f~~~~r~~t~l~~~~v~~g 985 (1605)
T KOG0260|consen 906 LSSEEVVNEISELLKLQNLLECEYKKLVRDRRVLLYIFEYGDAKWPLPENLQRIIWNALKKFSIDERKPTDLIPFKVVKG 985 (1605)
T ss_pred chhhhHhhhhhhhHHHHHHHHHHHHhhhhhhhhhhhhcccCCcccccchhHHHHHHHHHhhcccccccccccchhhhhhh
Confidence
Q ss_pred ------------------------------------------------------------CCcccCCceeccccccchhH
Q 000525 864 ------------------------------------------------------------PTGEIGDQPVGSLSACAISE 883 (1443)
Q Consensus 864 ------------------------------------------------------------~~~~~~ge~VG~~aAqSi~E 883 (1443)
.+.+.|||.||++||||+||
T Consensus 986 ~~~l~e~l~iv~g~~~~sraqrl~~~lLrs~l~~krv~~e~rls~eaf~w~~~~Ie~~f~qa~a~pgemvg~lAaqsvge 1065 (1605)
T KOG0260|consen 986 VKELAEKLVIVRGEDYISRAQRLFNILLRSTLATKRVLEEYRLSSEAFEWVLGEIEARFLQAEASPGEMVGALAAQSVGE 1065 (1605)
T ss_pred hhhhhheeEEeeCchhHHHHHHHHHHHHHhhHHHHHHHHHhcccHHHHHHHhhhhhhheeeeecCccchHhHHHHHHhCC
Confidence 02378999999999999999
Q ss_pred HHHhcc---ccccc---cccccccccchhhhccCCCCCCCccEeeeehhhhccccccCchhhHHHHHhhhcccchhhhhc
Q 000525 884 AAYSAL---DQPIS---LLETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDIVS 957 (1443)
Q Consensus 884 p~tq~l---~~~~~---~l~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e~~a~~Vk~~LE~~tL~di~~ 957 (1443)
|+|||+ +|.++ .+.+.|+|||+||+|.+++.+ ++.+++||....+|.. +.|+.|+.+||.+||.+++.
T Consensus 1066 PatqmTlntfh~aGVssknVt~gvprlkei~Nv~k~~k--tpsLtV~l~g~~~k~~----e~ak~v~~~le~ttl~~vt~ 1139 (1605)
T KOG0260|consen 1066 PATQMTLNTFHYAGVSSKNVTLGVPRLKEIINVAKNAK--TPSLTVYLTGEAAKDN----EWAKLVQCCLEHTTLKDVTR 1139 (1605)
T ss_pred chhhcccchhcccceeeeeeeccCcchhhhhhhhccCC--CceEEEEecchhhcch----HHHHHHhhhcccccHHhhhc
Confidence 999996 66655 367899999999999999766 4799999987766543 57999999999999999999
Q ss_pred eEEEEEcCCCC--------------c------ccccCceEEEEEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCC
Q 000525 958 TSMIIYSPQTG--------------S------MKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVP 1017 (1443)
Q Consensus 958 ~i~i~y~P~~~--------------~------~~~~sp~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~ 1017 (1443)
...|.|+|+.. | ..+.+||.+++++|+..|..++|++++|.++|..++..
T Consensus 1140 ~t~i~ydpdp~~tvI~ed~e~v~a~~e~pd~D~~~ispwlLrlelDr~~m~dk~ltm~~ia~~i~~~f~~---------- 1209 (1605)
T KOG0260|consen 1140 ATEIYYDPDPQSTVIDEDREFVVAYYEMPDEDVGRISPWLLRLELDRASMTDKKLTMEQIAEKINRGFGS---------- 1209 (1605)
T ss_pred cCcceecCCCcceeeccchhhHHhhhcCcccchhhcChHHHHhhhhhhhcccccccHHHHHHHHHhhccC----------
Confidence 99999998752 1 12557999999999999999999999999999988731
Q ss_pred ceeeecCccccccccccCCCceEEEEEeecccccchhhHHHHHHHhccccccceeeccccceEEEEeecccccccCCCCC
Q 000525 1018 DMLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDD 1097 (1443)
Q Consensus 1018 ~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~~~~~~l~~l~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~ 1097 (1443)
++. |...+|+++ ...+++++.. +++.+..+..|...++. +..++|++.|.+|+|...+.. .-+
T Consensus 1210 d~~-----~i~~ddna~---klv~r~ri~~-~~e~D~~l~~Ie~~ml~---~~~l~G~~~i~kV~m~~~~~G-----~f~ 1272 (1605)
T KOG0260|consen 1210 DLA-----CIFSDDNAE---KLVLRLRIAK-EEEDDVFLKCIEANMLG---DMTLRGIPDIFKVYMSPTEDG-----EFK 1272 (1605)
T ss_pred CCc-----eeecccCCc---ceEEEEEecC-ccchhHHHHHHHHhhhh---hcccCCccccceEEEeecCCC-----cee
Confidence 122 222234443 3455555544 33455677787776766 889999999999999842210 001
Q ss_pred CCceEEEEEeeccccccchhHHHHhhhhccccccccccccCCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHH
Q 000525 1098 SFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEH 1177 (1443)
Q Consensus 1098 ~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rH 1177 (1443)
.-+||+|+|+|.+ |.++|. .+.||..||+|||+.||+++|||||+|.+++.|+..|+...|.+|++||
T Consensus 1273 ~~~ew~LeTdg~~-----------l~~v~s-~~~vD~~rt~sn~l~ei~~vlgIea~r~a~~~e~~~vi~f~gsyVnyrh 1340 (1605)
T KOG0260|consen 1273 PVDEWDLETDGVN-----------LRRVLS-EPDVDPARTTSNDLVEIAEVLGIEAVRKALLRELLNVISFDGSYVNYRH 1340 (1605)
T ss_pred ecceeEEecCchh-----------HHhhhc-cCCCCcccccccchhhhhhhhcHHHHHhhhhhhhhheEeecccchhHHH
Confidence 2369999999876 566677 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccceeeEeecchhhhhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccce
Q 000525 1178 LLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHF 1257 (1443)
Q Consensus 1178 l~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~f 1257 (1443)
+.|++|+||++|.++++||||++++.. .+||++|||+|++.|++||++++.|..+||+|+|++|+.+|.|| |.|
T Consensus 1341 laLl~dvmT~~g~lm~itRhg~nr~~t-----gaLmrcSfEetv~il~~aa~~~ekd~~rgvsEnImlgqlap~gT-g~~ 1414 (1605)
T KOG0260|consen 1341 LALLCDVMTARGHLMAITRHGINRQDT-----GALMRCSFEETVDILMDAAAHAEKDPCRGVSENIMLGQLAPMGT-GCF 1414 (1605)
T ss_pred HHHHHHHHhcccceeeeeccccchhhc-----cccccccHHHHHHHHHHHHhhhccCCCccceeeeeecccccCCC-cce
Confidence 999999999999999999999999776 99999999999999999999999999999999999999999999 999
Q ss_pred EEEEccCCCCCCcc
Q 000525 1258 DIIYSGEGRTLSKP 1271 (1443)
Q Consensus 1258 ~ll~~~~~~~~~~~ 1271 (1443)
+|+.+.+.+.+..+
T Consensus 1415 d~~ld~e~l~~~~~ 1428 (1605)
T KOG0260|consen 1415 DLMLDAEKLKKGIE 1428 (1605)
T ss_pred eeeccHHhhhccCc
Confidence 99999887755443
No 4
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=100.00 E-value=6.1e-228 Score=2038.17 Aligned_cols=1168 Identities=22% Similarity=0.305 Sum_probs=870.0
Q ss_pred ceeeeeEEEEcCChHHHHhccceEEecC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccceeecCccc
Q 000525 14 SGILTGISLGISTDTEKEKLSVMEIGAV-----------SEVTNPRLGLPNPTNECSSCGAKDRKACEGHFGFIKFPFTI 82 (1443)
Q Consensus 14 ~~~I~~I~F~~~S~eEI~~~Sv~~I~~~-----------~Gl~D~rLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~PV 82 (1443)
.+.+..|+||+||++||+++||++||+| |||||++||+-+....|.||++ +...||||||||||+.||
T Consensus 10 ~~~~~~v~Fg~yt~~ei~klSv~kIt~p~~~D~lGhPi~GGLYDl~LGp~~~~~~C~TC~~-~~~~CPGH~GHIeL~~pv 88 (1640)
T KOG0262|consen 10 MSFQPSVSFGSYTDQEIRKLSVKKITNPITFDNLGHPIPGGLYDLALGPLDNSDVCSTCNQ-DELNCPGHMGHIELPVPV 88 (1640)
T ss_pred cccccceeeeccCHHHHhhcceeEecCceeecccCCCCCCcccccccCCccchhhhhhhcc-hhhcCCCccCeeeecccc
Confidence 3445669999999999999999999975 8999999998777789999994 899999999999999999
Q ss_pred cccccHHHHHHHHhccccccccccCcch--------hhhc------------------------------c---------
Q 000525 83 LHPYFLSDIAKLLNSICPKCKTIRKERQ--------KGAG------------------------------S--------- 115 (1443)
Q Consensus 83 fHpgf~~~i~kIL~~iC~~C~rlll~~~--------~k~l------------------------------~--------- 115 (1443)
|||+||+.++++|++.|++||+|+++.. .+.+ +
T Consensus 89 ynPlfF~~ly~lLr~sCl~Chhf~~k~~~v~~~~cqLrll~~G~i~ea~~Le~i~~~~~~d~~d~~~~~~k~~~~~~v~~ 168 (1640)
T KOG0262|consen 89 YNPLFFDFLYNLLRGSCLFCHHFRCKNVDVHILFCQLRLLEYGLIEEAEDLESITSETVEDNEDESLNEIKSCRAQYVTE 168 (1640)
T ss_pred cCHHHHHHHHHHHHHHHHhhhhcccCcHHHHHHHHHHHHHHhchHHHHHHHHHhhhhhhccCcchhHHHHHhhhhhhccH
Confidence 9999999999999999999999988741 0000 0
Q ss_pred --------cc---------------------ccccccccccccCCCCCCcccccccccccccCccceeehhhhhhhc-c-
Q 000525 116 --------SR---------------------KEQPRVCKYCVRNPAQWYPRMRFKLSSKDLSGKTAIIVEIDEKLSK-K- 164 (1443)
Q Consensus 116 --------~~---------------------~~~~~~C~~C~~~~~~~~p~i~~~~~~~~~~~k~~ii~e~~~~~~~-k- 164 (1443)
+. .-..++|++|... .|.+++. -+.|.-+..-......+ +
T Consensus 169 ~i~~~~~~~~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~----~p~~rk~-----~~~kv~~~~~~~~~~~~~~~ 239 (1640)
T KOG0262|consen 169 AISEALLDKSEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHS----NPKLRKD-----GFRKVFIDALSSKVGANVIR 239 (1640)
T ss_pred HHHHHhhcCCCccchhhHHHHHHHHHHHHHHhhccccCCcccCC----Cchhhcc-----ccceeeeehhcccccccchh
Confidence 00 0114789999762 2332211 11111000000000000 0
Q ss_pred -----CCCCccccccccCcccc--------------ccccccCCCccccCHHHHHHHhccCC---hhhHhhccC------
Q 000525 165 -----NKKLPDDYWGFIPFDAQ--------------QEENSVKPNRKVLSCKQVSYLLKDVD---PSIREEFIL------ 216 (1443)
Q Consensus 165 -----~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~LsP~eV~~iLkkI~---~ed~~~~~~------ 216 (1443)
+......+.+.-.+... +.....+..++.|+|.+|+++|+.+. .+++..+++
T Consensus 240 ~~~i~~~~~~~~~~d~~~~G~~E~~~~g~d~~e~~~~~~~~~~t~~~~l~~tevR~~l~~lf~ne~~~l~~lf~l~~~~~ 319 (1640)
T KOG0262|consen 240 GAKIKKDVGSKGFEDSGIDGSNEVEEDGKDLFEKSTEPAEFEKTGKKYLLPTEVREHLRDLFKNEGELLSYLFPLWDSGS 319 (1640)
T ss_pred heeeehhcccccccccccCCccccccccccccccccccccccccccccccHHHHHHHHHHHHhhhHHHHHHhhccccccc
Confidence 00000000000000000 00111223568899999999999994 344544333
Q ss_pred ----CCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHHH----HHHHH----HHHHhh-h
Q 000525 217 ----SKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIELS----HLVQD----CLKISK-L 283 (1443)
Q Consensus 217 ----rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~~----~~~~~----~~~~~~-~ 283 (1443)
+-|+|||.+|||||+++||..+++ +...|+.+|..|+++++.+.....+. .++.+ .++... +
T Consensus 320 ~k~~p~d~FFld~l~VpPtrfRP~s~~g-----d~~~en~Qt~~L~kVle~s~~i~~~~~~m~~kl~~~~k~~l~~~~g~ 394 (1640)
T KOG0262|consen 320 GKIDPSDMFFLDNLLVPPTRFRPPSMLG-----DEVHENPQTLNLNKVLESSVLIRKLLKDMKGKLDEELKLILERLRGI 394 (1640)
T ss_pred cccCccceeeeeccccCCcccCCchhcc-----hhhhcChHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHhhhhH
Confidence 236999999999999999998763 34678999999999987542211111 00000 000000 0
Q ss_pred hcccccCCchhHhhhc---------c-CCccc-CcCCcc--------hhhccccCCCCCCCCceeEeCCCCCcccccccc
Q 000525 284 HLDKSSRKDSAEVRQK---------K-NIDIS-NSSGLR--------WIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIP 344 (1443)
Q Consensus 284 ~~d~~~~~~~~~~~q~---------~-~~~~~-~~~G~r--------~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP 344 (1443)
+ +.....|..+|. + ++..+ .++|++ .||++||||||||+|||||||||||.+||||||
T Consensus 395 ~---~kl~~aw~~LQ~~vn~lfDs~~~~k~~r~~~pGikQiLEKKeGLFRkhMMGKRVN~AaRSVIsPDPnI~tnEIGIP 471 (1640)
T KOG0262|consen 395 F---SKLINAWLQLQASVNVLFDSKMASKWSRDSPPGIKQILEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEIGIP 471 (1640)
T ss_pred H---HHHHHHHHHHHHHHHHHhccccccccccCCCchHHHHHHHhhhhHHHHhhccccchhhccccCCCCCccccccCCc
Confidence 0 000012333332 1 11111 235655 479999999999999999999999999999999
Q ss_pred HHHHhhcCcceeechhhHHHhhhhh-cccccccCcceEe-eCCeEEEec-------c--ccccc----------CCCEEe
Q 000525 345 CQVAERLQISERLNSWNWERLSVCI-SFRLLEKGELYVC-RKGGLVRIR-------R--IDALE----------LGDIIY 403 (1443)
Q Consensus 345 ~~~a~~Lt~pe~Vt~~Ni~~l~~~~-~~~~~~~g~~~i~-~~g~~~~~~-------~--~~~l~----------~g~iV~ 403 (1443)
..||++|||||+||+||+++||+++ |++-+++||+++. ++|.+..+- . |++|. -+.+|+
T Consensus 472 ~vFA~KLTyPepVt~~NV~elr~aViNGP~~hPGA~~iqd~dg~~t~l~~~~~~qR~alA~qLLtpst~~~~~~~~K~V~ 551 (1640)
T KOG0262|consen 472 PVFAKKLTYPEPVTPWNVNELRKAVINGPDVHPGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTGNPTEFGTKKVH 551 (1640)
T ss_pred hHHHhhccCCCcCCcccHHHHHHHHhcCCCCCCCcceeecCCCceeecCCCCHHHHHHHHHHhhccccCCCcccCCceee
Confidence 9999999999999999999999984 6777999999875 667655432 1 33432 357999
Q ss_pred ceeccCceEEEeCCCCCCccccccccEEEecCCceEEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcc
Q 000525 404 RPLTDGDIVLINRPPSIHPHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLI 483 (1443)
Q Consensus 404 Rhl~dgD~vl~NRqPsLHk~Simah~v~v~p~~~t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~ 483 (1443)
||+.|||+||+||||||||+|||||+|||+|+++|+||||++|++|||||||||||+|+|||+.|||||++|+++..|++
T Consensus 552 RHvknGDvvlmNRQPTLHKPSimaHkaRVL~gEktlRlHYANCkaYNADFDGDEMN~HfPQse~araEa~~ian~dsqYL 631 (1640)
T KOG0262|consen 552 RHVKNGDVVLMNRQPTLHKPSIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIARAEAYNIANTDSQYL 631 (1640)
T ss_pred eeccCCcEEEEcCCCccccchhhhhhheecCCcceeeeeecccccccCCCCcchhcccCCchhhHHHHHHHHhccCCcee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCcccccchhHHHHHHhhccCccccCHHHHHHHHhhCC------CccCCCceecccCCccchHHHHHhhcC----C
Q 000525 484 NQQSGRNLLSLGQDSLTAAHLLMEDSVLLSHLQMQQLQMFCP------HRFLSPDIFKISKDSVWSGKQLFSMLL----P 553 (1443)
Q Consensus 484 sp~~g~pl~gl~QD~l~g~~llt~~d~fl~~~~~~~l~~~~~------~~l~~pai~Kp~~~~lwTGKql~s~~l----p 553 (1443)
.|++|.|++||||||++++++||.||+||+|++|+||+..+. ..+++|+|+|| .+|||||||+|++| |
T Consensus 632 vPt~G~PlrGLIQDHiVsgv~LT~rd~Fftre~y~qLv~~~l~~~~~rI~~lpPtIlkP--~~LWTGKQVIsTil~Ni~P 709 (1640)
T KOG0262|consen 632 VPTDGTPLRGLIQDHIVSGVLLTMRDSFFTREDYQQLVFAGLSDTFKRIKLLPPTILKP--APLWTGKQVISTILKNIIP 709 (1640)
T ss_pred ccCCCCchhhhhhhheeeeEEEEecccccCHHHHHHHHHHhhhhhccceeccCcccccc--ccccccchHHHHHHHhcCC
Confidence 999999999999999999999999999999999999987643 26889999999 79999999999998 4
Q ss_pred C---CCccc-------------cCC-----CcEEEeCCeeccc-cCcccccCCCccHHHHHHHHhcHH-HHHHHHHHHHH
Q 000525 554 P---DFEYT-------------FPS-----KDVYISGGKLISA-EGSSWLRDYEGNLFQYLIKRYRDK-VLDFLYAAQEV 610 (1443)
Q Consensus 554 ~---~~~~~-------------~~~-----~~v~i~~gell~~-~~k~~lg~~~~~l~~~l~~~~g~~-a~~~l~~~q~l 610 (1443)
+ .+|.. .++ +.|+|++|||||| +||+.+|++.+||+|++++.||++ +.++|+.+.||
T Consensus 710 ~~~p~iNl~~kaKip~~~W~~~s~e~~l~Es~v~ir~GellcGVLDKa~~Gat~yGLvH~~~ElYG~~~s~~lLs~~srl 789 (1640)
T KOG0262|consen 710 EGHPPINLESKAKIPGKAWRVHSEEPKLNESQVLIREGELLCGVLDKAQFGATAYGLVHCCHELYGGETSGKLLSVFSRL 789 (1640)
T ss_pred CCCCcccchhcccCchhhcCCCCCcccCCcceEEEecCceEEEeechhhcCchhhhhhhhhhhhhCccchhhHHHHHHHH
Confidence 3 34432 112 5599999999998 899999999999999999999998 67999999999
Q ss_pred HHHHHhcccceeecCccccccccch-HHHHHHHHH-hhHHHHHhhhhhhhhHHHhHHhhhhccCCcccccccccchhhHH
Q 000525 611 LCEWLSVRGMTVSLSDLYLASHSCS-RKILMDEIF-YGLREAQDTCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYE 688 (1443)
Q Consensus 611 ~~~~L~~~GfSigi~D~~~~~~~~~-~~~~~~~i~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E 688 (1443)
++.||+++|||+|++|+.+.++++. |++++++.. .+.++|++..++.. +.-.+.+.+.++. .+.-.
T Consensus 790 FT~ylq~~GFT~GvdDlll~~~~D~kR~~il~e~~~vG~qa~~~~~~l~~---da~~del~~~le~---------~y~~d 857 (1640)
T KOG0262|consen 790 FTAYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKEAFGLDV---DAPPDELRSRLEA---------IYLKD 857 (1640)
T ss_pred HHHHHHHhccccccceeeechhhhHHHHHHHHhhhcccHHHHHHHhCCCC---CCCHHHHHHHHHH---------HHhcc
Confidence 9999999999999999999999864 667776653 45556655443211 1111111111110 00000
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH----hhCCCCCcceeeeccCCccchhhHhHhhhcccccccCCCCccccCcccc
Q 000525 689 KQRSAALSQASVDAFKHVFWDIQNLAY----KYGSKDNSLLAMFKAGSKGNLLKLVQHSLCLGLQHSLAPLSFRFPHELS 764 (1443)
Q Consensus 689 ~~~~~~L~~~~~~~~~~~~~~~~~~~~----~~~~~~N~~~~M~~sGSKGS~~Nl~Qi~~~lGqQ~~~g~~~~r~p~~~~ 764 (1443)
....+.|...+...+..+.++|.+.|. -..+|.|++.+|+.||||||++|++||+||||||.++|+ |+|.|+|
T Consensus 858 ~~~~~~LD~~~k~~~n~~ts~I~~~cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeLEGk---RvPlMvS 934 (1640)
T KOG0262|consen 858 ADKLAMLDRVMKSELNGYTSEIVKKCVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQELEGK---RVPLMVS 934 (1640)
T ss_pred hhHHHHHHHHHHHHHhhhhHHHHhhhccchhhhcCCcchHHHHHHhcCCcccccHHHHHHhhhhHhhcCC---ccceeec
Confidence 112233444444444555555555543 346899999999999999999999999999999999996 9999999
Q ss_pred ccccccCCCCCCccccCCccccccccccccCCCChhhHHHhcccCCCccccccc--CCCCcchHHHHHHHhheEeeecce
Q 000525 765 CAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNA--DLPGTLTRRLMFFMRDLCTAYDGT 842 (1443)
Q Consensus 765 ~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m~gReGliDtav--a~sGYLqRrLvk~lEdl~v~YD~t 842 (1443)
|++||+|.+++++|+|| |||..+|++|+.|+|||||||||||||||||| |+|||||||||||||+|+|+||.|
T Consensus 935 GKtLPsF~p~e~spraG-----GfI~~RFlTGi~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V~YD~T 1009 (1640)
T KOG0262|consen 935 GKTLPSFAPYETSPRAG-----GFIDGRFLTGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVHYDLT 1009 (1640)
T ss_pred CCccCCcCCCCCCCCCC-----CcccceeecCCCchHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhhcEEeccce
Confidence 99999999999999998 77889999999999999999999999999998 999999999999999999999999
Q ss_pred EEccCCceEEEEEeccCCCCC-----------------------------------------------------------
Q 000525 843 VRNAYGNQIVQFSYNIEGTST----------------------------------------------------------- 863 (1443)
Q Consensus 843 VR~s~G~~iiq~~yg~~g~~~----------------------------------------------------------- 863 (1443)
|||++|+ ||||.|||||.+.
T Consensus 1010 VRDsDgs-vVQF~YGEDglDitKssfl~~~~f~~~Ny~avl~~~~~~~v~s~~d~~~a~~~~k~i~kw~kk~~w~~~~k~ 1088 (1640)
T KOG0262|consen 1010 VRDSDGS-VVQFMYGEDGLDITKSSFLNKKEFPTDNYEAVLLKYKSESVLSAFDIKKASKYIKKILKWKKKHMWFELDKK 1088 (1640)
T ss_pred EEcCCCc-EEEEeecCccccccHHhhcchhhhhhhhHHHHHhhhChHHHhhhhhhHHHHHHHHHHHHHHhhhccchhhcc
Confidence 9999995 9999999999540
Q ss_pred ----------------------------------------------------------CCcccCCceeccccccchhHHH
Q 000525 864 ----------------------------------------------------------PTGEIGDQPVGSLSACAISEAA 885 (1443)
Q Consensus 864 ----------------------------------------------------------~~~~~~ge~VG~~aAqSi~Ep~ 885 (1443)
.+.+.||||||++||||||||.
T Consensus 1089 ~~cpdpv~~k~~p~~y~gsvsekf~~~i~~f~~~~~k~~~s~~~~~~~lr~ll~~K~~~SLa~PGE~VGvlAAQSIGEPS 1168 (1640)
T KOG0262|consen 1089 IACPDPVLAKYNPDKYLGSVSEKFRKKIDDFDDENAKKEKSEEPSEEKLRRLLQLKYIRSLADPGEPVGVLAAQSIGEPS 1168 (1640)
T ss_pred cCCCChhhhhcchhhhhccccHHHHHHHHHHHHHhhhhhccccchHHHHHHHHHHHHHHHhcCCCCcceeeeecccCCCc
Confidence 0347899999999999999999
Q ss_pred Hhcc---ccccc---cccccccccchhhhc-cCCCCCCCccEeeeehhhhccccccCchhhHHHHHhhhcccchhhhhce
Q 000525 886 YSAL---DQPIS---LLETSPLLNLKNVLE-CGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDIVST 958 (1443)
Q Consensus 886 tq~l---~~~~~---~l~t~gl~rLkEIl~-~~k~~~~~~~~~~l~Ls~~~~k~~~~~e~~a~~Vk~~LE~~tL~di~~~ 958 (1443)
|||| +|.++ .++|.|+|||+|||+ |+++++| |+|++-+...- ...+|..++.+|.+++|++++..
T Consensus 1169 TQMTLNTFHfAGrGemNVTLGIPRLREIlMtASanIkT--P~mt~pi~~g~------s~~ra~~i~~~l~rV~L~evlk~ 1240 (1640)
T KOG0262|consen 1169 TQMTLNTFHFAGRGEMNVTLGIPRLREILMTASANIKT--PSMTVPIKNGV------SDERADDITKELRRVTLKEVLKK 1240 (1640)
T ss_pred ceeehhheeeccccceeeeecchHHHHHHHHHhhccCC--CceeeeccCCc------cHHHHHHHHHHHHHHHHHHHHhh
Confidence 9996 66655 478999999999997 4566665 56665443221 12468999999999999999975
Q ss_pred EEE--EE--cCCCCcccccCceEEEEEeeH--HHHHHcCCCHHHHHHHHHHhh------------hhh--hhhhcc--cC
Q 000525 959 SMI--IY--SPQTGSMKHFSPWICHFHVRK--EIMKRTGLKEHSIIDSLYRQC------------KAA--RTELKI--SV 1016 (1443)
Q Consensus 959 i~i--~y--~P~~~~~~~~sp~v~~~~Ldk--e~l~~~~L~i~~I~~~i~~~~------------~~~--~~~l~~--~~ 1016 (1443)
+.+ .+ .+... ..-+.++|.+.. +.=..+.+.-++|.+.+.+++ +.. ++.... ..
T Consensus 1241 v~vte~~t~~~~~~----~~~y~lr~~~~~~~~y~~e~~v~~e~i~~~m~~~Flk~L~~aI~k~~~k~~~~~~~~~dd~~ 1316 (1640)
T KOG0262|consen 1241 VGVTEKITMVENQS----CKKYKLRFDLLPREEYQEEYDVRPEDIEEVMENRFLKLLERAIKKKLKKAKYTRGMSNDDAD 1316 (1640)
T ss_pred eeeeEEEEeecccc----ceEEEEEEeecCHHHhhhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhccccccCC
Confidence 442 22 12111 112667776641 122244555444444332221 100 000100 00
Q ss_pred Ccee--------eecCccc-----------------------------cc--------------c---------------
Q 000525 1017 PDML--------ISNKDCS-----------------------------SI--------------N--------------- 1030 (1443)
Q Consensus 1017 ~~i~--------i~~~~c~-----------------------------~~--------------~--------------- 1030 (1443)
|.+. +...+-+ +. +
T Consensus 1317 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ddddas~~k~~~k~~~~~dYe~~de~e~~~~~~~e~~~~~e~~e~d~e~g~ 1396 (1640)
T KOG0262|consen 1317 PDDGNEVDNNDEVGGEDNEDSDDESEDDEDDDDASDAKLHKKTEEEADYESEDEDERVEEREDEGDEDEESDEDDEEVGL 1396 (1640)
T ss_pred ccccccCCccccccCCccccccccccccCcccchhHHHHhhhhccccCcCCCchhhhhhhhhcccccccccccchhhccc
Confidence 0000 0000000 00 0
Q ss_pred -------------------------------------ccccCCCceEEEEEeecccccchhhHHHHHHHhccccccceee
Q 000525 1031 -------------------------------------MQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMPFLLKTVVK 1073 (1443)
Q Consensus 1031 -------------------------------------~~~~~~~~~~i~v~~~~~~~~~~~~l~~l~~~iip~ll~~vVk 1073 (1443)
+++.++..||-.. +.-........+-.|.+.+++ .++|.
T Consensus 1397 dg~~~~~~~~~e~~~~~~~~er~~qs~~~~~~fi~~y~fd~~~~~wcev~-~~lp~~~~k~~mssiVe~~~~---~~vI~ 1472 (1640)
T KOG0262|consen 1397 DGTPEPEEEDQEGQPEVNAVERREQSVKKRHDFISRYTFDKESGKWCEVE-LKLPLDKEKLDMSSIVESIAP---KSVIH 1472 (1640)
T ss_pred CCCCCcccccccCCchhhHHHHHHHHHHHHHHHhhhhccccccCcEEEEE-EEecCCCcchHHHHHHHHHhc---ceeee
Confidence 0111122233211 100111223566777777888 89999
Q ss_pred ccccceEEEEeecccccccCCCCCCCceEEEEEeeccccccchhHHHHhhhhccccccccccccCCCcHHHHHHHHcHHH
Q 000525 1074 GFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDA 1153 (1443)
Q Consensus 1074 G~~~I~rv~I~~~d~~~~~~~~~~~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt~sn~I~ei~~~lGIEA 1153 (1443)
.+|+|+|+++...+. +....+ +|.|+|.+ +.+...+.+.+|.++.|||||++|+++|||||
T Consensus 1473 q~~gIeRc~~~~~~~-------~~k~~~-~l~TeGVn-----------l~a~~~~~d~LDv~~lySNDI~ail~tyGVEA 1533 (1640)
T KOG0262|consen 1473 QVPGIERCVVSEPQD-------DVKEKS-VLLTEGVN-----------LPALFDHADILDVNRLYSNDIHAILNTYGVEA 1533 (1640)
T ss_pred ccCCceeeeccCCcc-------cccccc-eehhcCcc-----------HHHHHHHHhhhhhhhhccchHHHHHHHhhHHH
Confidence 999999999874321 111223 78899887 33444447999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcccCCccCHHHHHHHHhhccceeeEeecchhhhhhhhccCCCcchhhhccccccHHHHHHHHhhCCC
Q 000525 1154 GLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAV 1233 (1443)
Q Consensus 1154 ar~~ii~el~~~~~~~G~~V~~rHl~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~ 1233 (1443)
||++|++|+.+||+.|||+||+|||.||||||||+|.+.+|||+||. +.+|||+++|||+|.++|.+||.+|+.
T Consensus 1534 ar~~Iv~Ev~~VF~vYGIsVd~RHLsLiADYMTf~G~y~pfnR~Gm~------~ssSP~qkMsFETt~~Fl~~Aa~~g~~ 1607 (1640)
T KOG0262|consen 1534 ARNAIVNEVNNVFKVYGISVDIRHLSLIADYMTFEGGYQPFNRMGME------SSSSPLQKMSFETTCQFLKQAALFGEE 1607 (1640)
T ss_pred HHHHHHHHHHHhhhheeeeecHHHHHHHHHHHhhccccccccccccc------cCCChhHhhhHHHHHHHHHHHHhcCcc
Confidence 99999999999999999999999999999999999999999999986 457999999999999999999999999
Q ss_pred cCCCCccceeccCCCCCccCccceEEEEccC
Q 000525 1234 DNLQGSVDALGWGKVPSVGTGGHFDIIYSGE 1264 (1443)
Q Consensus 1234 D~l~gvs~~ii~Gk~~~~GTgg~f~ll~~~~ 1264 (1443)
|+|.++|++|++|+++..|| |+|||+.+.+
T Consensus 1608 D~L~sPSArLvvG~~~r~GT-G~Fdll~~v~ 1637 (1640)
T KOG0262|consen 1608 DELSSPSARLVVGLPVRGGT-GSFDLLQKVD 1637 (1640)
T ss_pred cccCCCcceeEeccccCCCc-ceeeeeccCC
Confidence 99999999999999999999 9999998765
No 5
>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=1.9e-188 Score=1793.68 Aligned_cols=778 Identities=26% Similarity=0.425 Sum_probs=636.9
Q ss_pred eeeeeEEEEcCChHHHHhccceEEecC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccceeecCcccc
Q 000525 15 GILTGISLGISTDTEKEKLSVMEIGAV-----------SEVTNPRLGLPNPTNECSSCGAKDRKACEGHFGFIKFPFTIL 83 (1443)
Q Consensus 15 ~~I~~I~F~~~S~eEI~~~Sv~~I~~~-----------~Gl~D~rLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~PVf 83 (1443)
++|++|+|++||+|||+++||++|+++ |||||||||++++...|+|||+ +..+||||||||||++|||
T Consensus 2 ~~I~~I~F~~~S~eEI~k~Sv~~It~~~~~d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~-~~~~CpGHFGhIeL~~PVf 80 (868)
T TIGR02390 2 KKIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGG-KVGECPGHFGHIELARPVV 80 (868)
T ss_pred ceeeEEEEeCCCHHHHHHhCeeEEecccccCCCCCcCCCCccCcccCCCCCCCCCCCCCC-CCCcCCCcceEEecccccc
Confidence 579999999999999999999999864 7999999999999999999996 7899999999999999999
Q ss_pred ccccHHHHHHHHhccccccccccCcchh-----hh---c---------------cccccccccccccccCCCCCCccccc
Q 000525 84 HPYFLSDIAKLLNSICPKCKTIRKERQK-----GA---G---------------SSRKEQPRVCKYCVRNPAQWYPRMRF 140 (1443)
Q Consensus 84 Hpgf~~~i~kIL~~iC~~C~rlll~~~~-----k~---l---------------~~~~~~~~~C~~C~~~~~~~~p~i~~ 140 (1443)
||+||+.|++||+|+|++|+++++++.. +. + .+.++..+.|++|++. .|.+++
T Consensus 81 hpgf~~~i~kiL~~vC~~C~rll~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~C~~Cg~~----~p~ir~ 156 (868)
T TIGR02390 81 HVGFAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKEEGGDLASTLIEKIVKEAAKRMKCPHCGEE----QKKIKF 156 (868)
T ss_pred chhHHHHHHHHHHHHhhhcCceeeCccccHHHHHHHHhcccchhhhHHHHHHHHHHHhhcCCCCCCCCCc----CceEEE
Confidence 9999999999999999999999986421 00 0 0123334679999763 344432
Q ss_pred ccccccccCccceeehhhhhhhccCCCCccccccccCccccccccccCCCccccCHHHHHHHhccCChhhHhhc-----c
Q 000525 141 KLSSKDLSGKTAIIVEIDEKLSKKNKKLPDDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPSIREEF-----I 215 (1443)
Q Consensus 141 ~~~~~~~~~k~~ii~e~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LsP~eV~~iLkkI~~ed~~~~-----~ 215 (1443)
. ++.. ++ ... +...+.|+|++|+++|++|+++|+.++ .
T Consensus 157 ~----------~~~~----------------~~---~~~--------~~~~~~L~p~~v~~ilk~I~~eD~~lLG~~p~~ 199 (868)
T TIGR02390 157 E----------KPTY----------------FY---EEG--------KEGDVKLTPSEIRERLEKIPDEDAELLGINPKV 199 (868)
T ss_pred e----------eeee----------------ee---ecc--------CCCCeecCHHHHHHHHHhCCHHHHHHhCCCCCC
Confidence 1 0000 00 000 013467999999999999999999874 3
Q ss_pred CCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHH---------HHHHHHHHHHhh-hhc
Q 000525 216 LSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIEL---------SHLVQDCLKISK-LHL 285 (1443)
Q Consensus 216 ~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~---------~~~~~~~~~~~~-~~~ 285 (1443)
.+||||||++|||||+++||++.+++ + ..+|||||.+|.+|++.|...++. ....++.+|... .+.
T Consensus 200 ~~Pe~~ilt~LPVPP~~iRPsv~~~~---g-~~~EDDLT~~L~~II~~N~~Lk~~~~~g~~~~~~~~~~~~LQ~~v~~~~ 275 (868)
T TIGR02390 200 ARPEWMVLTVLPVPPVTVRPSITLET---G-ERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYF 275 (868)
T ss_pred CCcceeeEeccccCCCCCcCeEEeCC---C-cccCChHHHHHHHHHHHHHHHHHHHHcCCchhhhHHHHHHHHHHHHHHH
Confidence 58999999999999999999987642 2 468999999999999876432221 112223333321 234
Q ss_pred ccccCCchhHhhhccCCccc----CcCCcc-hhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCcceeechh
Q 000525 286 DKSSRKDSAEVRQKKNIDIS----NSSGLR-WIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSW 360 (1443)
Q Consensus 286 d~~~~~~~~~~~q~~~~~~~----~~~G~r-~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~pe~Vt~~ 360 (1443)
|+.....+ ...++.++..+ .+.|+. |||+|||||||||||||||||||||++||||||..||++|||||+||+|
T Consensus 276 d~~~~~~~-~~~~~~~~~~~~i~~~l~gK~G~~R~nl~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~Vt~~ 354 (868)
T TIGR02390 276 DNELPGIP-PARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPW 354 (868)
T ss_pred cCCCCCCC-ccccCCCCCchhhHhhhcccccccccccccccccccCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEehh
Confidence 54432211 01111112111 123332 8999999999999999999999999999999999999999999999999
Q ss_pred hHHHhhhhhc-ccccccCcceEe-eCCeEEEecc------cccccCCCEEeceeccCceEEEeCCCCCCccccccccEEE
Q 000525 361 NWERLSVCIS-FRLLEKGELYVC-RKGGLVRIRR------IDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKV 432 (1443)
Q Consensus 361 Ni~~l~~~~~-~~~~~~g~~~i~-~~g~~~~~~~------~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v 432 (1443)
|+++|++++. ..-.++||+++. ++|+.+.++. +.+|++||+|||||+|||+|||||||||||||||||+|||
T Consensus 355 N~~~l~~lv~ng~~~~pga~~i~~~~g~~~~l~~~~~~~~~~~l~~g~~v~rhl~dgd~vl~NRqPsLHr~si~a~~~~v 434 (868)
T TIGR02390 355 NIDELREYVLNGPDSWPGANYVIRPDGRRIKIRDENKEELAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKV 434 (868)
T ss_pred hHHHHHHHHHcCCccCCCceEEEcCCCcEEechhhhHHHHHhhcccCCEEEEehhcCccceeccCCccccccceeEEEEE
Confidence 9999999874 445678998864 6777766643 4579999999999999999999999999999999999999
Q ss_pred ecCCceEEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHHhhccCcccc
Q 000525 433 LPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDSVLL 512 (1443)
Q Consensus 433 ~p~~~t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~llt~~d~fl 512 (1443)
+|+ +||||||++|+||||||||||||+|+|||++|||||++||++++|++||++|+|++|++||+|+|+|+||.+|+||
T Consensus 435 ~~~-~t~r~n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~~d~f~ 513 (868)
T TIGR02390 435 LPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLF 513 (868)
T ss_pred ecC-ceEeeccccCCccccCcccceeeEecCCCHHHHHHHHHHhhchhceecCCCCCeeEEeehhhhhheeeeeeccccC
Confidence 997 5999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHhhCCC--ccCCCceecccCCccchHHHHHhhcCCCCCccccC-----------------CCcEEEeCCeec
Q 000525 513 SHLQMQQLQMFCPH--RFLSPDIFKISKDSVWSGKQLFSMLLPPDFEYTFP-----------------SKDVYISGGKLI 573 (1443)
Q Consensus 513 ~~~~~~~l~~~~~~--~l~~pai~Kp~~~~lwTGKql~s~~lp~~~~~~~~-----------------~~~v~i~~gell 573 (1443)
++++++||+++... .+|+|||+|| +++||||||||++||.++|+... ++.|+|+||||+
T Consensus 514 ~~~~~~~l~~~~~~~~~~~~p~i~kp--~~lwTGKqi~s~~lp~~~n~~~~~~~~~~~~~~~~~~~~~d~~v~i~~g~ll 591 (868)
T TIGR02390 514 TKEEVQTILGVAGYFGDPPEPAIEKP--KEYWTGKQIFSAFLPEDLNFEGRAKICSGSDACKKEECPHDAYVVIKNGKLL 591 (868)
T ss_pred CHHHHHHHHhcCCccccCCCceecCC--cccccHHHHHHHhcCCCCcceecccccccccccccccCCCcceEEEecCeEE
Confidence 99999999987543 5789999999 79999999999999998887521 345999999999
Q ss_pred cc-cCcccccCCCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCccccccccchHHHHHHHHHhhHHHHH
Q 000525 574 SA-EGSSWLRDYEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQ 651 (1443)
Q Consensus 574 ~~-~~k~~lg~~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~~~~~~~~~~~~~~~~i~~~~~~a~ 651 (1443)
+| +||+++|++.++|+|.++++||++ |++||+++|+|+++||+++|||||++|++++++.. +++++.+++|+
T Consensus 592 ~G~ldK~~lg~~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~~~~~~~------~~~~~~i~~~~ 665 (868)
T TIGR02390 592 KGVIDKKAIGAEKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAK------EEIEELIEKAE 665 (868)
T ss_pred eeeecHHHhccCcccHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhccEEeehhheeeCHHHH------HHHHHHHHHHH
Confidence 87 899999999999999999999996 88999999999999999999999999999987543 22233345555
Q ss_pred hhhhhhhhHHHhHHhhhhccCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCcceeeeccC
Q 000525 652 DTCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKYGSKDNSLLAMFKAG 731 (1443)
Q Consensus 652 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~sG 731 (1443)
+.+. ++ ...|..+.++..++.+ ...++|.+++ +.|+++++++++++.+.++++|++++|+.||
T Consensus 666 ~~~~--~~----~~~~~~g~l~~~~~~~---~~~~~e~~i~--------~~l~~~r~~~~~~~~~~l~~~N~~~~M~~sG 728 (868)
T TIGR02390 666 KRVD--NL----IERYRNGELEPLPGRT---VEETLEMKIM--------EVLGKARDEAGEVAEKYLDPENHAVIMARTG 728 (868)
T ss_pred HHHH--HH----HHHHHcCCCccCcCCC---HHHHHHHHHH--------HHHHHHHHHHHHHHHHhcCCCcchhhhhhcc
Confidence 4432 11 2233444443322221 1223444333 3455667888999999999999999999999
Q ss_pred CccchhhHhHhhhcccccccCCCCccccCccccccccccCCCCCCccccCCccccccccccccCCCChhhHHHhcccCCC
Q 000525 732 SKGNLLKLVQHSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRD 811 (1443)
Q Consensus 732 SKGS~~Nl~Qi~~~lGqQ~~~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m~gRe 811 (1443)
||||++|++||+||||||+++|+ |+|.++++|+||+|++++..+.+ +|||.|||++||+|+|||||||||||
T Consensus 729 sKGS~~Ni~Qi~~~lGQQ~~~g~---ri~~~~~~rtlp~f~~~d~~~~~-----~GfV~~sF~~GL~p~EfFfH~m~gRe 800 (868)
T TIGR02390 729 ARGSLLNITQMAAMVGQQSVRGG---RIRRGYRNRTLPHFKKGDIGAKA-----RGFVRSSFKKGLDPTEYFFHAAGGRE 800 (868)
T ss_pred CCcccccHHHHHhccCccccCCC---cCccccccCCCCCCCCCCCCccc-----CceecccccCCCCHHHHHHHHhhhcc
Confidence 99999999999999999999996 99999999999999988876654 59999999999999999999999999
Q ss_pred ccccccc--CCCCcchHHHHHHHhheEeeecceEEccCCceEEEEEeccCCCCCCCcccCCceecc
Q 000525 812 SSFSDNA--DLPGTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGTSTPTGEIGDQPVGS 875 (1443)
Q Consensus 812 GliDtav--a~sGYLqRrLvk~lEdl~v~YD~tVR~s~G~~iiq~~yg~~g~~~~~~~~~ge~VG~ 875 (1443)
||||||+ |+||||||||||+||||+|+|||||||++|+ ||||.|||||.+ |....-++||.+
T Consensus 801 GLiDTAvKTa~sGYLqRrLvk~lEdl~v~yD~tVR~~~g~-iiQf~YG~dg~d-~~~~~~~~~~~~ 864 (868)
T TIGR02390 801 GLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGN-LIQFKYGEDGVD-PMKSDHGKPVDV 864 (868)
T ss_pred ccccccccccccchhHHHHHHHHhheEEecCCeEEeCCCc-EEEEeccCCCcC-HHHhccCccccc
Confidence 9999997 9999999999999999999999999999995 999999999943 433344566653
No 6
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=6.3e-188 Score=1794.44 Aligned_cols=782 Identities=26% Similarity=0.413 Sum_probs=638.7
Q ss_pred CCCceeeeeEEEEcCChHHHHhccceEEecC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccceeecC
Q 000525 11 EVPSGILTGISLGISTDTEKEKLSVMEIGAV-----------SEVTNPRLGLPNPTNECSSCGAKDRKACEGHFGFIKFP 79 (1443)
Q Consensus 11 ~~~~~~I~~I~F~~~S~eEI~~~Sv~~I~~~-----------~Gl~D~rLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~ 79 (1443)
+.++++|.+|+||+||+|||+++||++|+++ |||+|||||++++...|+|||+ +..+||||||||||+
T Consensus 3 ~~~~~~I~~I~F~~~S~eEI~klSv~~It~~~~~d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~-~~~~CPGHFGhIeL~ 81 (882)
T PRK08566 3 MMIPKRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGG-RAGECPGHFGHIELA 81 (882)
T ss_pred CCCceeeeeEEEecCCHHHHHHhCeEEEecccccCCCCCcCCCCCCCcccCCCCCCCCCCCCCC-CCCcCCCcceEEecc
Confidence 3467899999999999999999999999863 7999999999999999999996 789999999999999
Q ss_pred ccccccccHHHHHHHHhccccccccccCcchh--------hh--------------ccccccccccccccccCCCCCCcc
Q 000525 80 FTILHPYFLSDIAKLLNSICPKCKTIRKERQK--------GA--------------GSSRKEQPRVCKYCVRNPAQWYPR 137 (1443)
Q Consensus 80 ~PVfHpgf~~~i~kIL~~iC~~C~rlll~~~~--------k~--------------l~~~~~~~~~C~~C~~~~~~~~p~ 137 (1443)
+|||||+||+.|++||+|+|++|+++++++.. +. +.+.++..++|++|++. .|.
T Consensus 82 ~PVfhpgf~~~v~~iL~~iC~~C~rll~~~~~~~~~~~~l~~~~~~~~~~~~l~k~i~k~~k~~~~C~~Cg~~----~~k 157 (882)
T PRK08566 82 RPVIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVCPHCGEK----QYK 157 (882)
T ss_pred ccccchhHHHHHHHHHHHhhhhhCceeccccchHHHHHHHhchhhhhhhHHHHHHHHHHHhcCCCCCCCcCCC----Cce
Confidence 99999999999999999999999999987421 00 01223445679999763 233
Q ss_pred cccccccccccCccceeehhhhhhhccCCCCccccccccCccccccccccCCCccccCHHHHHHHhccCChhhHhhc---
Q 000525 138 MRFKLSSKDLSGKTAIIVEIDEKLSKKNKKLPDDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPSIREEF--- 214 (1443)
Q Consensus 138 i~~~~~~~~~~~k~~ii~e~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LsP~eV~~iLkkI~~ed~~~~--- 214 (1443)
+++. +. ..+|... +..++.|+|++|+++|++|+++|+.++
T Consensus 158 i~~~--------~~------------------~~~~~~~-----------~~~~~~L~p~~V~~ilk~I~~eD~~lLg~~ 200 (882)
T PRK08566 158 IKFE--------KP------------------TTFYEER-----------KEGLVKLTPSDIRERLEKIPDEDLELLGIN 200 (882)
T ss_pred EEEe--------cc------------------eeEEEec-----------CCCceeCCHHHHHHHHHhCCHHHHHHhCCC
Confidence 3211 00 0011110 013578999999999999999999774
Q ss_pred --cCCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHH---------HHHHHHHHHHhh-
Q 000525 215 --ILSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIEL---------SHLVQDCLKISK- 282 (1443)
Q Consensus 215 --~~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~---------~~~~~~~~~~~~- 282 (1443)
..+||||||++|||||+++||++.+++ + ...|||||.+|.+|+..|....+. ....++.+|...
T Consensus 201 ~~~~~Pe~~il~~lPVpP~~iRPsv~~~~---g-~~~eDDLT~~L~~II~~N~~Lk~~~~~g~~~~~~~~~~~~LQ~~v~ 276 (882)
T PRK08566 201 PEVARPEWMVLTVLPVPPVTVRPSITLET---G-QRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVT 276 (882)
T ss_pred CCCCCcceeEEeeeecCCCCCcCcEEeCC---C-cccCchHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence 358999999999999999999987642 2 467899999999999876433221 112223333321
Q ss_pred hhcccccCCchhHhhhccCCccc----CcCCcc-hhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCcceee
Q 000525 283 LHLDKSSRKDSAEVRQKKNIDIS----NSSGLR-WIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERL 357 (1443)
Q Consensus 283 ~~~d~~~~~~~~~~~q~~~~~~~----~~~G~r-~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~pe~V 357 (1443)
.+.|+.....+. ..++.++..+ .+.|+. |||+|||||||||||||||||||+|++||||||..||++|||||+|
T Consensus 277 ~~~d~~~~~~~~-~~~~~~~~~~~i~~~l~gK~G~fR~nl~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v 355 (882)
T PRK08566 277 TYFDNEIPGIPP-ARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERV 355 (882)
T ss_pred HHhcCCccCCcc-cccCCCCCccchHHhcccCCCccccccccccccCcCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEE
Confidence 234444322110 0111112111 123332 8999999999999999999999999999999999999999999999
Q ss_pred chhhHHHhhhhhc-ccccccCcceEe-eCCeEEEecc------cccccCCCEEeceeccCceEEEeCCCCCCcccccccc
Q 000525 358 NSWNWERLSVCIS-FRLLEKGELYVC-RKGGLVRIRR------IDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALT 429 (1443)
Q Consensus 358 t~~Ni~~l~~~~~-~~~~~~g~~~i~-~~g~~~~~~~------~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~ 429 (1443)
|+||+++|++++. ....++||+++. ++|+.+.+.. +.+|++||+|||||+|||+|||||||||||||||||+
T Consensus 356 ~~~N~~~l~~~v~ng~~~~pga~~i~~~~g~~~~l~~~~~~~~~~~l~~g~~v~Rhl~dgd~vl~NRqPsLHr~si~a~~ 435 (882)
T PRK08566 356 TEWNIEELREYVLNGPEKHPGANYVIRPDGRRIKLTDKNKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHR 435 (882)
T ss_pred chhhHHHHHHHHHcCCCcCCCceEEEcCCCceeeehhhhHHHHHHhccccceehhhhhcCceeeecCCCcccccccceeE
Confidence 9999999999864 444677998864 6777666532 3579999999999999999999999999999999999
Q ss_pred EEEecCCceEEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHHhhccCc
Q 000525 430 VKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDS 509 (1443)
Q Consensus 430 v~v~p~~~t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~llt~~d 509 (1443)
|||+|+ +||||||++|+||||||||||||+|+|||++|||||++||++++|++||++|+|++|++||+|+|+|+||.+|
T Consensus 436 ~~v~~~-~t~r~n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~~d 514 (882)
T PRK08566 436 VRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKS 514 (882)
T ss_pred EEEecC-ceEeeccccCCCccCCccCcEEEEecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeehHHHHHHHHHHhcc
Confidence 999998 5999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCHHHHHHHHhhCCC---ccCCCceecccCCccchHHHHHhhcCCCCCccccC-----------------CCcEEEeC
Q 000525 510 VLLSHLQMQQLQMFCPH---RFLSPDIFKISKDSVWSGKQLFSMLLPPDFEYTFP-----------------SKDVYISG 569 (1443)
Q Consensus 510 ~fl~~~~~~~l~~~~~~---~l~~pai~Kp~~~~lwTGKql~s~~lp~~~~~~~~-----------------~~~v~i~~ 569 (1443)
+||+++|+++|+++... .+|+|||+|| +++||||||||++||+++++... ++.|+|+|
T Consensus 515 ~f~~~~~~~~l~~~~~~~~~~~~~pai~~p--~~lwTGKqi~s~~lp~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~i~~ 592 (882)
T PRK08566 515 TLFTKEEALDLLRAAGIDELPEPEPAIENG--KPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKEDCEHDAYVVIKN 592 (882)
T ss_pred ccCCHHHHHHHHHhCCccccccCCcccCCC--cccccHHHHHHHHcCCCCCceeeccccccccccccccCCCCceEEEec
Confidence 99999999999998653 5789999999 79999999999999998876421 35699999
Q ss_pred Ceeccc-cCcccccCCCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCccccccccchHHHHHHHHHhhH
Q 000525 570 GKLISA-EGSSWLRDYEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGL 647 (1443)
Q Consensus 570 gell~~-~~k~~lg~~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~~~~~~~~~~~~~~~~i~~~~ 647 (1443)
|||+++ ++|+++|++.++|+|.++++||++ |++||+++|+|+++||+.+|||||++|+.++++..++ +++.+
T Consensus 593 gell~g~ldK~~lg~~~~~li~~i~~~yG~~~a~~fl~~~~~l~~~~l~~~GfSigi~D~~~~~~~~~~------~~~~i 666 (882)
T PRK08566 593 GKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEE------IDEII 666 (882)
T ss_pred CEEEeccccHHHhhcccchHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCEEeehhhcccCHHHHHH------HHHHH
Confidence 999986 899999999999999999999996 8899999999999999999999999999998765432 22224
Q ss_pred HHHHhhhhhhhhHHHhHHhhhhccCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCcceee
Q 000525 648 REAQDTCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKYGSKDNSLLAM 727 (1443)
Q Consensus 648 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M 727 (1443)
++|++.+. + ....|..+.++..++.. ...++|.+++. .|.++++++++++.++++++|++++|
T Consensus 667 ~~~~~~~~--~----~~~~~~~g~l~~~~~~~---~~~~~e~~i~~--------~l~~~r~~~~~~~~~~l~~~N~~~~M 729 (882)
T PRK08566 667 EEAEKRVE--E----LIEAYENGELEPLPGRT---LEETLEMKIMQ--------VLGKARDEAGEIAEKYLGLDNPAVIM 729 (882)
T ss_pred HHHHHHHH--H----HHHHHHcCCCccccCCC---HHHHHHHHHHH--------HHHHHHHHHHHHHHHhcCCCCcceee
Confidence 44444321 1 12233444443322221 11234444443 34456678899999999999999999
Q ss_pred eccCCccchhhHhHhhhcccccccCCCCccccCccccccccccCCCCCCccccCCccccccccccccCCCChhhHHHhcc
Q 000525 728 FKAGSKGNLLKLVQHSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSV 807 (1443)
Q Consensus 728 ~~sGSKGS~~Nl~Qi~~~lGqQ~~~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m 807 (1443)
+.||||||++|++||+||||||+++|+ |+|.++++|+||+|++++..+++ +|||.|||++||+|+|||||||
T Consensus 730 ~~SGsKGS~~N~~Qi~~~lGqQ~~~g~---ri~~~~~~rtLP~f~~~d~~~~~-----~GfV~~sF~~GL~p~EfffH~m 801 (882)
T PRK08566 730 ARTGARGSMLNLTQMAACVGQQSVRGE---RIRRGYRDRTLPHFKPGDLGAEA-----RGFVRSSYKSGLTPTEFFFHAM 801 (882)
T ss_pred eccccccCHHHHHHHHhccCceecCCC---cCccCccCccCCCCCCCCCCccc-----CceeeccccCCCCHHHHHHHHh
Confidence 999999999999999999999999996 99999999999999998876665 5999999999999999999999
Q ss_pred cCCCccccccc--CCCCcchHHHHHHHhheEeeecceEEccCCceEEEEEeccCCCCCCCcccCCceecc
Q 000525 808 TSRDSSFSDNA--DLPGTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGTSTPTGEIGDQPVGS 875 (1443)
Q Consensus 808 ~gReGliDtav--a~sGYLqRrLvk~lEdl~v~YD~tVR~s~G~~iiq~~yg~~g~~~~~~~~~ge~VG~ 875 (1443)
||||||||||+ |+||||||||||+||||+|+||+||||++|+ ||||.||+||.+ |....-+.||.+
T Consensus 802 ~GReGliDTAvkTa~sGYlqRrLvk~ledl~v~yD~tVR~s~g~-iiQf~YG~dg~d-~~~~~~~~~~~~ 869 (882)
T PRK08566 802 GGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGN-IVQFKYGEDGVD-PMKSDHGKPVDV 869 (882)
T ss_pred hhcccccccceeeccCccchHHHHHHHhheEEeeCCceEcCCCc-EEEEeccCCCcC-HHHhcCCCcccH
Confidence 99999999998 9999999999999999999999999999995 999999999943 322333456553
No 7
>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=3.1e-156 Score=1482.45 Aligned_cols=939 Identities=18% Similarity=0.225 Sum_probs=660.0
Q ss_pred eEEEEcCChHHHHhccceEEecC------------CCCCCCCC-CCC--------------CCCCCCCCCCCCCCCCCC-
Q 000525 19 GISLGISTDTEKEKLSVMEIGAV------------SEVTNPRL-GLP--------------NPTNECSSCGAKDRKACE- 70 (1443)
Q Consensus 19 ~I~F~~~S~eEI~~~Sv~~I~~~------------~Gl~D~rL-G~~--------------~~~~~C~TCg~~~~~~Cp- 70 (1443)
+|++++.|||+|+++|+-||+.| +||.|+|+ ||+ .++..|.+||- ...+|+
T Consensus 1 ~i~i~laSPe~I~~ws~geV~~petiny~t~kPe~~GLfcerIFGp~k~~ec~Cgkyk~~~~~~~~C~~Cgv-e~t~~~v 79 (1140)
T TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGV-EVTESKV 79 (1140)
T ss_pred CeEEEecCHHHHHhhhceEEeccceecCCCCccCCCCcccchhcCCccCceeccccccccCcCCcCCCCCCC-Ccccchh
Confidence 48999999999999999999875 79999999 987 35567999995 789999
Q ss_pred --CccceeecCccccccccHHH-----------HHHHHhccccccccccCcchhhhccccc----ccc-cccc-cccc-C
Q 000525 71 --GHFGFIKFPFTILHPYFLSD-----------IAKLLNSICPKCKTIRKERQKGAGSSRK----EQP-RVCK-YCVR-N 130 (1443)
Q Consensus 71 --GHFGhIeL~~PVfHpgf~~~-----------i~kIL~~iC~~C~rlll~~~~k~l~~~~----~~~-~~C~-~C~~-~ 130 (1443)
+|||||||+.||+|++|++. ..+.|+++|.+|+.+..+.....+.+.. ..+ .... +-.. .
T Consensus 80 rr~rmGhI~La~Pv~Hiwy~k~~ps~~~~ll~~~~k~le~v~y~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (1140)
T TIGR02386 80 RRERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFR 159 (1140)
T ss_pred hhhcccceeecCCceeehhcCCCchHHHHHhCCCHHHhhheeeccceEEeCCCCCchhhhhhhchhHHHHHHHHhccCcc
Confidence 99999999999999999998 5899999999999886653211111000 000 0000 0000 0
Q ss_pred CCCCCcccccccccccccCccceeehhhhhhhccCCCCccccccccCccccccccccCCCccccCHHHHHHHhccCChhh
Q 000525 131 PAQWYPRMRFKLSSKDLSGKTAIIVEIDEKLSKKNKKLPDDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPSI 210 (1443)
Q Consensus 131 ~~~~~p~i~~~~~~~~~~~k~~ii~e~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LsP~eV~~iLkkI~~ed 210 (1443)
...+...++... ....+..+.. .+. +.|. . .......++.+...++.+.|.+-
T Consensus 160 ~~~G~~ai~~~l------~~~dl~~~~~--------~~~-~~~~---~-----~~~~~~~~~~~krl~~~~~f~~s---- 212 (1140)
T TIGR02386 160 AGMGAEAIKELL------EKIDLDKEIE--------ELK-IQLR---E-----SKSDQKRKKLLKRLEIVEAFKDS---- 212 (1140)
T ss_pred cccchHHHHHHH------hcCCHHHHHH--------HHH-HHHH---h-----ccchhhHHhhhhHHHHHHHHHhc----
Confidence 000000000000 0000000000 000 0000 0 00001113456666666666552
Q ss_pred HhhccCCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHHH---------HHHHHHHHHh
Q 000525 211 REEFILSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIELS---------HLVQDCLKIS 281 (1443)
Q Consensus 211 ~~~~~~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~~---------~~~~~~~~~~ 281 (1443)
..+||||||++||||||++||++.++ |+++++||||.+|++|+..|...+.+. ......+|..
T Consensus 213 ----~~~Pewmil~~lPV~Pp~lRP~v~l~----gg~~~~sDLn~lyr~II~~Nn~Lk~~~~~~ap~~ii~~~~~~LQ~a 284 (1140)
T TIGR02386 213 ----GNRPEWMVLDVIPVIPPELRPMVQLD----GGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEA 284 (1140)
T ss_pred ----CCChHHhhhhcccCCCCccCCcEEeC----CCccccCchHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence 46899999999999999999999875 346789999999999998875443321 1222333332
Q ss_pred h-hhcccccCCchhHhhhccCCcccC----cCCcc-hhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCcce
Q 000525 282 K-LHLDKSSRKDSAEVRQKKNIDISN----SSGLR-WIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISE 355 (1443)
Q Consensus 282 ~-~~~d~~~~~~~~~~~q~~~~~~~~----~~G~r-~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~pe 355 (1443)
. ...||.....+. .+..+++.++ ++|++ |||+|||||||||||||||+|||+|+++|||||..||++||+|
T Consensus 285 V~~liDn~~~g~~~--~~~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GlP~~mA~~L~~P- 361 (1140)
T TIGR02386 285 VDALFDNGRRGKPV--VGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKP- 361 (1140)
T ss_pred HHHHhcccccCCCc--cCcCCCchhhHHHhhcCCCCcccccccccccCCCCCCeEcCCCCcccccccChHHHHHHcCch-
Confidence 1 345554333221 1112222221 23442 8999999999999999999999999999999999999999987
Q ss_pred eechhhHHHhhhhhcccccccC-cceEeeCCeEEEecccccccCCCEEeceeccCceEEEeCCCCCCccccccccEEEec
Q 000525 356 RLNSWNWERLSVCISFRLLEKG-ELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLP 434 (1443)
Q Consensus 356 ~Vt~~Ni~~l~~~~~~~~~~~g-~~~i~~~g~~~~~~~~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v~p 434 (1443)
||+.+|++. | +..++...+++ ....+.+|+++ ||+.+||+|||||||||||||||||+|++++
T Consensus 362 ----f~i~~L~~~--------~~~~~i~~ak~~i---~~~~~~v~~vl-~~vi~~d~VLlNRqPTLHRlsIqAf~~~l~~ 425 (1140)
T TIGR02386 362 ----FIIKRLIDR--------ELAANIKSAKKMI---EQEDPEVWDVL-EDVIKEHPVLLNRAPTLHRLGIQAFEPVLVE 425 (1140)
T ss_pred ----HHHHHHHHc--------CcccchHHHHHHH---HhcCCccceEE-EEccCCcEEEecCCCcccccccceeEEEEec
Confidence 677777751 1 11111111100 11234555555 7888999999999999999999999999998
Q ss_pred CCceEEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHHhhccCc-----
Q 000525 435 ISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDS----- 509 (1443)
Q Consensus 435 ~~~t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~llt~~d----- 509 (1443)
+ +||||||+||+||||||||||||+|||||++|||||++||.+++|++||++|+|+++++||+++|+|+||.++
T Consensus 426 g-ktirlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~ 504 (1140)
T TIGR02386 426 G-KAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKPGAKG 504 (1140)
T ss_pred C-ceEEEcccccCcccCCCCcceeEeecCCCHHHHHHHHHHhCCcccEecCCCCCceEEeechhhheeeEeeeccccccC
Confidence 6 5999999999999999999999999999999999999999999999999999999999999999999999885
Q ss_pred ---cccCHHHHHHHHhhCCCccCCCceecc--cCCccc--hHHHHHhhcCCCCCccccCCCcEEEeCCeeccccCccccc
Q 000525 510 ---VLLSHLQMQQLQMFCPHRFLSPDIFKI--SKDSVW--SGKQLFSMLLPPDFEYTFPSKDVYISGGKLISAEGSSWLR 582 (1443)
Q Consensus 510 ---~fl~~~~~~~l~~~~~~~l~~pai~Kp--~~~~lw--TGKql~s~~lp~~~~~~~~~~~v~i~~gell~~~~k~~lg 582 (1443)
+|++++++..... ...++.|+++++ .++++| |||||||.+||.+++|....+ .++|+.+|
T Consensus 505 ~~~~F~~~~e~~~~~~--~~~i~l~~~i~~~~~g~~~~tt~Gr~if~~ilP~~~~~~n~~~-----------~l~Kk~lg 571 (1140)
T TIGR02386 505 EGKIFSNVDEAIRAYD--NGKVHLHALIGVRTSGEILETTVGRVIFNEILPEGFPYINDNE-----------PLSKKEIS 571 (1140)
T ss_pred cCceeCCHHHHHHHHH--cCCccCCCceEEeccccEEEccchHHHHHHHcCCccccccccc-----------ccchHHHH
Confidence 7999999987542 334566666664 235677 699999999999887763211 24676664
Q ss_pred CCCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCccccccccchHHHHHHHHHhhHHHHHhhhhhhhhHH
Q 000525 583 DYEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTCNFQQLMV 661 (1443)
Q Consensus 583 ~~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~ 661 (1443)
+|+|.++++||.+ |++|||.+++|+++|++.+|||||++|+.++++ +++++++.++.+.+.
T Consensus 572 ----~LI~~i~~~~G~~~t~~~LD~lk~Lgf~~at~~GfSigi~Dl~ip~~---K~~ii~~a~~~v~~i----------- 633 (1140)
T TIGR02386 572 ----SLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDE---KYEILKEADKEVAKI----------- 633 (1140)
T ss_pred ----HHHHHHHHHhChHHHHHHHHHHHHHHHHHHHhcCeeeeeccCCCCHH---HHHHHHHHHHHHHHH-----------
Confidence 7999999999996 889999999999999999999999999998864 344554333222221
Q ss_pred HhHHhhhhccCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC----CCcceeeeccCCccchh
Q 000525 662 DSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKYGSK----DNSLLAMFKAGSKGNLL 737 (1443)
Q Consensus 662 ~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~----~N~~~~M~~sGSKGS~~ 737 (1443)
...|..+.+.. ..++. ..++.|.++.+++++.+.+.+.+ .|++++|+.||||||++
T Consensus 634 --~~~y~~G~lt~----------~er~~--------kvi~iw~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS~~ 693 (1140)
T TIGR02386 634 --QKFYNKGLITD----------EERYR--------KVVSIWSETKDKVTDAMMKLLKKDTYKFNPIFMMADSGARGNIS 693 (1140)
T ss_pred --HHHHHcCCCCh----------HHHHH--------HHHHHHHHHHHHHHHHHHHhcccccCCCCcHhhhhhcccccCHH
Confidence 11233332211 11222 23456777788888888888875 49999999999999999
Q ss_pred hHhHhhhcccccccCCCCccccCccccccccccCCCCCCccccCCccccccccccccCCCChhhHHHhcccCCCcccccc
Q 000525 738 KLVQHSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDN 817 (1443)
Q Consensus 738 Nl~Qi~~~lGqQ~~~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m~gReGliDta 817 (1443)
|++||+||+|||+... |+++| -||.|||++||+|+|||||||||||||+|||
T Consensus 694 ni~QL~GmrGlma~p~-----------Grii~-----------------~PI~ssF~eGLtp~EyF~st~GaRkGLiDTA 745 (1140)
T TIGR02386 694 QFRQLAGMRGLMAKPS-----------GDIIE-----------------LPIKSSFREGLTVLEYFISTHGARKGLADTA 745 (1140)
T ss_pred HHHHHHhCCCcccCCC-----------CCccc-----------------cchhhccccCCCHHHHhhhccchhccccchh
Confidence 9999999999997421 12222 3689999999999999999999999999999
Q ss_pred c--CCCCcchHHHHHHHhheEeeecc--e-----EE---ccCCc------------------------------------
Q 000525 818 A--DLPGTLTRRLMFFMRDLCTAYDG--T-----VR---NAYGN------------------------------------ 849 (1443)
Q Consensus 818 v--a~sGYLqRrLvk~lEdl~v~YD~--t-----VR---~s~G~------------------------------------ 849 (1443)
+ |+|||||||||+++||++|.||. | |. +..+.
T Consensus 746 lKTAdSGYLtRRLVdv~qDviV~~dDCgT~~gi~v~~~~~~~~~~i~~l~~ri~GR~~~~di~~~~~~~~i~~~~~~i~~ 825 (1140)
T TIGR02386 746 LKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEVEAIVEGKDEIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITE 825 (1140)
T ss_pred eeecccceeeeehhhhhcceEEEeCCCCCCCCEEEEEeecCCceEEeehhheeEEEEEhhheEeCCCCcEEEeCCCCcCH
Confidence 8 99999999999999999999982 2 11 11111
Q ss_pred --------------------------eEEEEEeccCCCCCCCcccCCceeccccccchhHHHHhcc---cccccc-----
Q 000525 850 --------------------------QIVQFSYNIEGTSTPTGEIGDQPVGSLSACAISEAAYSAL---DQPISL----- 895 (1443)
Q Consensus 850 --------------------------~iiq~~yg~~g~~~~~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~~----- 895 (1443)
.|+|.+||.|- .....+..||+||++||||||||+||+| +|..++
T Consensus 826 ~~~~~i~~~~i~~v~iRS~ltC~s~~gvC~~CYG~~L-a~~~~V~~GeaVGiiAAQSIGEPGTQLTmRTFHtGGv~~~~~ 904 (1140)
T TIGR02386 826 EIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDL-ATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASG 904 (1140)
T ss_pred HHHHHHHHcCCCEEEecCCeeeCCCCCCccccCCCcc-cCCcEecccccceeEeeeecCCCcchhehhheeecccccccc
Confidence 13333333331 0123467899999999999999999985 776554
Q ss_pred ccccccccchhhhccCCCCCCCccEeeeehhhhccccccCchhhHHHHHhhhcccchhhhhceEEEEEcCCCCcccccCc
Q 000525 896 LETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSP 975 (1443)
Q Consensus 896 l~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e~~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp 975 (1443)
..|.|+||+.|+.+|++-. .+.+. ++ +.-.+
T Consensus 905 DIT~GlpRv~elfear~p~---~~a~i---ae---------------------------~~G~v---------------- 935 (1140)
T TIGR02386 905 DITQGLPRVKELFEARTPK---DKAVI---AE---------------------------VDGTV---------------- 935 (1140)
T ss_pred ccccCchhhhhhhhcccCC---CceEE---Ee---------------------------cCCEE----------------
Confidence 3358999999999996521 11111 00 00011
Q ss_pred eEEEEEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCCceeeecCccccccccccCCCceEEEEEeecccccchhh
Q 000525 976 WICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSID 1055 (1443)
Q Consensus 976 ~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~~~~~~ 1055 (1443)
+| +..+. ++ . ..+.|.+. + ...
T Consensus 936 ---~~-~~~~~---~~------------~------------~~i~i~~~----------------------~---~~~-- 957 (1140)
T TIGR02386 936 ---EI-IEDIV---KN------------K------------RVVVIKDE----------------------N---DEE-- 957 (1140)
T ss_pred ---EE-eeccc---CC------------c------------EEEEEECC----------------------C---Cce--
Confidence 11 00000 00 0 00111110 0 000
Q ss_pred HHHHHHHhccccccceeeccccceEEEEeecccccccCCCCCCCceEEEEEeeccccccchhHHHHhhhhcccccccccc
Q 000525 1056 LETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWT 1135 (1443)
Q Consensus 1056 l~~l~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~ 1135 (1443)
.+..+ |.=+++.+.. |+.+-.. . . | ++
T Consensus 958 ----~~y~i-----------p~~~~l~v~~--------------gd~V~~G---------~---~-l------~~----- 984 (1140)
T TIGR02386 958 ----KKYTI-----------PFGAQLRVKD--------------GDSVSAG---------D---K-L------TE----- 984 (1140)
T ss_pred ----eEEec-----------cCCceEEecC--------------CCEEccC---------C---c-c------cC-----
Confidence 00011 1112222221 1121110 0 0 0 11
Q ss_pred ccCCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHHHHHHHhhccceeeEe-----------ecchhhhh----
Q 000525 1136 RSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFV-----------GLNAKGLA---- 1200 (1443)
Q Consensus 1136 rt~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rHl~LlAd~MT~~G~~~-----------gi~r~G~~---- 1200 (1443)
-+-|++||++++||||++++|++||++|+..||++||.+|+++|++.||.++++. -+.++++.
T Consensus 985 --g~~~~~~il~v~G~~a~~~~lv~evq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~l~g~~v~~~~~~~~n~ 1062 (1140)
T TIGR02386 985 --GSIDPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENR 1062 (1140)
T ss_pred --CCCCHHHHHHhcCHHHHHHHHHHHHHHHHHhCCccccchhHhHHHHHHhCcEEEEeCCCcCCCCCCeeeHHHHHHHHH
Confidence 2347899999999999999999999999999999999999999999999998775 34444433
Q ss_pred ------------------hhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccc
Q 000525 1201 ------------------LQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGH 1256 (1443)
Q Consensus 1201 ------------------~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~ 1256 (1443)
..|.||.+.|+|+.||||+|+++|.+||.+|+.|+|.|++||||+|+.+|+|| |.
T Consensus 1063 ~~~~~g~~~~~~~~~llGitkasl~t~SflsaASFqeTtkvLt~Aai~gk~D~L~GlkENVIiG~liPaGT-G~ 1135 (1140)
T TIGR02386 1063 KLLEQGKKPASAIPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGT-GL 1135 (1140)
T ss_pred HHHhCCCCCccceeeeeeeeehhccCCCcccccchhhHHHHHHHHHhcCCCCCCCCcccceEecCcccCCC-Cc
Confidence 23568888999999999999999999999999999999999999999999999 64
No 8
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=4.4e-154 Score=1464.15 Aligned_cols=938 Identities=19% Similarity=0.255 Sum_probs=655.0
Q ss_pred eeeeEEEEcCChHHHHhccceEEecC------------CCCCCCCCCCCCCCCCCCCCCCCCC------CCCC-------
Q 000525 16 ILTGISLGISTDTEKEKLSVMEIGAV------------SEVTNPRLGLPNPTNECSSCGAKDR------KACE------- 70 (1443)
Q Consensus 16 ~I~~I~F~~~S~eEI~~~Sv~~I~~~------------~Gl~D~rLG~~~~~~~C~TCg~~~~------~~Cp------- 70 (1443)
.+..|++++.|||+|+++|+-||+.| +||.+.|...+.++..| .||. +. ..|+
T Consensus 6 ~~~~i~i~laspe~I~~ws~GeV~~petinyrt~kPe~~GLfcerIFgp~kd~eC-~Cgk-yk~~~~~~~~C~~cgve~~ 83 (1156)
T PRK00566 6 DFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYEC-LCGK-YKRVRYKGIICERCGVEVT 83 (1156)
T ss_pred CcceEEEEccCHHHHHHhhcceEccccccccCCCccCCCCcccchhcCcccCcEE-eCcc-ccccCcCCcCCCCCCceee
Confidence 67899999999999999999999875 79999999667888999 9993 32 4799
Q ss_pred ------CccceeecCccccccccHHHH-----------HHHHhccccccccccCcchhhhcccccc----ccc-cccccc
Q 000525 71 ------GHFGFIKFPFTILHPYFLSDI-----------AKLLNSICPKCKTIRKERQKGAGSSRKE----QPR-VCKYCV 128 (1443)
Q Consensus 71 ------GHFGhIeL~~PVfHpgf~~~i-----------~kIL~~iC~~C~rlll~~~~k~l~~~~~----~~~-~C~~C~ 128 (1443)
+|||||+|+.||.|+.|++.+ .+.|+++|.+|+.+..+.....+.+... .+. ....-+
T Consensus 84 ~~~vrr~rmGhI~La~Pv~Hiwy~k~~ps~i~~ll~~~~k~le~v~y~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (1156)
T PRK00566 84 RSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYG 163 (1156)
T ss_pred echhhhhhcceeeecCceeeeeecCCCchHHHHHhCCCHHHhhheeecceEEEeCCCCCchhhhcccCHHHHHHHHHHhc
Confidence 999999999999999999944 8999999999988765432111110000 000 000000
Q ss_pred cCCCCCCcccccccccccccCccceeehhhhhhhccCCCCccccccccCccccccccccCCCccccCHHHHHHHhccCCh
Q 000525 129 RNPAQWYPRMRFKLSSKDLSGKTAIIVEIDEKLSKKNKKLPDDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDP 208 (1443)
Q Consensus 129 ~~~~~~~p~i~~~~~~~~~~~k~~ii~e~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LsP~eV~~iLkkI~~ 208 (1443)
. .|... +. ...+.+. . .. -.+...... . +..-.........++.+...++.+.|.+.
T Consensus 164 ~---------~~~~~----~G-a~ai~~l---l-~~-~dl~~~~~~-l-~~~~~~~~~~~~~~~~~krl~~~~~f~~s-- 220 (1156)
T PRK00566 164 D---------EFVAK----MG-AEAIKEL---L-KN-IDLEAEAEE-L-REELKETGSEQKRKKALKRLKVVEAFRKS-- 220 (1156)
T ss_pred c---------ccccc----cc-HHHHHHH---H-Hh-CCHHHHHHH-H-HHHHHhcccchhHHHHHHHHHHHHHHHcC--
Confidence 0 00000 00 0000000 0 00 000000000 0 00000000000112334444555554443
Q ss_pred hhHhhccCCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHH---------HHHHHHHHH
Q 000525 209 SIREEFILSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIEL---------SHLVQDCLK 279 (1443)
Q Consensus 209 ed~~~~~~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~---------~~~~~~~~~ 279 (1443)
..+||||||++||||||++||++.++ |+++++||||.+|++|+..|...+.+ .......+|
T Consensus 221 ------~~~Pewmil~~lPV~Pp~lRP~v~l~----~g~~~~sDLn~lyr~II~rNnrLk~~~~~~ap~~ii~~~~~~LQ 290 (1156)
T PRK00566 221 ------GNKPEWMILDVLPVIPPDLRPLVQLD----GGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQ 290 (1156)
T ss_pred ------CCCccEeeEeecccCCCcccCceEeC----CCcccCCchHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence 46899999999999999999999875 34778899999999999876543332 112223333
Q ss_pred Hh-hhhcccccCCchhHhhhccCCccc----CcCCcc-hhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCc
Q 000525 280 IS-KLHLDKSSRKDSAEVRQKKNIDIS----NSSGLR-WIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQI 353 (1443)
Q Consensus 280 ~~-~~~~d~~~~~~~~~~~q~~~~~~~----~~~G~r-~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~ 353 (1443)
.. ..+.||...+.+.+. ..+++.+ .+.|++ |||+|||||||||||||||+|||+|+++|||||..||++||+
T Consensus 291 ~aV~~lidn~~~g~~~~~--~~~rplksls~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~ 368 (1156)
T PRK00566 291 EAVDALFDNGRRGRPVTG--PNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFK 368 (1156)
T ss_pred HHHHHHhccCccCCCccc--ccCCchhHHHHhhcCCCccccccccccccCCCCCceEeCCCCcccccccChHHHHHHhCc
Confidence 32 134555533222110 1112211 123443 899999999999999999999999999999999999999998
Q ss_pred ceeechhhHHHhhhhhcccccccCc-ceEeeCCeEEEecccccccCCCEEeceeccCceEEEeCCCCCCccccccccEEE
Q 000525 354 SERLNSWNWERLSVCISFRLLEKGE-LYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKV 432 (1443)
Q Consensus 354 pe~Vt~~Ni~~l~~~~~~~~~~~g~-~~i~~~g~~~~~~~~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v 432 (1443)
| ||+.+|.. +|. ..++...+++ ......+|+++ ||+.+||+|||||||||||||||||++++
T Consensus 369 P-----f~i~~L~~--------~g~~~~ik~ak~~~---~~~~~~v~~vl-e~vi~gd~VLlNRqPTLHR~sIqAf~~~l 431 (1156)
T PRK00566 369 P-----FIMKKLVE--------RGLATTIKSAKKMV---EREDPEVWDVL-EEVIKEHPVLLNRAPTLHRLGIQAFEPVL 431 (1156)
T ss_pred H-----HHHHHHHH--------cCCccchHhhhhhh---hhhcCcceEEE-EEecCCCEEEecCCCcccccccceeEEEE
Confidence 8 67877764 121 1111111111 11234566666 66779999999999999999999999999
Q ss_pred ecCCceEEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHHhhccCc---
Q 000525 433 LPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDS--- 509 (1443)
Q Consensus 433 ~p~~~t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~llt~~d--- 509 (1443)
+++ +||||||+||+||||||||||||+|||||++|||||++||.+.+|++||++|+|+++++||+++|+|+||.++
T Consensus 432 ~~g-ktirLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~ 510 (1156)
T PRK00566 432 IEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTREREGA 510 (1156)
T ss_pred ecC-ceEEECccccCccccccccceeEEecCCCHHHHHHHHHHhCCcccEEecCCCCeeEEeehhhhhhhheeecccccc
Confidence 986 5999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred -----cccCHHHHHHHHhhCCCccCCCceecccC---CccchHHHHHhhcCCCCCccccCCCcEEEeCCeeccccCcccc
Q 000525 510 -----VLLSHLQMQQLQMFCPHRFLSPDIFKISK---DSVWSGKQLFSMLLPPDFEYTFPSKDVYISGGKLISAEGSSWL 581 (1443)
Q Consensus 510 -----~fl~~~~~~~l~~~~~~~l~~pai~Kp~~---~~lwTGKql~s~~lp~~~~~~~~~~~v~i~~gell~~~~k~~l 581 (1443)
+|++++|+.+++......++.|..+++.. ...|||||||+.+||++++|... +|. ++|+++
T Consensus 511 ~~~~~~F~~~~e~~~~~~~~~i~l~~~i~~~~~~~~~i~tt~Gk~if~~ilP~~~~~~n~-------~g~----ldKk~L 579 (1156)
T PRK00566 511 KGEGMVFSSPEEALRAYENGEVDLHARIKVRITSKKLVETTVGRVIFNEILPEGLPFINV-------NKP----LKKKEI 579 (1156)
T ss_pred cCCCceeCCHHHHHHHHHcCCCCCCCeEEecCCCCceEEcCcHHHHHHhhccccceeecc-------cce----ecHHHH
Confidence 89999999998765433444444444311 23699999999999998766531 222 578888
Q ss_pred cCCCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCccccccccchHHHHHHHHHhhHHHHHhhhhhhhhH
Q 000525 582 RDYEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTCNFQQLM 660 (1443)
Q Consensus 582 g~~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~ 660 (1443)
| +|+|.++++||.+ |++|||.+++|+++|++.+|||||++|+.++++ +++++++.++.+.+.
T Consensus 580 g----~LI~~i~~~yG~~~t~~~LD~ik~Lgf~yat~~GfSigi~Dl~ip~~---K~~ii~~a~~~v~~i---------- 642 (1156)
T PRK00566 580 S----KIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPE---KKEIIEEAEKEVAEI---------- 642 (1156)
T ss_pred H----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEeehhhcCcChH---HHHHHHHHHHHHHHH----------
Confidence 6 5999999999996 899999999999999999999999999999864 345554433222221
Q ss_pred HHhHHhhhhccCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC----CCcceeeeccCCccch
Q 000525 661 VDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKYGSK----DNSLLAMFKAGSKGNL 736 (1443)
Q Consensus 661 ~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~----~N~~~~M~~sGSKGS~ 736 (1443)
...|..+.+.. ...+ +..++.|.++.+++++.+.+++.+ .|++++|+.||||||+
T Consensus 643 ---~~~y~~G~lt~----------~er~--------~kvi~~w~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS~ 701 (1156)
T PRK00566 643 ---EKQYRRGLITD----------GERY--------NKVIDIWSKATDEVAKAMMKNLSKDQESFNPIYMMADSGARGSA 701 (1156)
T ss_pred ---HHHHHcCCCCc----------hHHH--------HHHHHHHHHHHHHHHHHHHHhCccccCCCCChheeeeccCCcCH
Confidence 11233343321 0111 223456777888888888887765 8999999999999999
Q ss_pred hhHhHhhhccccccc-CCCCccccCccccccccccCCCCCCccccCCccccccccccccCCCChhhHHHhcccCCCcccc
Q 000525 737 LKLVQHSLCLGLQHS-LAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFS 815 (1443)
Q Consensus 737 ~Nl~Qi~~~lGqQ~~-~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m~gReGliD 815 (1443)
+|++||+||+|||.. .|+ . ++ .||.|||++||+|+|||||||||||||+|
T Consensus 702 ~ni~QL~GmrGlma~p~G~------------i----------------ie-~pI~ssFreGLt~~EyFfst~GaRkGLiD 752 (1156)
T PRK00566 702 SQIRQLAGMRGLMAKPSGE------------I----------------IE-TPIKSNFREGLTVLEYFISTHGARKGLAD 752 (1156)
T ss_pred HHHHHHHhhcCccccCCCC------------E----------------ee-hhhhhhhhcCCCHHHHhhcCcchhhcccc
Confidence 999999999999863 221 1 11 47999999999999999999999999999
Q ss_pred ccc--CCCCcchHHHHHHHhheEeeec--ce-----EEcc-CCceEE---------------------------------
Q 000525 816 DNA--DLPGTLTRRLMFFMRDLCTAYD--GT-----VRNA-YGNQIV--------------------------------- 852 (1443)
Q Consensus 816 tav--a~sGYLqRrLvk~lEdl~v~YD--~t-----VR~s-~G~~ii--------------------------------- 852 (1443)
||+ |+|||||||||+++||++|.|| || |+.. +|..++
T Consensus 753 TALKTAdSGYLtRRLVdvaqDviV~~~DCgT~~gi~~~~~~~~~~~i~~l~~~~~GR~~~~di~~~~t~~~i~~~~~~i~ 832 (1156)
T PRK00566 753 TALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLID 832 (1156)
T ss_pred hheeeccceeeehhHHHhhCceEEEECCCCCcCCEEEEEeccCCEEEeEhhheeEeEEEhhheecCCCCcEEEcCCCccC
Confidence 998 9999999999999999999997 23 2211 111233
Q ss_pred ------------------------------EEEeccCCCCCCCcccCCceeccccccchhHHHHhcc---cccccccccc
Q 000525 853 ------------------------------QFSYNIEGTSTPTGEIGDQPVGSLSACAISEAAYSAL---DQPISLLETS 899 (1443)
Q Consensus 853 ------------------------------q~~yg~~g~~~~~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~~l~t~ 899 (1443)
|.+||.|- .....+.-||+||++||||||||+||+| +|..++.-|.
T Consensus 833 ~~~~~~i~~~~i~~v~iRS~ltC~s~~gvC~~CYG~~L-a~~~~v~iGeaVGiIAAQSIGEPGTQLTmRTFHtGGvdIT~ 911 (1156)
T PRK00566 833 EEIADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDL-ATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVDITG 911 (1156)
T ss_pred HHHHHHHHHcCCCEEEEcCCeeecCCCcccHhhhCccc-cCCCCcccCcceeEEeeeecCCCccceeeeeeeecceeccC
Confidence 22333321 0112467899999999999999999985 7777776789
Q ss_pred ccccchhhhccCCCCCCCccEeeeehhhhccccccCchhhHHHHHhhhcccchhhhhceEEEEEcCCCCcccccCceEEE
Q 000525 900 PLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICH 979 (1443)
Q Consensus 900 gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e~~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp~v~~ 979 (1443)
|+||+.|+.+|++-. .+.+ + ++ +.-.+.+.-
T Consensus 912 Glprv~elfear~pk---~~a~-i--se---------------------------~~G~v~~~~---------------- 942 (1156)
T PRK00566 912 GLPRVAELFEARKPK---GPAI-I--AE---------------------------IDGTVSFGK---------------- 942 (1156)
T ss_pred CccchhhheeeccCC---CceE-E--Ee---------------------------cCCEEEecc----------------
Confidence 999999999996421 1111 0 00 001111100
Q ss_pred EEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCCceeeecCccccccccccCCCceEEEEEeecccccchhhHHHH
Q 000525 980 FHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSIDLETI 1059 (1443)
Q Consensus 980 ~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~~~~~~l~~l 1059 (1443)
+. ++ ...+.|.+.+ ++. ..
T Consensus 943 -----~~---~~------------------------~~~i~i~~~~----------~~~------------~~------- 961 (1156)
T PRK00566 943 -----ET---KG------------------------KRRIVITPDD----------GEE------------RE------- 961 (1156)
T ss_pred -----cc---CC------------------------ceEEEEeCCC----------Cce------------EE-------
Confidence 00 00 0001111000 000 00
Q ss_pred HHHhccccccceeeccccceEEEEeecccccccCCCCCCCceEEEEEeeccccccchhHHHHhhhhccccccccccccCC
Q 000525 1060 QMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHP 1139 (1443)
Q Consensus 1060 ~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt~s 1139 (1443)
-. +|.-+++.+.. ++.+-..+. | ++ -+
T Consensus 962 --y~-----------vp~~~~~~v~~--------------gd~v~~G~~-------------l------~~-------g~ 988 (1156)
T PRK00566 962 --YL-----------IPKGKHLLVQE--------------GDHVEAGDK-------------L------TD-------GS 988 (1156)
T ss_pred --EE-----------ccCCCeeeecC--------------CCEEccCCc-------------c------cC-------CC
Confidence 01 12112222221 112111000 0 11 12
Q ss_pred CcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHHHHHHHhhccceeeE----------------------------
Q 000525 1140 DNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEF---------------------------- 1191 (1443)
Q Consensus 1140 n~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rHl~LlAd~MT~~G~~---------------------------- 1191 (1443)
-|++||++++||||++++|++||++|+..||++|+.+|+++|++.||.++++
T Consensus 989 ~~~~~il~v~G~~~~~~~lv~eiq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~~~g~~v~~~~~~~~n~~~~~ 1068 (1156)
T PRK00566 989 IDPHDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIA 1068 (1156)
T ss_pred CCHHHHHHhcCHHHHHHHHHHHHHHHHHhCCcccccceeehHHHHHhCCeEEecCCCcCCCCCceeeHHHHHHHHHHHHH
Confidence 3689999999999999999999999999999999999999999999987543
Q ss_pred ------------eecchhhhhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccceE
Q 000525 1192 ------------VGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHFD 1258 (1443)
Q Consensus 1192 ------------~gi~r~G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~f~ 1258 (1443)
+|||+ .||.+.|+|+.||||+|+++|.+||.+|++|+|.|++||||+|+.+|+|| |...
T Consensus 1069 ~g~~~~~~~~~llGItk-------a~l~t~SflsaASFQeTtkvLt~AAi~gk~D~L~GlkENVIiG~liPaGT-G~~~ 1139 (1156)
T PRK00566 1069 EGKEPATGRPVLLGITK-------ASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGT-GLAR 1139 (1156)
T ss_pred CCCCCCcccceeeeeee-------cccccCcccccccccchHHHHHHHHhcCCCCcCCCcccceEecCcccCCC-Ccch
Confidence 45554 55567799999999999999999999999999999999999999999999 7653
No 9
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=1.8e-139 Score=1323.87 Aligned_cols=774 Identities=19% Similarity=0.223 Sum_probs=555.0
Q ss_pred CCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHHH---------HHHHHHHHHhh-hhc
Q 000525 216 LSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIELS---------HLVQDCLKISK-LHL 285 (1443)
Q Consensus 216 ~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~~---------~~~~~~~~~~~-~~~ 285 (1443)
.+|+||||++||||||++||++..+ |+++.+||||.+|+.|+..|...+.+. ......+|... ..+
T Consensus 310 ~~PewmiL~vlPV~Pp~lRP~V~l~----gg~~atsDLn~lyr~II~rNnrLk~l~~~~ap~~ii~nekr~LQeaVd~li 385 (1460)
T PRK14906 310 NDPADMILDVIPVIPPDLRPMVQLD----GGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLF 385 (1460)
T ss_pred CCHHHHhhhcccCCCCCcCCcEEEC----CCcccCCchHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHH
Confidence 5899999999999999999999875 347788999999999998875443321 12223333321 335
Q ss_pred ccccCCchhHhhhccCCcccC----cCCcc-hhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCcceeechh
Q 000525 286 DKSSRKDSAEVRQKKNIDISN----SSGLR-WIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSW 360 (1443)
Q Consensus 286 d~~~~~~~~~~~q~~~~~~~~----~~G~r-~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~pe~Vt~~ 360 (1443)
||.....+. ....+++.++ +.|++ |||+|||||||||||||||+|||+|+++|||||..||.+||+|+
T Consensus 386 DN~~~g~p~--~~~~~rplKsls~~LkGK~GRFRqNLlGKRVDySgRSVIspdP~L~l~e~GlP~~mA~eLf~Pf----- 458 (1460)
T PRK14906 386 DNGRRGRPV--TGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPF----- 458 (1460)
T ss_pred cCCCcCCCC--ccccCCchhHHHHHhcccCcccccccccccccCcCCceEeCCCCCccccccCcHHHHHhcCchh-----
Confidence 555433221 0111122111 23432 89999999999999999999999999999999999999999984
Q ss_pred hHHHhhhhhcccccccCcceEeeCCeEEEecccccccCCCEEeceeccCceEEEeCCCCCCccccccccEEEecCCceEE
Q 000525 361 NWERLSVCISFRLLEKGELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPISSVVT 440 (1443)
Q Consensus 361 Ni~~l~~~~~~~~~~~g~~~i~~~g~~~~~~~~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v~p~~~t~r 440 (1443)
++.+|...... ..++...+.+. ......+.|.||+++||+|||||||||||||||||+++++++ +|||
T Consensus 459 ~i~~L~~~~~~-------~nik~ak~~i~----~~~~~v~~vle~vi~gd~VLlNRqPTLHRlsIqAf~~~L~~g-ktIr 526 (1460)
T PRK14906 459 VMKRLVELEYA-------ANIKAAKRAVD----RGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEG-KAIK 526 (1460)
T ss_pred HHHHHHHhccc-------ccHHHHhhHHh----hcCCcceeeeeeeeccceeEeccCcccchhccceeeEEecCC-ceEE
Confidence 55666542100 00100000000 112234567788999999999999999999999999999986 5999
Q ss_pred ecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHHhhcc-Cc-------ccc
Q 000525 441 INPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLME-DS-------VLL 512 (1443)
Q Consensus 441 ~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~llt~-~d-------~fl 512 (1443)
|||+||+||||||||||||+|||||++|||||+.||++.+|++||++|+|+++++||+++|+|+||. ++ .|.
T Consensus 527 LhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F~ 606 (1460)
T PRK14906 527 LHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFA 606 (1460)
T ss_pred ecccccCccccCCcCceeeeecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeeeeeeeeeEEeeeccccccccCceeC
Confidence 9999999999999999999999999999999999999999999999999999999999999999996 43 799
Q ss_pred CHHHHHHHHhhCC-CccCCCceeccc-------------------CCccchHHHHHhhcCCCCCccccCCCcEEEeCCee
Q 000525 513 SHLQMQQLQMFCP-HRFLSPDIFKIS-------------------KDSVWSGKQLFSMLLPPDFEYTFPSKDVYISGGKL 572 (1443)
Q Consensus 513 ~~~~~~~l~~~~~-~~l~~pai~Kp~-------------------~~~lwTGKql~s~~lp~~~~~~~~~~~v~i~~gel 572 (1443)
+.+++..+..+.. ..++.|..+++. ....|+||+||+.+||.++.|. |+.
T Consensus 607 ~~~e~~~a~~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~tt~Gr~Ifn~ilP~d~~fv---------N~~- 676 (1460)
T PRK14906 607 DFDDALNAYDARADLDLQAKIVVRLSRDMTVRGSYGDLEETKAGERIETTVGRIIFNQVLPEDYPYL---------NYK- 676 (1460)
T ss_pred CHHHHHHHHhcCCCccccccEEEecCcccccccccccccCCCCCceEECCCCEEEEecccCCCcccc---------cce-
Confidence 9999998876532 333333222210 0247999999999999876443 222
Q ss_pred ccccCcccccCCCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCccccccccchHHHHHHHHHhhHHHHH
Q 000525 573 ISAEGSSWLRDYEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQ 651 (1443)
Q Consensus 573 l~~~~k~~lg~~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~~~~~~~~~~~~~~~~i~~~~~~a~ 651 (1443)
++|+.+| +|++.++++||.+ +++|||.+++++++|++.+|||||++|+.++++ +.+++++.+..+.+.
T Consensus 677 ---l~KK~Lg----~LI~~i~~~~G~~~t~~fLD~Ik~LGf~yaT~sG~SIgi~Di~ip~~---K~~iI~~A~~~V~ei- 745 (1460)
T PRK14906 677 ---MVKKDIG----RLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDD---KPEILAEADEKVAAI- 745 (1460)
T ss_pred ---eeHHHHH----HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCCEEEeecccccChH---HHHHHHHHHHHHHHH-
Confidence 3566664 5999999999986 889999999999999999999999999988753 344544333222221
Q ss_pred hhhhhhhhHHHhHHhhhhccCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCcceeeeccC
Q 000525 652 DTCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKYGSKDNSLLAMFKAG 731 (1443)
Q Consensus 652 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~sG 731 (1443)
...|..+.+.. ...|. ..++.|.++.+++++.+.+++.+.|++++|+.||
T Consensus 746 ------------~~~y~~G~iT~----------~Er~~--------kVi~iw~~a~d~v~~~~~~~l~~~N~i~mMa~SG 795 (1460)
T PRK14906 746 ------------DEDYEDGFLSE----------RERHK--------QVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSG 795 (1460)
T ss_pred ------------HHHHHcCCCcH----------HHHHH--------HHHHHHHHHHHHHHHHHHHhcccCCCeEeeeecc
Confidence 12233343311 11122 2345677888999999999999999999999999
Q ss_pred CccchhhHhHhhhccccccc-CCCCccccCccccccccccCCCCCCccccCCccccccccccccCCCChhhHHHhcccCC
Q 000525 732 SKGNLLKLVQHSLCLGLQHS-LAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSR 810 (1443)
Q Consensus 732 SKGS~~Nl~Qi~~~lGqQ~~-~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m~gR 810 (1443)
||||..|+.||+||+|||.. .|+ .++ .||.|||++||+|.||||||||||
T Consensus 796 ARGS~~QI~QLaGmRGlma~p~G~----------------------------iIe-~PI~SnFrEGLt~~EyFiSt~GaR 846 (1460)
T PRK14906 796 ARGNIKQIRQLAGMRGLMADMKGE----------------------------IID-LPIKANFREGLSVLEYFISTHGAR 846 (1460)
T ss_pred CcccHHHHHHHHhcccceecCCCC----------------------------ccc-cccccccccCCCHHHHHHHccccc
Confidence 99999999999999999863 231 111 578999999999999999999999
Q ss_pred Cccccccc--CCCCcchHHHHHHHhheEeeec--ce-----EEcc--C--------------------C-----------
Q 000525 811 DSSFSDNA--DLPGTLTRRLMFFMRDLCTAYD--GT-----VRNA--Y--------------------G----------- 848 (1443)
Q Consensus 811 eGliDtav--a~sGYLqRrLvk~lEdl~v~YD--~t-----VR~s--~--------------------G----------- 848 (1443)
|||+|||+ |+|||||||||+++||++|..+ || |..- . |
T Consensus 847 KGL~DTALKTAdSGYLTRRLVdVaQDViV~e~DCgT~~Gi~v~~~~~~~~l~~ri~GR~~~~di~~~~g~~i~~~~~~I~ 926 (1460)
T PRK14906 847 KGLVDTALRTADSGYLTRRLVDVAQDVIVREEDCGTDEGVTYPLVKPKGDVDTNLIGRCLLEDVCDPNGEVLLSAGDYIE 926 (1460)
T ss_pred chhhhhhhhccccchHHHHHHHhhhheEEEeccCCCCCCEEEEEeecccchhheeeeEEEHhhhcCCCCCEEEeCCCeeC
Confidence 99999998 9999999999999999999754 22 2110 0 0
Q ss_pred ---------------------------ceEEEEEeccCCCCCCCcccCCceeccccccchhHHHHhcc---cccccc---
Q 000525 849 ---------------------------NQIVQFSYNIEGTSTPTGEIGDQPVGSLSACAISEAAYSAL---DQPISL--- 895 (1443)
Q Consensus 849 ---------------------------~~iiq~~yg~~g~~~~~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~~--- 895 (1443)
..|+|.+||.|- .....+.-||+||++||||||||+||+| +|..++
T Consensus 927 ~~~~~~~i~~~gi~~v~iRS~ltC~s~~gvC~kCYG~dL-atg~~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGv~~~ 1005 (1460)
T PRK14906 927 SMDDLKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDL-ATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVAGD 1005 (1460)
T ss_pred cHHHHHHHHHCCCCEEEEeCCeeECCCCCChhhCcCCcc-cCCcEeccccceeeeeeeecCCCcceeeeeeeeccccccc
Confidence 014555555542 1123467899999999999999999985 776554
Q ss_pred ccccccccchhhhccCCCCCCCccEeeeehhhhccccccCchhhHHHHHhhhcccchhhhhceEEEEEcCCCCcccccCc
Q 000525 896 LETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSP 975 (1443)
Q Consensus 896 l~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e~~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp 975 (1443)
-.|.|+||+.|+.+|++... +.+ + + ++.-.+.| ...
T Consensus 1006 dit~GLpRv~eLfEar~pk~---~a~-i--~---------------------------e~~G~v~i--~~~--------- 1041 (1460)
T PRK14906 1006 DITQGLPRVAELFEARKPKG---EAV-L--A---------------------------EISGTLQI--TGD--------- 1041 (1460)
T ss_pred ccccCcchhhhheeeccCCC---cee-e--e---------------------------ccCCEEEe--ccC---------
Confidence 34699999999999965221 111 0 0 01111111 000
Q ss_pred eEEEEEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCCceeeecCccccccccccCCCceEEEEEeecccccchhh
Q 000525 976 WICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSID 1055 (1443)
Q Consensus 976 ~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~~~~~~ 1055 (1443)
++ . ..+.|.+.+ ++. . ..
T Consensus 1042 --------------~~------------~------------~~i~i~~~~----------~~~-~-~y------------ 1059 (1460)
T PRK14906 1042 --------------KT------------E------------KTLTIHDQD----------GNS-R-EY------------ 1059 (1460)
T ss_pred --------------CC------------c------------eEEEEECCC----------Cce-e-EE------------
Confidence 00 0 001111110 000 0 00
Q ss_pred HHHHHHHhccccccceeeccccceEEEEeecccccccCCCCCCCceEEEEEeeccccccchhHHHHhhhhcccccccccc
Q 000525 1056 LETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWT 1135 (1443)
Q Consensus 1056 l~~l~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~ 1135 (1443)
.+|. ...+ .|+|+ +|+.+-.. . .+ ++
T Consensus 1060 -------~v~~--~~~~--~~~v~-------------------~gd~v~~G---------~--------~l--~~----- 1085 (1460)
T PRK14906 1060 -------VVSA--RVQF--MPGVE-------------------DGVEVRVG---------Q--------QI--TR----- 1085 (1460)
T ss_pred -------EccC--Cccc--ccccC-------------------CCCEEccC---------C--------Cc--cC-----
Confidence 0110 0000 01111 11121110 0 00 11
Q ss_pred ccCCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHHHHHHHhhccce-------------eeEeecchhh----
Q 000525 1136 RSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSAT-------------GEFVGLNAKG---- 1198 (1443)
Q Consensus 1136 rt~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rHl~LlAd~MT~~-------------G~~~gi~r~G---- 1198 (1443)
-+-|.++++++.|++|+..+|++|+++|+..||+.|+.+|+.+|+..|+.+ |+.+...++-
T Consensus 1086 --G~~~p~~il~~~g~~~~~~ylv~eVQ~VYr~QGV~InDKHiEvIvRQMl~kV~I~d~Gdt~fl~Ge~vd~~~~~~~n~ 1163 (1460)
T PRK14906 1086 --GSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTAN 1163 (1460)
T ss_pred --CCCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCceeccccHHHHHHHHhceEEEecCCCcCCCCCCeeeHHHHHHHHH
Confidence 123679999999999999999999999999999999999999999999998 3322211110
Q ss_pred ----------------hhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccc
Q 000525 1199 ----------------LALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGH 1256 (1443)
Q Consensus 1199 ----------------~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~ 1256 (1443)
+...|.||.+.|.|+.|||++|+++|.+||..|++|+|.|..||+|+|+.||+|| |.
T Consensus 1164 ~~~~~g~~pa~~~p~llGITKasL~t~SflSaASFQeTtrVLt~AAi~gk~D~L~GLKENVIiG~lIPAGT-G~ 1236 (1460)
T PRK14906 1164 NLILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGT-GL 1236 (1460)
T ss_pred HHHHcCCCCceeeeEEeeeeecccccccccccccccchHHHHHHHHhcCCCCcCCCCccceEecceecCCC-Cc
Confidence 1123578888999999999999999999999999999999999999999999999 64
No 10
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=8.4e-139 Score=1361.09 Aligned_cols=903 Identities=17% Similarity=0.223 Sum_probs=577.6
Q ss_pred cCCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHH---------HHHHHHHHHHhh-hh
Q 000525 215 ILSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIEL---------SHLVQDCLKISK-LH 284 (1443)
Q Consensus 215 ~~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~---------~~~~~~~~~~~~-~~ 284 (1443)
..+||||||++||||||++||++..+ ++++.+||||.+|+.|+..|...+.+ .......+|... ..
T Consensus 1663 ~~rPewmil~~lPV~Pp~lRP~v~l~----~g~~~~sDLn~ly~~II~~NnrLk~~~~~~ap~~ii~~~~~~LQ~~V~~l 1738 (2836)
T PRK14844 1663 GNRPEWMILTTIPILPPDLRPLVSLE----SGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSL 1738 (2836)
T ss_pred CCChhheeeeccccCCCcccCcEEeC----CCcccCCchHHHHHHHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHHHH
Confidence 36899999999999999999999874 34688999999999999887544332 122233333322 24
Q ss_pred cccccCCch----------hHhhhccCCcccCcCCcc-hhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCc
Q 000525 285 LDKSSRKDS----------AEVRQKKNIDISNSSGLR-WIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQI 353 (1443)
Q Consensus 285 ~d~~~~~~~----------~~~~q~~~~~~~~~~G~r-~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~ 353 (1443)
+||...+.+ ..+.|+ +.|++ |||+|||||||||||||||+|||+|+++|||||..||++||+
T Consensus 1739 ~Dn~~~g~~~~~~~~r~~lksls~~-------LkGK~GRFR~NLlGKRVDySgRSVI~pdP~L~l~evGlP~~mA~eL~~ 1811 (2836)
T PRK14844 1739 FDNSRRNALVNKAGAVGYKKSISDM-------LKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFK 1811 (2836)
T ss_pred hcCCCCCCCccCCCCCCccccHHHH-------hcCCCCcccccccccccccCCCceEeCCCCcccceeeCCHHHHHhccc
Confidence 455433211 122222 23432 899999999999999999999999999999999999999998
Q ss_pred ceeechhhHHHhhhhhcccccccCcceEeeCCeEEEecccccccCCCEEeceeccCceEEEeCCCCCCccccccccEEEe
Q 000525 354 SERLNSWNWERLSVCISFRLLEKGELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVL 433 (1443)
Q Consensus 354 pe~Vt~~Ni~~l~~~~~~~~~~~g~~~i~~~g~~~~~~~~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v~ 433 (1443)
| ||+++|+.... .+. +. ..+ ++-....+.+|++++||+ +||+|||||||||||||||||+++++
T Consensus 1812 P-----f~i~~L~~~~~----~~~---i~-~a~--~li~~~~~~v~dile~vi-~gd~VLlNRqPTLHR~sIqAf~~~l~ 1875 (2836)
T PRK14844 1812 P-----FVYSKLKMYGM----APT---IK-FAS--KLIRAEKPEVWDMLEEVI-KEHPVLLNRAPTLHRLGIQAFEPILI 1875 (2836)
T ss_pred H-----HHHHHHHHcCc----ccc---hH-HHH--HHHHhhCCcceEEEEEEe-cCCEEEecCCCccccccccceeeEee
Confidence 7 67888886411 010 00 000 011123456788886665 69999999999999999999999999
Q ss_pred cCCceEEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHHhhccCcccc-
Q 000525 434 PISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDSVLL- 512 (1443)
Q Consensus 434 p~~~t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~llt~~d~fl- 512 (1443)
++ +||||||+||+||||||||||||+|||||++|||||+.||++.+|++||++|+|+++++||+++|+|+||.++.++
T Consensus 1876 ~g-ktirlhp~vC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~ilG~y~LT~~~~~~~ 1954 (2836)
T PRK14844 1876 EG-KAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQEPKED 1954 (2836)
T ss_pred cC-ceEEecccCCCcccCCCCCceeeeecCCcHHHHHHHHHHhCCcccEEecCCCceeEeehhhhhhhhhhhcccccccc
Confidence 86 5999999999999999999999999999999999999999999999999999999999999999999999998754
Q ss_pred ---CHHHHHHHHhh-CCCccCCCceecccCCccc---------------hHHHHHhhcCCCCCccccCCCcEEEeCCeec
Q 000525 513 ---SHLQMQQLQMF-CPHRFLSPDIFKISKDSVW---------------SGKQLFSMLLPPDFEYTFPSKDVYISGGKLI 573 (1443)
Q Consensus 513 ---~~~~~~~l~~~-~~~~l~~pai~Kp~~~~lw---------------TGKql~s~~lp~~~~~~~~~~~v~i~~gell 573 (1443)
.+.++.++++. ....++.++.+|| ..+| .|||||+.+||.+.++.. .+-||.
T Consensus 1955 ~~~~f~~~~~~~~a~~~~~~~i~~~i~~--~~~~~~~~~~~~~~~~~tt~GR~if~~ilP~~~~~~~-----~~~n~~-- 2025 (2836)
T PRK14844 1955 DLPSFGAFCEVEHSLSDGTLHIHSSIKY--RMEYINSSGETHYKTICTTPGRLILWQIFPKHENLGF-----DLINQV-- 2025 (2836)
T ss_pred cccccCCHHHHHHHHHcCCcccCceEEe--eeccccCCCCcccceEecccHHHHHHHHcCCccccCc-----ceEeee--
Confidence 44666666544 3446667777787 3444 499999999998654421 122332
Q ss_pred cccCcccccCCCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCccccccccchHHHHHHHHHhhHHHHHh
Q 000525 574 SAEGSSWLRDYEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQD 652 (1443)
Q Consensus 574 ~~~~k~~lg~~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~~~~~~~~~~~~~~~~i~~~~~~a~~ 652 (1443)
++|+.+ ++|++.++++||.+ ++.|||++++|+++|++.+|||+|++|+.++++ +.++++ +|++
T Consensus 2026 --l~KK~l----~~II~~~~~~yG~~~t~~fLD~lk~LGf~yaT~~G~SIgi~Di~iP~~---K~~iI~-------~a~~ 2089 (2836)
T PRK14844 2026 --LTVKEI----TSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPET---KATHVD-------HARG 2089 (2836)
T ss_pred --echhHH----HHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhccEEeeHhHcccCHH---HHHHHH-------HHHH
Confidence 456655 57999999999986 789999999999999999999999999998754 233433 3333
Q ss_pred hhhhhhhHHHhHHhhhhccCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC------CCCCccee
Q 000525 653 TCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKYG------SKDNSLLA 726 (1443)
Q Consensus 653 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~------~~~N~~~~ 726 (1443)
.+. + ....|..|.++. ..++ +..++.|.++.+++++.+.+.+ .+.|++++
T Consensus 2090 ~v~--~----i~~~y~~G~it~----------~Er~--------~kvi~iW~~~~d~v~~~~~~~l~~~~~~~~~N~i~m 2145 (2836)
T PRK14844 2090 EIK--K----FSMQYQDGLITR----------SERY--------NKVIDEWSKCTDMIANDMLKAISIYDGNSKYNSVYM 2145 (2836)
T ss_pred HHH--H----HHHHHHcCCCCH----------HHHH--------HHHHHHHHHHHHHHHHHHHHhhhhccccCCCCceee
Confidence 221 1 112244443321 0112 2345677788888888776644 35799999
Q ss_pred eeccCCccchhhHhHhhhcccccccCCCCccccCccccccccccCCCCCCccccCCccccccccccccCCCChhhHHHhc
Q 000525 727 MFKAGSKGNLLKLVQHSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHS 806 (1443)
Q Consensus 727 M~~sGSKGS~~Nl~Qi~~~lGqQ~~~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~ 806 (1443)
|+.||||||+.|+.|++||+||+... . |..++ .+|.|||.+||+|.||||||
T Consensus 2146 Ma~SGARGS~sQI~QLaGmRGLmakp--------~-------------------G~iIe-~PI~SNFrEGLsv~EyFiSt 2197 (2836)
T PRK14844 2146 MVNSGARGSTSQMKQLAGMRGLMTKP--------S-------------------GEIIE-TPIISNFREGLNVFEYFNST 2197 (2836)
T ss_pred eecccCccCHHHHHHHHhcceeeecC--------C-------------------CCeee-cchhhhhccCCCHHHhhhhc
Confidence 99999999999999999999997532 1 11122 67999999999999999999
Q ss_pred ccCCCccccccc--CCCCcchHHHHHHHhheEeee-c-ce-----EEcc-CCce--------------------------
Q 000525 807 VTSRDSSFSDNA--DLPGTLTRRLMFFMRDLCTAY-D-GT-----VRNA-YGNQ-------------------------- 850 (1443)
Q Consensus 807 m~gReGliDtav--a~sGYLqRrLvk~lEdl~v~Y-D-~t-----VR~s-~G~~-------------------------- 850 (1443)
|||||||+|||+ |+|||||||||+++||++|.- | || |..- +|+.
T Consensus 2198 ~GaRKGL~DTALKTAdSGYLTRRLVDVaQDviI~e~DCgT~~Gi~v~~~~~~~~~i~~L~~ri~GR~~a~di~~p~t~~~ 2277 (2836)
T PRK14844 2198 HGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKEL 2277 (2836)
T ss_pred cccccchhhhhhhcccccchhhhhhhhhceEEEEecccCCCCceEEEEeccCCeEEeEhhheeEEEEEHhHeEcCCCCCE
Confidence 999999999998 999999999999999999964 3 22 2110 1212
Q ss_pred -------------------------------------EEEEEeccCCCCCCCcccCCceeccccccchhHHHHhcc---c
Q 000525 851 -------------------------------------IVQFSYNIEGTSTPTGEIGDQPVGSLSACAISEAAYSAL---D 890 (1443)
Q Consensus 851 -------------------------------------iiq~~yg~~g~~~~~~~~~ge~VG~~aAqSi~Ep~tq~l---~ 890 (1443)
|+|.+||.|- .....+.-||+||++||||||||+||+| +
T Consensus 2278 i~~~~~~I~~~~~~~i~~~gi~~v~IRS~ltC~s~~gvC~~CYG~~L-a~~~~V~iGeaVGiIAAQSIGEPGTQLTMRTF 2356 (2836)
T PRK14844 2278 LVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISPGVCSLCYGRDL-ATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTF 2356 (2836)
T ss_pred EEeCCCccCHHHHHHHHHcCCCEEEEcCCeeECCCCCChhhccCccc-cCCCcccccccceeeeecccCCCcceeeeehe
Confidence 4444444441 1123467899999999999999999985 6
Q ss_pred ccccccc-----------ccccccchhh---hccCCCCCCCccEeeeehhhhcc--ccccCchhhHHHHHhhhcccchhh
Q 000525 891 QPISLLE-----------TSPLLNLKNV---LECGSKKSNADQTMSLFLSNKLG--KRRHGFEYGALEVKNHLECLMLSD 954 (1443)
Q Consensus 891 ~~~~~l~-----------t~gl~rLkEI---l~~~k~~~~~~~~~~l~Ls~~~~--k~~~~~e~~a~~Vk~~LE~~tL~d 954 (1443)
|..++.. ..|..++.+. .+.......-.+...+.+..... ..++...+.|......=+.+.-++
T Consensus 2357 HtGGvas~~~~~~~i~~~~~G~v~~~~~~~v~~~~g~~iv~sr~~~~~i~d~~g~~~~~~~i~yga~l~v~~g~~V~~g~ 2436 (2836)
T PRK14844 2357 HIGGVMTRGVESSNIIASINAKIKLNNSNIIIDKNGNKIVISRSCEVVLIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGD 2436 (2836)
T ss_pred eeccccccccccceeEeccCceEEeccceeEEcCCCcEEEEecccEEEEEecCCcEEEEEecccccEEEecCCCEecCCC
Confidence 6544310 1222222221 11100000001111111111100 000001111111111112222222
Q ss_pred hhceEEEEEcCCCCcc-cccCceEEEE-------EeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCCceeeecCcc
Q 000525 955 IVSTSMIIYSPQTGSM-KHFSPWICHF-------HVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDC 1026 (1443)
Q Consensus 955 i~~~i~i~y~P~~~~~-~~~sp~v~~~-------~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~~i~i~~~~c 1026 (1443)
+-..|+|..... ++.+ -.++| .+..+.=...+++-..|++..... .-+...|.+.|...+=
T Consensus 2437 ----~la~wdp~~~piisE~~-G~v~f~d~~~g~t~~~~~D~~tg~~~~~i~~~~~~~------~~~~~~P~i~i~~~~g 2505 (2836)
T PRK14844 2437 ----KVAEWDPYTLPIITEKT-GTVSYQDLKDGISITEVMDESTGISSKVVKDWKLYS------GGANLRPRIVLLDDNG 2505 (2836)
T ss_pred ----EEEEEcCCCcceEeecc-eEEEEEEEecceeEEEEecccCCceEEEEeeccccc------cccccCceEEEEcCCC
Confidence 234566665422 1111 11111 111222122233222222221100 0011234455543210
Q ss_pred c-c---c---cccccCCCceEEEEEeecccccchhhH-HHHHHHhccccc---cceeeccccceEEEEeeccccccc---
Q 000525 1027 S-S---I---NMQKECNDAFCVTVMIVENFKRTSIDL-ETIQMWVMPFLL---KTVVKGFREIKKVDILWKDKQKAS--- 1092 (1443)
Q Consensus 1027 ~-~---~---~~~~~~~~~~~i~v~~~~~~~~~~~~l-~~l~~~iip~ll---~~vVkG~~~I~rv~I~~~d~~~~~--- 1092 (1443)
. . . ..+.... .-.|.|. + .....- +.|.+ +|.-. .-+..|+|+|...+-.+.++....
T Consensus 2506 ~~~~~~~~~~~~y~lp~-ga~l~v~--~---g~~v~~Gdilak--ipr~~~~t~DIT~GLpRv~eLFEar~pk~~a~ise 2577 (2836)
T PRK14844 2506 KVMTLASGVEACYFIPI-GAVLNVQ--D---GQKVHAGDVITR--TPRESVKTRDITGGLPRVIELFEARRPKEHAIVSE 2577 (2836)
T ss_pred ceecccCCcceeeecCC-CceEeec--c---Cceecccceeec--ccccccccCccCCCCccchheeeeecCCCceEEec
Confidence 0 0 0 0000000 0011110 0 000000 00000 11100 124467777776655443321100
Q ss_pred -----CC--CC-CCCceEEEEEee-cc-c-cccchhHHHHhhhhcccccc--c---cccccCCCcHHHHHHHHcHHHHHH
Q 000525 1093 -----KS--HD-DSFGELYLRVSM-SG-Q-CHITSLWSALMNDCHQIMDM--I---DWTRSHPDNIRSFCLAYGIDAGLQ 1156 (1443)
Q Consensus 1093 -----~~--~~-~~~~el~l~~~g-s~-~-~~~~~~~~vll~~~l~~~~~--i---d~~rt~sn~I~ei~~~lGIEAar~ 1156 (1443)
.+ .. ++..++++..+. .. . .-....+..+ .+.+| | |.-..-+-|+++|++++||||+++
T Consensus 2578 i~G~V~~~~~~~~~~~~i~i~~~~~~~~~~~y~vp~~~~~-----~v~~gd~V~~G~~l~~G~~~p~dil~v~G~ea~~~ 2652 (2836)
T PRK14844 2578 IDGYVAFSEKDRRGKRSILIKPVDEQISPVEYLVSRSKHV-----IVNEGDFVRKGDLLMDGDPDLHDILRVLGLEALAH 2652 (2836)
T ss_pred CCcEEEecccccCCceEEEEECCCCCccceEEEccCCceE-----EecCCCEEcCCCCccCCCCCHHHHHHhhCHHHHHH
Confidence 00 00 111122222110 00 0 0000000000 00000 0 111124568999999999999999
Q ss_pred HHHHHHHHHhcccCCccCHHHHHHHHhhccce-------------ee---------------------------Eeecch
Q 000525 1157 FFLTNLESAISDTGKNILPEHLLIVANTLSAT-------------GE---------------------------FVGLNA 1196 (1443)
Q Consensus 1157 ~ii~el~~~~~~~G~~V~~rHl~LlAd~MT~~-------------G~---------------------------~~gi~r 1196 (1443)
+|++|++.|+..||++||.+|+++|++.|+.+ |+ ++||||
T Consensus 2653 ylv~Evq~VYr~QGV~IndKHiEvIvrQMl~kV~I~d~Gdt~~l~Ge~v~~~~~~~~n~~~~~~g~~pa~~~pvllGITk 2732 (2836)
T PRK14844 2653 YMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRENDAMSNSGKRPAHYLPILQGITR 2732 (2836)
T ss_pred HHHHHHHHHHHhcCeeecccEeeeehhhhhceeEEecCCCcccCCCceecHHHHHHHHHHHHhcCCCCceeeeeeeceee
Confidence 99999999999999999999999999999988 44 345554
Q ss_pred hhhhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCcc
Q 000525 1197 KGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGG 1255 (1443)
Q Consensus 1197 ~G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg 1255 (1443)
.||.+.|+|+.||||+|+++|.+||..|+.|+|.|+.||||+|+++|+|| |
T Consensus 2733 -------asL~t~SflSaASFQeTtkVLt~AAi~Gk~D~L~GlKENVIiG~lIPaGT-G 2783 (2836)
T PRK14844 2733 -------ASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGT-G 2783 (2836)
T ss_pred -------ccccCCChhhcCCcccchHHHHHHHhcCCCCcCCCcccceEecCcccCCc-C
Confidence 46677899999999999999999999999999999999999999999999 5
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=3.4e-137 Score=1351.18 Aligned_cols=523 Identities=19% Similarity=0.217 Sum_probs=399.3
Q ss_pred cCCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHHH---------HHHHHHHHHhh-hh
Q 000525 215 ILSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIELS---------HLVQDCLKISK-LH 284 (1443)
Q Consensus 215 ~~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~~---------~~~~~~~~~~~-~~ 284 (1443)
..+||||||++||||||++||++..+ |+++++||+|.+|++|+..|...+.+. ......||... ..
T Consensus 1620 ~~~PewmiL~~lPV~Pp~lRP~v~l~----gg~~a~sDln~lyr~II~rNnrLk~l~~~~ap~~ii~nek~~LQ~aVd~l 1695 (2890)
T PRK09603 1620 GNRPEWMMLTVLPVLPPDLRPLVALD----GGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVL 1695 (2890)
T ss_pred CCChHheeeeeeccCCCcccCcEEeC----CCcccCCCccHHHHHHHHHHHHHHHHHHcCCCceehHHHHHHHHHHHHHH
Confidence 36899999999999999999999875 347789999999999998875443321 12223333321 34
Q ss_pred cccccCCchhHhhhccCCcccC----cCCc-chhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCcceeech
Q 000525 285 LDKSSRKDSAEVRQKKNIDISN----SSGL-RWIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNS 359 (1443)
Q Consensus 285 ~d~~~~~~~~~~~q~~~~~~~~----~~G~-r~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~pe~Vt~ 359 (1443)
+||...+.+. ....+++.++ +.|+ .|||+|||||||||||||||+|||+|+++|||||..||.+||+|+.
T Consensus 1696 ~DN~~~~~~~--~~~~~rplKsls~~LkGK~GRFRqNLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~P~~--- 1770 (2890)
T PRK09603 1696 FDNGRSTNAV--KGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHL--- 1770 (2890)
T ss_pred hccccccccc--cCCCCCcchhHHHHhcCCCCccccccccccccCcCCceEeCCCCcccccccChHHHHHHhCChHH---
Confidence 5555432220 1111222221 2344 2899999999999999999999999999999999999999999955
Q ss_pred hhHHHhhhhhcccccccCcc-eEeeCCeEEEecccccccCCCEEeceeccCceEEEeCCCCCCccccccccEEEecCCce
Q 000525 360 WNWERLSVCISFRLLEKGEL-YVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPISSV 438 (1443)
Q Consensus 360 ~Ni~~l~~~~~~~~~~~g~~-~i~~~g~~~~~~~~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v~p~~~t 438 (1443)
+.+|.. +|.. .++...+++ ......+|.|+|||++||+|||||||||||||||||+|+++|+ +|
T Consensus 1771 --i~~L~~--------~G~~~~lk~ak~~i----~~~~~~v~~vlr~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~g-kt 1835 (2890)
T PRK09603 1771 --LSKLEE--------RGYATTLKQAKRMI----EQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDG-KA 1835 (2890)
T ss_pred --HHHHHH--------cCCccCHHHHHHHH----HhccCccEEEEEeeecCCeEEecCCCccccccceeeeEEEecC-ce
Confidence 344432 2211 111000000 1123445778899999999999999999999999999999997 69
Q ss_pred EEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHHhhccCcc--------
Q 000525 439 VTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDSV-------- 510 (1443)
Q Consensus 439 ~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~llt~~d~-------- 510 (1443)
|||||+||+||||||||||||+|+|||++|||||++||.+.+|++||++|+|+++++||+++|+|+||.++.
T Consensus 1836 IrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~LM~s~~nilsP~~G~Pi~~p~QD~vlG~y~LT~~~~~~~~~~~~ 1915 (2890)
T PRK09603 1836 IQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKL 1915 (2890)
T ss_pred EEeccccCCcccCCCCCceeEEeecCCHHHHHHHHHHhcccceEEEcCCCceeEEeecceeeeeEEeeccccCCCCccce
Confidence 999999999999999999999999999999999999999999999999999999999999999999999985
Q ss_pred ccCHHHHHHHHhhCCC--ccCCCceecccCCccch--HHHHHhhcCCCCCccccCCCcEEEeCCeeccccCcccccCCCc
Q 000525 511 LLSHLQMQQLQMFCPH--RFLSPDIFKISKDSVWS--GKQLFSMLLPPDFEYTFPSKDVYISGGKLISAEGSSWLRDYEG 586 (1443)
Q Consensus 511 fl~~~~~~~l~~~~~~--~l~~pai~Kp~~~~lwT--GKql~s~~lp~~~~~~~~~~~v~i~~gell~~~~k~~lg~~~~ 586 (1443)
|.+.+++...+..... ..+.|+++|| ..+|| ||||||.+||.++++.+ -||. ++|+.+|
T Consensus 1916 F~~~~e~~~~~~~~~~~~~~~i~~~~~p--~~l~Tt~GK~ifs~ilP~~~~~~~-------~n~~----ldKK~Lg---- 1978 (2890)
T PRK09603 1916 FSSVNEIITAIDTKELDIHAKIRVLDQG--NIIATSAGRMIIKSILPDFIPTDL-------WNRP----MKKKDIG---- 1978 (2890)
T ss_pred eCCHHHHHHHHHcCCCccCCcceeecCC--cEEEcCccceeeeccCcccccccc-------Eeee----echHHHH----
Confidence 4556666544333221 2345666677 78999 99999999998654331 1332 4777775
Q ss_pred cHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCccccccccchHHHHHHHHHhhHHHHHhhhhhhhhHHHhHH
Q 000525 587 NLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTCNFQQLMVDSHM 665 (1443)
Q Consensus 587 ~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~~~ 665 (1443)
+|+|.++++||.+ |+.|||.+++|+++|++.+|||||++|+.++++ +++++++....+.+. ..
T Consensus 1979 ~LI~~i~~~yG~~~t~~fLD~lk~LGf~yat~~G~SIgI~Dl~ip~~---K~~iI~~A~~eV~ei-------------~~ 2042 (2890)
T PRK09603 1979 VLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKD---KQKMVEKAKVEVKKI-------------QQ 2042 (2890)
T ss_pred HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHhCCEeeeeccCcccHH---HHHHHHHHHHHHHHH-------------HH
Confidence 6999999999996 899999999999999999999999999998754 344543332222111 12
Q ss_pred hhhhccCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC----CCCCcceeeeccCCccchhhHhH
Q 000525 666 NFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKYG----SKDNSLLAMFKAGSKGNLLKLVQ 741 (1443)
Q Consensus 666 ~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~----~~~N~~~~M~~sGSKGS~~Nl~Q 741 (1443)
.|..+.+... ..+ +..++.|.++.+++++.+.+.+ ++.|++++|+.||||||.+|++|
T Consensus 2043 ~y~~G~it~~----------Er~--------~kvid~w~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS~~NI~Q 2104 (2890)
T PRK09603 2043 QYDQGLLTDQ----------ERY--------NKIIDTWTEVNDKMSKEMMTAIAKDKEGFNSIYMMADSGARGSAAQIRQ 2104 (2890)
T ss_pred HHHcCCCCcc----------HHH--------HHHHHHHHHHHHHHHHHHHHHhhhcCCCCCcHHHHHhccccccHHHHHH
Confidence 2344433211 111 2335567777777777666554 35799999999999999999999
Q ss_pred hhhcccccccCCCCccccCccccccccccCCCCCCccccCCccccccccccccCCCChhhHHHhcccCCCccccccc--C
Q 000525 742 HSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNA--D 819 (1443)
Q Consensus 742 i~~~lGqQ~~~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m~gReGliDtav--a 819 (1443)
|+||+|||.... +..++ .+|.|||++||+|+|||||||||||||+|||+ |
T Consensus 2105 LaGmrGqMakp~---------------------------G~iie-~PI~snFrEGLtp~EyFfst~GaRKGLiDTALKTA 2156 (2890)
T PRK09603 2105 LSAMRGLMTKPD---------------------------GSIIE-TPIISNFKEGLNVLEYFNSTHGARKGLADTALKTA 2156 (2890)
T ss_pred HHHcCCcEECCC---------------------------CCccc-ChhhcCcccCCCHHHHHHhccccccchhhhhhhcc
Confidence 999999986321 01111 46889999999999999999999999999998 9
Q ss_pred CCCcchHHHHHHHhheEeeec
Q 000525 820 LPGTLTRRLMFFMRDLCTAYD 840 (1443)
Q Consensus 820 ~sGYLqRrLvk~lEdl~v~YD 840 (1443)
+|||||||||+++||++|..|
T Consensus 2157 dSGYLTRRLVdvaQDviI~e~ 2177 (2890)
T PRK09603 2157 NAGYLTRKLIDVSQNVKVVSD 2177 (2890)
T ss_pred ccchhhhhHHHhhcceEEEec
Confidence 999999999999999999875
No 12
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=100.00 E-value=3.8e-125 Score=1188.52 Aligned_cols=718 Identities=21% Similarity=0.275 Sum_probs=561.9
Q ss_pred eeeEEEEcCChHHHHhccceEEecC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccceeecCcccccc
Q 000525 17 LTGISLGISTDTEKEKLSVMEIGAV-----------SEVTNPRLGLPNPTNECSSCGAKDRKACEGHFGFIKFPFTILHP 85 (1443)
Q Consensus 17 I~~I~F~~~S~eEI~~~Sv~~I~~~-----------~Gl~D~rLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~PVfHp 85 (1443)
+..|+||++||+||++ |+.+|+.| +||+|+|||+++++..| |||. +...||||||||||+.||+||
T Consensus 4 ~~~i~~gl~sp~~ir~-~s~ev~~pet~~~~~~P~~~Gl~d~ri~~~~~~~~C-~Cg~-~~~~~~~~~GhIeLa~Pv~hi 80 (808)
T COG0086 4 IFDIKFGLASPEEIRS-WSGEVKKPETINYRTKPERGGLFDERIFGPDKDYEC-TCGK-YKRICPGGFGHIELAAPVAHI 80 (808)
T ss_pred cceeEEecCCHHHHHh-cceEEcCccccCCCCcccCCCccchhhcCCCCCcee-cCCC-CcCcCCCCceeEEeecceEEe
Confidence 3449999999999999 77999875 79999999999999999 9995 889999999999999999999
Q ss_pred ccHHHHHHHHhccccccccccCcchhhhc-cccc----------cccccccccccCCCCCCcccccccccccccCcccee
Q 000525 86 YFLSDIAKLLNSICPKCKTIRKERQKGAG-SSRK----------EQPRVCKYCVRNPAQWYPRMRFKLSSKDLSGKTAII 154 (1443)
Q Consensus 86 gf~~~i~kIL~~iC~~C~rlll~~~~k~l-~~~~----------~~~~~C~~C~~~~~~~~p~i~~~~~~~~~~~k~~ii 154 (1443)
+|++.+..+|+++|.+|++++.......+ .... .....|++|++.. +.+.+ .+.
T Consensus 81 ~f~k~~~~~L~~~~~~~~~v~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~Ga~~----~~~~~--------~~~--- 145 (808)
T COG0086 81 WFFKSIPSLLDMTCRDCERVLYFEAYVVLGTDLEKIQLLNETEYVYDSFCAHCGAEA----IKILL--------EKP--- 145 (808)
T ss_pred chhhccHHHHhhhHHhhhhhhhHhHHHHhccchhhhcccchheeeccccCCCCCchh----HHHHH--------hCc---
Confidence 99999999999999999999987432111 0000 1125688887631 11110 000
Q ss_pred ehhhhhhhccCCCCccccccccCccccccccccCCCccccCHHHHHHHhccCChhhHhhc-cCCCCcceeeccccCCCCC
Q 000525 155 VEIDEKLSKKNKKLPDDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPSIREEF-ILSKDAPFLKCFPVTPNNH 233 (1443)
Q Consensus 155 ~e~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LsP~eV~~iLkkI~~ed~~~~-~~rPE~ffLt~LPVPP~~i 233 (1443)
+++... + . +.++|.++.++|++|+..+...+ .++||||||+++||||+++
T Consensus 146 ----------------~~~~~~-------~-----~-~~~~~~~~~~~~~~l~~~d~~~~~~~~pewmil~vlpV~Pp~~ 196 (808)
T COG0086 146 ----------------DLETER-------E-----E-ETLSPTKVKKLLKRLKVVDAFLLSGNRPEWMILTVLPVPPPDL 196 (808)
T ss_pred ----------------chhhhh-------h-----h-cccCHHHHHHHHhhccHHHHHHhcCCCcceeEEEeeccCCCCC
Confidence 000000 0 1 56899999999999998777654 6899999999999999999
Q ss_pred CccccccccccccccccchhHHHHHHHHHhhCCcHHHH--------HHHHHHHHHhh-hhcccccCCch-------hHhh
Q 000525 234 RVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIELS--------HLVQDCLKISK-LHLDKSSRKDS-------AEVR 297 (1443)
Q Consensus 234 RPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~~--------~~~~~~~~~~~-~~~d~~~~~~~-------~~~~ 297 (1443)
||++.+++ +++++||||.+|..|+..|...+.+. ......||.+. .+.|| ..+.+ +++.
T Consensus 197 RP~i~ld~----g~~a~~dl~~~~~~ii~~n~rlk~~~~~~~~~iv~~~~~~lQ~~v~~~~Dn-~~~~~~~~~rPlksl~ 271 (808)
T COG0086 197 RPSIQLDG----GRFAESDLNDLYRRVINRNNRLKRLLELAAPIIVRNEKRMLQEAVDALFDN-RRPRAVTGGRPLKSLS 271 (808)
T ss_pred CcceecCC----CccchhHHHHHHHHHHHHHHHhHHhhhhcchHHHHHHHHHHHHHHHHHhhc-CCCCCccCCCccccHH
Confidence 99998863 37899999999999998876544332 22233444432 45666 22111 2333
Q ss_pred hc-cCCcccCcCCcchhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCcceeechhhHHHhhhhhccccccc
Q 000525 298 QK-KNIDISNSSGLRWIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEK 376 (1443)
Q Consensus 298 q~-~~~~~~~~~G~r~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~pe~Vt~~Ni~~l~~~~~~~~~~~ 376 (1443)
|+ +||.+ |||+|||||||||||||||+|||||+++|||||..||++||+|+.||+||++.|++
T Consensus 272 ~~LkgK~G-------rFR~nL~GKRVd~SgRsVI~~~P~l~~~e~GvP~~~A~~L~~p~~v~~~~~~~~~~--------- 335 (808)
T COG0086 272 QRLKGKQG-------RFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGLRT--------- 335 (808)
T ss_pred HHhcCCCc-------eeeccccccccCCCCceeecCCCCccccccCCHHHHHHHhccCEEEEehhhhhhhc---------
Confidence 33 33332 89999999999999999999999999999999999999999999999999999995
Q ss_pred CcceEee-CCeEEEecccccccCCCEEeceeccCceEEEeCCCCCCccccccccEEEecCCceEEecccCCCCCCCCCCC
Q 000525 377 GELYVCR-KGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPISSVVTINPLCCSPFHGDFDG 455 (1443)
Q Consensus 377 g~~~i~~-~g~~~~~~~~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v~p~~~t~r~n~~~c~pyNADFDG 455 (1443)
|++++.+ .++ .+..+|.|+||+++||+|||||||||||+|||+|++++++..+|||+||+||.||||||||
T Consensus 336 ~a~~~~~~~~~--------~~~~~w~Vl~evi~gd~Vl~NR~PtLHrlsImq~~e~vl~~gkt~rLh~lVc~~yNADFDG 407 (808)
T COG0086 336 GAKYAKRMVER--------RLPEVWDVLREVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDG 407 (808)
T ss_pred CCceEEecccc--------cccccchHHHHHhcCCccccccCChHHHHHHHhhceeeccccceeecchhhccccccccCc
Confidence 6666542 222 2778999999999999999999999999999999999999778999999999999999999
Q ss_pred CceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHHhhccCccccCHHHHHHHHhh---CCCccCCCc
Q 000525 456 DCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDSVLLSHLQMQQLQMF---CPHRFLSPD 532 (1443)
Q Consensus 456 DeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~llt~~d~fl~~~~~~~l~~~---~~~~l~~pa 532 (1443)
||||+|+|||.+|+|||+.||.+++|++||++|+|+++.+||+++|.|+||..|+|++..+++++++. ....-+.||
T Consensus 408 DeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~~~~~~~~~ei~l~~~~~~~~e~~~a 487 (808)
T COG0086 408 DEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLKDEYADDREKAEA 487 (808)
T ss_pred hhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEeccEEEEEecccCCCCcceEEEeccccccchhhhHH
Confidence 99999999999999999999999999999999999999999999999999999999999999988543 222456789
Q ss_pred eecccCCccchHHHHHhhcCCCC--Cccc--------------cC-CCcEEEeCCeeccc-cCcccccCCCccHHHHHHH
Q 000525 533 IFKISKDSVWSGKQLFSMLLPPD--FEYT--------------FP-SKDVYISGGKLISA-EGSSWLRDYEGNLFQYLIK 594 (1443)
Q Consensus 533 i~Kp~~~~lwTGKql~s~~lp~~--~~~~--------------~~-~~~v~i~~gell~~-~~k~~lg~~~~~l~~~l~~ 594 (1443)
|.++ ..+|||||+++.+++.. ..+. .+ +..+.|.||+++.+ +++. +..+++
T Consensus 488 i~~~--~~~~~~k~i~~~i~~~~~~~~i~~t~~~~~~~~~~~~~~~d~~~~i~~~~l~~~~i~k~---------~~~i~~ 556 (808)
T COG0086 488 IAKK--IELTTGKVIVSTISPDLAELSIIVTTDGRRIFNRGLPEDKDVLVKIVNGKLIKGVIDKK---------IVTIYR 556 (808)
T ss_pred Hhcc--cceeeeeEEEEEeeccCCcceEEEecchhhhhhccCCcccceeeEEeccccceeeehhh---------HHHHHH
Confidence 9998 79999999999888764 2211 11 13377888888753 3432 336889
Q ss_pred HhcHH-HH-HHHHHHHHHHHHHHhccc-ceeecCccccccccchHHHHHHHHHhhHHHHHhhhhhhhhHHHhHHhhhhcc
Q 000525 595 RYRDK-VL-DFLYAAQEVLCEWLSVRG-MTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTCNFQQLMVDSHMNFLMSA 671 (1443)
Q Consensus 595 ~~g~~-a~-~~l~~~q~l~~~~L~~~G-fSigi~D~~~~~~~~~~~~~~~~i~~~~~~a~~~~~~~~~~~~~~~~~~~~~ 671 (1443)
.||++ +. .+++.+.+|...|+...| |+++++|...... ..+++.+ .+|+..+. + ....|..+.
T Consensus 557 ~~g~~~~~~~~~~~~dkl~~~~~~~~~~~~~~i~~~d~~~~-~~~~e~v-------~~ae~~v~--~----~i~~~~~g~ 622 (808)
T COG0086 557 EYGPEVASKALVKLLDKLKNLGIKGIGGFGIGIGRKDIEAE-DEKDEIV-------IEAEGSVL--K----LILQYEEGD 622 (808)
T ss_pred HhCchhhHHHHHHHHHHHHHhheeeeccceEEeecccccch-HHHHHHH-------HHHHHHHH--H----HHHHhhcCC
Confidence 99984 56 888888899999999988 9999999862211 1122233 33333211 1 112233443
Q ss_pred CCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCcceeeeccCCccchhhHhHhhhccccccc
Q 000525 672 KDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKYGSKDNSLLAMFKAGSKGNLLKLVQHSLCLGLQHS 751 (1443)
Q Consensus 672 ~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~sGSKGS~~Nl~Qi~~~lGqQ~~ 751 (1443)
.+..+... .....|.....++.+++ .+..+.+.++...+ +..|..+|++||..|++||++|+|||.+
T Consensus 623 lt~~~~~~---i~e~~e~~~~e~l~~ai--------~~~~~~~~~~~g~~--~~~i~~m~~~Gs~~n~sq~~~~iG~~gv 689 (808)
T COG0086 623 LTRTERNN---IVEIIEVLGIEALRNAI--------IEEIKITLEEQGLD--FVDIRHMGLSGARMNISQIVQLIGQQGV 689 (808)
T ss_pred ccccCCCC---eEEEeehHHHHHHHHHH--------HHHHhhhHHhcCCc--chhHHHHhhhhhccCHHHHHHHhhhhee
Confidence 33322111 12244555555665543 33344455555555 7788888999999999999999999999
Q ss_pred CCCCccccCccccccccccCCCCCCccccCCccccccccccccCCCChhhHHHhcccCCCccccccc--CCCCcchHHHH
Q 000525 752 LAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNA--DLPGTLTRRLM 829 (1443)
Q Consensus 752 ~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m~gReGliDtav--a~sGYLqRrLv 829 (1443)
.|+ +.+.+ ++|+|+..+..+. +.|||.+||++||+|.|||||+|+||+||+|||+ |+|||||||||
T Consensus 690 ~g~---r~~~~----~~~~Fe~~~~~~~-----a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa~sGYl~RrLv 757 (808)
T COG0086 690 MGE---KISVL----ARAAFEVTVKHLE-----AEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYLTRRLV 757 (808)
T ss_pred ecc---CCCcc----cccccccccccce-----eeeeeecccCCCCCcceEEeecCccccchHHHhhhhcccCcceEEee
Confidence 885 55544 8999988776543 4599999999999999999999999999999998 99999999999
Q ss_pred HHHhheEeeecceEEccCCceEEEEEeccCCC
Q 000525 830 FFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGT 861 (1443)
Q Consensus 830 k~lEdl~v~YD~tVR~s~G~~iiq~~yg~~g~ 861 (1443)
+++|||+|.||++||++.| .++||.||+||.
T Consensus 758 ~~~qdl~v~~d~~~~~g~~-~~~~~~~ged~~ 788 (808)
T COG0086 758 DVAQDLIVQEDDCVTDGIG-VVIQFEYGEDGE 788 (808)
T ss_pred chhcceEEEecCeEeecCc-eEEEEecCcccc
Confidence 9999999999999999888 499999999983
No 13
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=100.00 E-value=3.8e-77 Score=714.01 Aligned_cols=271 Identities=19% Similarity=0.296 Sum_probs=210.5
Q ss_pred cCCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHH---------HHHHHHHHHHh-hhh
Q 000525 215 ILSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIEL---------SHLVQDCLKIS-KLH 284 (1443)
Q Consensus 215 ~~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~---------~~~~~~~~~~~-~~~ 284 (1443)
..+||||||++|||||+++||++.++ |++.++||+|.+|++|+..|.....+ .......+|.. ...
T Consensus 239 ~~~PewmiL~~lPV~Pp~lRP~v~l~----~g~~~~sDLn~ly~~II~rNn~L~~~~~~~~p~~ii~~~~~~LQ~aVd~l 314 (627)
T PRK02625 239 GSRPEWMVLDVIPVIPPDLRPMVQLD----GGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDAL 314 (627)
T ss_pred CCCccEEEEEeeecCCCcccCceEeC----CCcccCCCHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHH
Confidence 36899999999999999999998875 34678899999999999876543222 11222333332 134
Q ss_pred cccccCCchhHhhhccCCccc----CcCCcc-hhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCcceeech
Q 000525 285 LDKSSRKDSAEVRQKKNIDIS----NSSGLR-WIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNS 359 (1443)
Q Consensus 285 ~d~~~~~~~~~~~q~~~~~~~----~~~G~r-~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~pe~Vt~ 359 (1443)
.|+...+.+. ....++..+ .+.|++ |||+|||||||||||||||||||+|++||||||.+||.+||+|
T Consensus 315 iDn~~~g~~~--~~~~~rp~ksls~~LkGKeGRFR~NLlGKRVDySgRSVIspdP~L~l~e~GvP~~mA~eL~~P----- 387 (627)
T PRK02625 315 IDNGRRGRTV--VGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQP----- 387 (627)
T ss_pred hcCCCCCCCc--ccccCCchhhHHHHhccCCccccccccccccccCCCceEeCCCCcccccccChHHHHHhcCcH-----
Confidence 4554332211 000112111 123442 8999999999999999999999999999999999999999988
Q ss_pred hhHHHhhhhhccccccc--CcceEeeCCeEEEecccccccCCCEEeceeccCceEEEeCCCCCCccccccccEEEecCCc
Q 000525 360 WNWERLSVCISFRLLEK--GELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPISS 437 (1443)
Q Consensus 360 ~Ni~~l~~~~~~~~~~~--g~~~i~~~g~~~~~~~~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v~p~~~ 437 (1443)
||+++|+.. .++.+ +|..+.. ... ...+.|+|||+|||+|||||||||||+|||||+++++++ +
T Consensus 388 f~i~~L~~~---g~~~~i~~ak~~i~---------~~~-~~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~-k 453 (627)
T PRK02625 388 FVIHRLIRQ---GIVNNIKAAKKLIQ---------RAD-PEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEG-R 453 (627)
T ss_pred HhHHHHHHc---CchhhHHHHHHHHH---------hcC-CcccEEEEEeecCcEEEecCCCccccccceeEeeEEcCC-C
Confidence 688887641 11110 1110000 011 224678899999999999999999999999999998876 5
Q ss_pred eEEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHHhhccCcc
Q 000525 438 VVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDSV 510 (1443)
Q Consensus 438 t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~llt~~d~ 510 (1443)
||||||+||+||||||||||||+|||||++|||||++||.+++|++||++|+|+++++||+++|+|+||.+|.
T Consensus 454 tirlhplvC~~fNADFDGDeMnvHvPqS~~A~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~LT~~~~ 526 (627)
T PRK02625 454 AIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENP 526 (627)
T ss_pred eEEeccccCCcccCCcCCCeEEEecCCCHHHHHHHHHHhcCccceEEcCCCceeEeechhhhhheeeeeccCc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999998873
No 14
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=100.00 E-value=8.1e-77 Score=673.85 Aligned_cols=274 Identities=30% Similarity=0.475 Sum_probs=224.1
Q ss_pred CcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHH---------HHHHHHHHHHhh-hhcccc
Q 000525 219 DAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIEL---------SHLVQDCLKISK-LHLDKS 288 (1443)
Q Consensus 219 E~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~---------~~~~~~~~~~~~-~~~d~~ 288 (1443)
|||||++|||||+|+||++..++ ....+||+|.+|.+|+..|...+.. ....++.+|... .+.|+.
T Consensus 1 e~fil~~lpVpP~~~RP~v~~~~----~~~~eddlt~~l~~Ii~~N~~L~~~~~~~~~~~~~~~~~~~LQ~~v~~~~d~~ 76 (295)
T smart00663 1 EWMILTVLPVPPPCLRPSVSLDG----GRFAEDDLTHLLRDIIKRNNRLKRLLELGAPEHIIRNEKRLLQEAVDTLFDNE 76 (295)
T ss_pred CeEEEeccccCCCCCCCcEEeCC----CcccCCcHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHccC
Confidence 79999999999999999987653 2568899999999999876433222 111223333321 234443
Q ss_pred cCCchhHhhhccCCcc----cCcCCc-chhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCcceeechhhHH
Q 000525 289 SRKDSAEVRQKKNIDI----SNSSGL-RWIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWE 363 (1443)
Q Consensus 289 ~~~~~~~~~q~~~~~~----~~~~G~-r~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~pe~Vt~~Ni~ 363 (1443)
+... ..++.++.. ..++|+ .+||+|||||||||||||||||||+|+++|||||.+||++||+||.||.||++
T Consensus 77 ~~~~---~~~~~~~~~~~i~~~l~gK~G~~R~nllGKRvd~s~RsVI~pdP~l~~~evgiP~~~A~~Lt~pe~v~~~n~~ 153 (295)
T smart00663 77 GLPR---ARQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNID 153 (295)
T ss_pred CCcc---cccCCCCCcccccccccCcCCccccccccccccccCceEEeCCCCcceeEeeCCHHHHHhCCcCEEEhHHHHH
Confidence 1110 111111111 112333 28999999999999999999999999999999999999999999999999999
Q ss_pred HhhhhhcccccccCcceEeeCCeEEEec------ccccccCCCEEeceeccCceEEEeCCCCCCccccccccEEEecCCc
Q 000525 364 RLSVCISFRLLEKGELYVCRKGGLVRIR------RIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPISS 437 (1443)
Q Consensus 364 ~l~~~~~~~~~~~g~~~i~~~g~~~~~~------~~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v~p~~~ 437 (1443)
+|++++.... +|++++.+ |+.+.++ .+..|++||+|+|||.|||+|||||||||||+|||||+|+|+++ +
T Consensus 154 ~l~~lv~ng~--pga~~i~~-g~~~~l~~~~~~~~~~~l~~g~~v~r~l~dgd~Vl~NRqPsLHr~si~a~~v~v~~~-~ 229 (295)
T smart00663 154 KLRKLVRNGP--NGAKYIIR-GKKTNLKLAKRSKIAKHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEG-K 229 (295)
T ss_pred HHHHHHhcCC--CCceEEEe-CcEEEchhhhhHHHHhcCccccEeheehhcCCEEEEecCCccccccceeEEEEEecC-c
Confidence 9999865443 68888876 6555543 24578999999999999999999999999999999999999997 6
Q ss_pred eEEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHH
Q 000525 438 VVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAH 503 (1443)
Q Consensus 438 t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~ 503 (1443)
||||||++|+||||||||||||+|+|||++|||||.+||.+.+|++||++|+|++|++||+++|+|
T Consensus 230 tir~n~~~c~~fNADFDGDeMnih~pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~ 295 (295)
T smart00663 230 TIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295 (295)
T ss_pred eEEecCccCCcccCCcCCCEEEEecCCCHHHHHHHHHHhhhhhccccCCCCCeeEeeecceeeecC
Confidence 999999999999999999999999999999999999999999999999999999999999999986
No 15
>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=100.00 E-value=2.4e-76 Score=706.32 Aligned_cols=269 Identities=19% Similarity=0.297 Sum_probs=209.7
Q ss_pred cCCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHH---------HHHHHHHHHHh-hhh
Q 000525 215 ILSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIEL---------SHLVQDCLKIS-KLH 284 (1443)
Q Consensus 215 ~~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~---------~~~~~~~~~~~-~~~ 284 (1443)
..+||||||++|||||+++||++.++ |++.++||+|.+|++|+..|.....+ .......+|.. ..+
T Consensus 232 ~~~PewmiL~~lPV~Pp~lRP~v~l~----~g~~~~sDln~lyr~II~rNn~L~~~~~~~~p~~i~~~~~~~LQ~aVd~l 307 (619)
T TIGR02387 232 SSRPEWMVLDVIPVIPPDLRPMVQLD----GGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDAL 307 (619)
T ss_pred CCCcceEEEEecccCCcccCCceEeC----CCcccCCCHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHH
Confidence 36899999999999999999998875 33678899999999999876543222 11222333332 134
Q ss_pred cccccCCchhHhhhccCCccc----CcCCc-chhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCcceeech
Q 000525 285 LDKSSRKDSAEVRQKKNIDIS----NSSGL-RWIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNS 359 (1443)
Q Consensus 285 ~d~~~~~~~~~~~q~~~~~~~----~~~G~-r~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~pe~Vt~ 359 (1443)
.|+...+.+. ....++..+ .+.|+ .|||+|||||||||||||||+|||+|+++|||||.+||.+||+|
T Consensus 308 idn~~~g~~~--~~~~~rp~ksls~~LkGKeGRFR~nLlGKRVDySgRSVI~pdP~L~l~qvGvP~~mA~eLf~P----- 380 (619)
T TIGR02387 308 IDNGRRGRTV--VGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQP----- 380 (619)
T ss_pred hcCCCCCCCc--ccccCCchhhHHHHhccCCccccccccccccccCCCceecCCCCcccceecChHHHHHhcCch-----
Confidence 4554332220 000112111 12344 28999999999999999999999999999999999999999987
Q ss_pred hhHHHhhhhhccccccc--Ccce-EeeCCeEEEecccccccCCCEEeceeccCceEEEeCCCCCCccccccccEEEecCC
Q 000525 360 WNWERLSVCISFRLLEK--GELY-VCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPIS 436 (1443)
Q Consensus 360 ~Ni~~l~~~~~~~~~~~--g~~~-i~~~g~~~~~~~~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v~p~~ 436 (1443)
||+++|++. .++.+ +|.. +.+. . ...+.|+|||+|||+|||||||||||+|||||+++++++
T Consensus 381 f~i~~L~~~---g~~~~i~~ak~~i~~~----------~-~~v~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~- 445 (619)
T TIGR02387 381 FVIHRLIRQ---GIVNNIKAAKKLIQRA----------D-DEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDG- 445 (619)
T ss_pred HhHHHHHhc---CcccchHHHHHHHHhc----------C-ChhHHHHHHHhcCCEEEecCCCccchhcceeeeeEEecC-
Confidence 578887751 11100 1111 0000 0 123569999999999999999999999999999998875
Q ss_pred ceEEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHHhhccCc
Q 000525 437 SVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDS 509 (1443)
Q Consensus 437 ~t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~llt~~d 509 (1443)
+||||||+||+||||||||||||+|||||++|||||++||.+++|++||++|+|+++++||+++|+|+||.++
T Consensus 446 ktirlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llg~y~LT~~~ 518 (619)
T TIGR02387 446 RAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALN 518 (619)
T ss_pred CeEEECcccCCcccCCCCCceeeeecCCCHHHHHHHHHHhhchhcEEecCCCceeEeechhhhhhhheeeccc
Confidence 5999999999999999999999999999999999999999999999999999999999999999999999876
No 16
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=100.00 E-value=2.2e-74 Score=697.09 Aligned_cols=271 Identities=21% Similarity=0.255 Sum_probs=209.4
Q ss_pred cCCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhCCcHHH-----------HHHHHHHHHHh-h
Q 000525 215 ILSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIEL-----------SHLVQDCLKIS-K 282 (1443)
Q Consensus 215 ~~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~~~~~~-----------~~~~~~~~~~~-~ 282 (1443)
..+||||||++|||||+++||++..+ |++.++||+|.+|++|+..|.....+ .......+|.. .
T Consensus 258 ~~~PewmiL~~lPV~Pp~lRP~v~l~----~g~~~~sDln~lyr~II~rNn~L~~~~~~~~~~p~~~i~~~~~~LQ~aVd 333 (663)
T CHL00018 258 NIEPEWMVLCLLPVLPPELRPIIQLD----GGKLMSSDLNELYRRVIYRNNTLTDLLTTSRSTPGELVMCQKKLLQEAVD 333 (663)
T ss_pred CCCccEEEEEeeeeCCCcccCceEcC----CCcccCCChHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHHHHHHH
Confidence 36899999999999999999998774 34678999999999999765432221 11122223322 1
Q ss_pred hhcccccCCchhHhhhccCCccc----CcCCc-chhhccccCCCCCCCCceeEeCCCCCccccccccHHHHhhcCcceee
Q 000525 283 LHLDKSSRKDSAEVRQKKNIDIS----NSSGL-RWIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERL 357 (1443)
Q Consensus 283 ~~~d~~~~~~~~~~~q~~~~~~~----~~~G~-r~~R~nl~GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~pe~V 357 (1443)
...|+.....+... ..++..+ .+.|+ .+||+|||||||||||||||+|||+|+++|||||.+||.+||+|+.
T Consensus 334 ~lidn~~~g~~~~~--~~~r~~ksls~~LkGK~GrFR~NLlGKRVDySgRSVIvpdP~L~l~e~GlP~~mA~eL~~P~~- 410 (663)
T CHL00018 334 ALLDNGIRGQPMRD--GHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFV- 410 (663)
T ss_pred HHhcCCCCCCcccc--CCCCCCCCccccccCcCccccccccccccccCCCceecCCCcccccccCChHHHHHHcCcHHH-
Confidence 33454433222110 0112211 13454 2899999999999999999999999999999999999999999974
Q ss_pred chhhHHHhhhhhccccccc--CcceEeeCCeEEEecccccccCCCEEeceeccCceEEEeCCCCCCccccccccEEEecC
Q 000525 358 NSWNWERLSVCISFRLLEK--GELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPI 435 (1443)
Q Consensus 358 t~~Ni~~l~~~~~~~~~~~--g~~~i~~~g~~~~~~~~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v~p~ 435 (1443)
+.+|.. ..+..+ +|... + ......++.|+|||+|||+|||||||||||+|||||+++++++
T Consensus 411 ----i~~Li~---~~~~~~~~~Ak~~------i----~~~~~~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~L~~g 473 (663)
T CHL00018 411 ----IRGLIR---QHLASNIRAAKSK------I----REKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEG 473 (663)
T ss_pred ----HHHHHh---cCccccHHHHHHH------H----HhcCCcccEeeeehhcCceeeecCCCcccccccceeeEEecCC
Confidence 333321 111110 01100 0 1123457899999999999999999999999999999988876
Q ss_pred CceEEecccCCCCCCCCCCCCceeeecCCChhHHHHHHHHcCccCCcccCCCCCcccccchhHHHHHHhhccCcc
Q 000525 436 SSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDSV 510 (1443)
Q Consensus 436 ~~t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraEa~~Lm~~~~~~~sp~~g~pl~gl~QD~l~g~~llt~~d~ 510 (1443)
+||||||+||+||||||||||||+|+|||++|||||+.||.+.+|++||++|+|+++++||+++|+|+||.+|.
T Consensus 474 -ktIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~ 547 (663)
T CHL00018 474 -RAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNR 547 (663)
T ss_pred -CeEEeCcccCCcccCCccCcEEEEecCCCHHHHHHHHHHhcCccceeEcCCCceeEeechhhhhhhheecccCC
Confidence 59999999999999999999999999999999999999999999999999999999999999999999998764
No 17
>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=1.3e-71 Score=649.38 Aligned_cols=345 Identities=48% Similarity=0.790 Sum_probs=293.1
Q ss_pred CceeccccccchhHHHHhccccccccccccccccchhhhccCCCCCCCccEeeeehhhhccccccCc--hhhHHHHHhhh
Q 000525 870 DQPVGSLSACAISEAAYSALDQPISLLETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGF--EYGALEVKNHL 947 (1443)
Q Consensus 870 ge~VG~~aAqSi~Ep~tq~l~~~~~~l~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~--e~~a~~Vk~~L 947 (1443)
|||||++||||||||||||+..+......++||||||+|+++++.++.+|++++||....++....+ +++|++|+++|
T Consensus 1 GE~VG~LAAqSIgEPAtQmtLntfh~agvs~vprLKEiLn~~~~~~~ktps~~v~L~~~~~~~~~~~~~~~~a~~Vq~~L 80 (381)
T cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESSPLELLKEVLECRSKSKSKENDRRVILSLHLCKCDHGFEYERAALEVKNHL 80 (381)
T ss_pred CCcchhHHHhhhcchHHHhhhccchhcCCccHHHHHHHhcccccCCCCCCCEEEEEeccccccccchHHHHHHHHHHHHh
Confidence 8999999999999999999866655555578999999999966555556777777766444444433 44899999999
Q ss_pred cccchhhhhceEEEEEcCCCC---------------------------cccccCceEEEEEeeHHHHHHcCCCHHHHHHH
Q 000525 948 ECLMLSDIVSTSMIIYSPQTG---------------------------SMKHFSPWICHFHVRKEIMKRTGLKEHSIIDS 1000 (1443)
Q Consensus 948 E~~tL~di~~~i~i~y~P~~~---------------------------~~~~~sp~v~~~~Ldke~l~~~~L~i~~I~~~ 1000 (1443)
|+++|++++.+++|.|+|+.. ...++|||++||++|++.
T Consensus 81 e~~tL~~v~~~~~I~Ydp~~~~t~i~~d~~~~~~~~~~~~~~~~~~~~~~~~~spw~~r~~l~~~~-------------- 146 (381)
T cd02737 81 ERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKKAIFSTSLKITKFSPWVCHFHLDKEC-------------- 146 (381)
T ss_pred hhccHHHhhheEEEEECCCcccccccccHHHHHhhhhhhhhcccccccccccCCcceEEEEEehhH--------------
Confidence 999999999999999999832 113567899999999880
Q ss_pred HHHhhhhhhhhhcccCCceeeecCccccccccccCCCceEEEEEee-cccccchhhHHHHHHHhccccccceeeccccce
Q 000525 1001 LYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMIV-ENFKRTSIDLETIQMWVMPFLLKTVVKGFREIK 1079 (1443)
Q Consensus 1001 i~~~~~~~~~~l~~~~~~i~i~~~~c~~~~~~~~~~~~~~i~v~~~-~~~~~~~~~l~~l~~~iip~ll~~vVkG~~~I~ 1079 (1443)
.. .++..||.+... ..+.+....++.+++.++|.||+++|||+|+|+
T Consensus 147 ---~~-----------------------------~~~~~ci~~~~~~~~~~~~~~~~~~~~~~i~~~lL~~~lkG~~~I~ 194 (381)
T cd02737 147 ---QK-----------------------------LSDGPCLTFSVSKEVSKSSEELLDVLRDRIIPFLLETVIKGDERIK 194 (381)
T ss_pred ---hc-----------------------------CCCCceEEeecCcccccchhHHHHHHHHHHHHHHhheeecccCCee
Confidence 00 012234443321 112233356677888899999999999999999
Q ss_pred EEEEeeccccccc---CCCCCCCceEEEEEeecccccc--chhHHHHhhhhccccccccccccCCCcHHHHHHHHcHHHH
Q 000525 1080 KVDILWKDKQKAS---KSHDDSFGELYLRVSMSGQCHI--TSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAG 1154 (1443)
Q Consensus 1080 rv~I~~~d~~~~~---~~~~~~~~el~l~~~gs~~~~~--~~~~~vll~~~l~~~~~id~~rt~sn~I~ei~~~lGIEAa 1154 (1443)
+|+|.|++.++.. ..+....+||+|+|+++..++. |..|+.+|++|++++++|||+|++||||++|+++||||||
T Consensus 195 kv~i~~~~~~~~~~~~~~~~~~~~E~vLe~~~~~~~~~t~G~~~~~vl~~c~~~~~~ID~~rt~sNdI~ev~~~lGIEAA 274 (381)
T cd02737 195 SVNILWEDSPSTSWVKSVGKSSRGELVLEVTVEESCKKTRGNAWNVVMDACIPVMDLIDWERSMPYSIQQIKSVLGIDAA 274 (381)
T ss_pred EEEEEecCCCcccccccccccccceEEEEEEeccccccccchhHHHHHHhhhcccccCcCCCcEECCHHHHHHHHhHHHH
Confidence 9999997765433 3345567899999999987776 9999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhcccCCccCHHHHHHHHhhccceeeEeecchhhhhhhhccCCCcchhhhccccccHHHHHHHHhhCCCc
Q 000525 1155 LQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVD 1234 (1443)
Q Consensus 1155 r~~ii~el~~~~~~~G~~V~~rHl~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D 1234 (1443)
|++|++||++||+.||++||+|||+||||+||++|++.||||+||+++++|++++|||++||||+|+++|++||.+|+.|
T Consensus 275 R~~ii~El~~v~~~~G~~Vd~rHL~LlAD~MT~~G~~~~~nR~Gi~~~~~s~~~~spl~~asFE~t~~~l~~AA~~g~~D 354 (381)
T cd02737 275 FEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRSLKISAPFTEACFSSPIKCFLKAAKKGASD 354 (381)
T ss_pred HHHHHHHHHHHHHhcCCcccHHHHHHHHHHhccCCceEEecchhhhhcccccccCCHHHHhhHHHHHHHHHHHHhccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccceeccCCCCCccCccc-eEEEE
Q 000525 1235 NLQGSVDALGWGKVPSVGTGGH-FDIIY 1261 (1443)
Q Consensus 1235 ~l~gvs~~ii~Gk~~~~GTgg~-f~ll~ 1261 (1443)
+|.|||++|+||+++|+|| |. |||+|
T Consensus 355 ~l~gvs~~ii~G~~~~vGT-G~~fdll~ 381 (381)
T cd02737 355 SLSGVLDACAWGKEAPVGT-GSKFEILW 381 (381)
T ss_pred CCCChHHheeeCCcCCCcC-CcceeeeC
Confidence 9999999999999999999 65 99987
No 18
>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=2.9e-64 Score=593.65 Aligned_cols=354 Identities=21% Similarity=0.336 Sum_probs=287.1
Q ss_pred CCcccCCceeccccccchhHHHHhcc---cccccc---ccccccccchhhhccCCCCCCCccEeeeehhhhccccccCch
Q 000525 864 PTGEIGDQPVGSLSACAISEAAYSAL---DQPISL---LETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFE 937 (1443)
Q Consensus 864 ~~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~~---l~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e 937 (1443)
.+.+.|||+||++||||||||+|||| +|.+++ +.|+|+|||+||+|++++++ +|.|++||.+.++ .++
T Consensus 21 ~~~~~~ge~vg~~aaQSiGEP~TQmTLnTFH~AGVas~NVTlGVPRLkEIInasK~ik--TP~~tv~L~~~~~----~d~ 94 (410)
T cd02584 21 RSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIK--TPSLTVYLEPGFA----KDE 94 (410)
T ss_pred HhhcCCCCCcchhhhhhcCCchhcccccccccccccccccccCccchHHHhhcccCCC--CCeEEEEecCccc----chH
Confidence 34678999999999999999999996 777664 67899999999999998655 6799999987653 245
Q ss_pred hhHHHHHhhhcccchhhhhceEEEEEcCCCCc----------------------ccccCceEEEEEeeHHHHHHcCCCHH
Q 000525 938 YGALEVKNHLECLMLSDIVSTSMIIYSPQTGS----------------------MKHFSPWICHFHVRKEIMKRTGLKEH 995 (1443)
Q Consensus 938 ~~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~----------------------~~~~sp~v~~~~Ldke~l~~~~L~i~ 995 (1443)
+.|+.|+.+||+++|++++.++++.|+|+.++ ...++||+++++||++.|.+++++++
T Consensus 95 ~~A~~v~~~IE~t~l~dv~~~~~i~ydp~~~~~~i~~d~~~i~~~~~~~d~~~~~~~~~~~~lrl~ld~~~~~~~~i~~~ 174 (410)
T cd02584 95 EKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEQDRLSPWLLRIELDRKKMTDKKLSME 174 (410)
T ss_pred HHHHHHHhheeEeEHHHhhhheEEEecCcccceeecccHHHHHHhhccCcccccccccCCeeEEEEECHHHHHHcCCCHH
Confidence 68999999999999999999999999998652 12457999999999999999999999
Q ss_pred HHHHHHHHhhhhhhhhhcccCCceeeecCccccccccccCCCceEEEEEeecccc------cchhhHHHHHHHhcccccc
Q 000525 996 SIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMIVENFK------RTSIDLETIQMWVMPFLLK 1069 (1443)
Q Consensus 996 ~I~~~i~~~~~~~~~~l~~~~~~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~------~~~~~l~~l~~~iip~ll~ 1069 (1443)
.|+.++...+. .++.+..++ ++ .+...+++.+..... .....+..+.+ ..|.+
T Consensus 175 ~i~~~i~~~~~----------~~~~v~~~~-----~~---~~~~~iri~~~~~~~~~~~~~~~~~~l~~~~~---~~l~~ 233 (410)
T cd02584 175 QIAKKIKEEFK----------DDLNVIFSD-----DN---AEKLVIRIRIINDDEEKEEDSEDDVFLKKIES---NMLSD 233 (410)
T ss_pred HHHHHHHHhcC----------CCeEEEEcC-----CC---cceeEEEEEecCccccccccchhHHHHHHHHH---hhCCC
Confidence 98888765431 123332221 10 122344443322110 11122333322 24559
Q ss_pred ceeeccccceEEEEeecccccccC--CCCCCCceEEEEEeeccccccchhHHHHhhhhccccccccccccCCCcHHHHHH
Q 000525 1070 TVVKGFREIKKVDILWKDKQKASK--SHDDSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCL 1147 (1443)
Q Consensus 1070 ~vVkG~~~I~rv~I~~~d~~~~~~--~~~~~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt~sn~I~ei~~ 1147 (1443)
++|+|+|+|+||+|...+..+... ......++|+|+|+|++ |.++|. +++|||+||+||||+||++
T Consensus 234 i~l~Gi~~I~r~~i~~~~~~~~~~~~g~~~~~~~~~l~teG~n-----------l~~v~~-~~~Vd~~rt~sNdI~ei~~ 301 (410)
T cd02584 234 MTLKGIEGIRKVFIREENKKKVDIETGEFKKREEWVLETDGVN-----------LREVLS-HPGVDPTRTTSNDIVEIFE 301 (410)
T ss_pred cEEeCCCCceEEEEEcCCceEecCCCCcccCCcceEEEecCcC-----------HHHHhC-CCCCccccCEeCCHHHHHH
Confidence 999999999999998432211111 11123458999999987 677777 8999999999999999999
Q ss_pred HHcHHHHHHHHHHHHHHHhcccCCccCHHHHHHHHhhccceeeEeecchhhhhhhhccCCCcchhhhccccccHHHHHHH
Q 000525 1148 AYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKA 1227 (1443)
Q Consensus 1148 ~lGIEAar~~ii~el~~~~~~~G~~V~~rHl~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asFe~t~~~l~~A 1227 (1443)
+|||||||++|++||++||+.||++||+|||+||||+||++|++.||||+|+++++. |||++||||+|+++|++|
T Consensus 302 ~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~-----S~l~~aSFE~t~~~L~~A 376 (410)
T cd02584 302 VLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDT-----GPLMRCSFEETVDILLEA 376 (410)
T ss_pred hcCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhhceEEeeEeeeeeeccCC-----ChhhhccchhHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999987765 999999999999999999
Q ss_pred HhhCCCcCCCCccceeccCCCCCccCccceEEEEc
Q 000525 1228 AKAGAVDNLQGSVDALGWGKVPSVGTGGHFDIIYS 1262 (1443)
Q Consensus 1228 A~~g~~D~l~gvs~~ii~Gk~~~~GTgg~f~ll~~ 1262 (1443)
|.+|+.|+|.||||||+||+++|+|| |+|+|+++
T Consensus 377 A~~g~~D~l~gvse~Ii~G~~~~~GT-G~f~l~~d 410 (410)
T cd02584 377 AAFGETDDLKGVSENIMLGQLAPIGT-GCFDLLLD 410 (410)
T ss_pred HhcCCCCcCCCchHheeecCcccccc-ceEEEEeC
Confidence 99999999999999999999999999 99999975
No 19
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=1.2e-64 Score=588.33 Aligned_cols=324 Identities=20% Similarity=0.275 Sum_probs=276.0
Q ss_pred CCcccCCceeccccccchhHHHHhcc---cccccc---ccccccccchhhhccCCCCCCCccEeeeehhhhccccccCch
Q 000525 864 PTGEIGDQPVGSLSACAISEAAYSAL---DQPISL---LETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFE 937 (1443)
Q Consensus 864 ~~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~~---l~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e 937 (1443)
.+.+.|||+||++||||||||+|||| +|++++ +.|+|+|||+||+|++++++ +|.|++||.+...+ ++
T Consensus 38 ~alv~PGeaVG~IAAQSIGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEIINa~k~i~--TP~~ti~L~~~~~~----~~ 111 (367)
T TIGR02389 38 RSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPS--TPSMTIYLEDEYEK----DR 111 (367)
T ss_pred HhcCCCccccchhhhhhcCCccccccccccccccccccCccccchhHHHHhhcccCCC--CCeEEEEecCcchh----hH
Confidence 45789999999999999999999996 777764 67899999999999998655 57899999876532 34
Q ss_pred hhHHHHHhhhcccchhhhhceEEEEEcCCCCcccccCceEEEEEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCC
Q 000525 938 YGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVP 1017 (1443)
Q Consensus 938 ~~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~ 1017 (1443)
..|+.|+.+||+++|+|++.++++.| ++|+++++||++.|+.+++++++|.+++.+... .+
T Consensus 112 ~~a~~v~~~iE~t~l~dv~~~~~~~~----------~~~~l~i~ld~~~l~~~~i~~~~i~~~i~~~~~-----~~---- 172 (367)
T TIGR02389 112 EKAEEVAKKIEATKLEDVAKDISIDL----------ADMTVIIELDEEQLKERGITVDDVEKAIKKAKL-----GK---- 172 (367)
T ss_pred HHHHHHHHHhhheeHHHHHhhhheec----------cCcEEEEEECHHHHHhcCCCHHHHHHHHHHhcc-----cc----
Confidence 68999999999999999999988876 247899999999999999999999998886531 00
Q ss_pred ceeeecCccccccccccCCCceEEEEEeecccccchhhHHHHHHHhccccccceeeccccceEEEEeecccccccCCCCC
Q 000525 1018 DMLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDD 1097 (1443)
Q Consensus 1018 ~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~~~~~~l~~l~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~ 1097 (1443)
..+.+. +...+.+.+.. +....|+.+++ .+++++|+|+|||+||+|..
T Consensus 173 -~~~~~~------------~~~~i~i~~~~---~~~~~l~~l~~----~l~~~~v~Gi~gI~r~~i~~------------ 220 (367)
T TIGR02389 173 -VIEIDM------------DGNTITIKPPK---PSLKELRKLKE----KIKNLHIKGIKGIKRVVIRK------------ 220 (367)
T ss_pred -cceeec------------CCCEEEEEecC---chHHHHHHHHH----HhhhceEeCCCCceEEEEEC------------
Confidence 111010 12234443322 33456777776 56699999999999999872
Q ss_pred CCceEEEEEeeccccccchhHHHHhhhhccccccccccccCCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHH
Q 000525 1098 SFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEH 1177 (1443)
Q Consensus 1098 ~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rH 1177 (1443)
.++||+|.|+|++ || +++. +++|||+||+||||+||+++|||||||++|++||++||+.||++||+||
T Consensus 221 ~~~~~~l~teG~n------l~-----~v~~-~~~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RH 288 (367)
T TIGR02389 221 EGDEYVIYTEGSN------LK-----EVLK-LEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRH 288 (367)
T ss_pred CCCeEEEEEeccC------HH-----HHHc-CCCCccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCeecHHH
Confidence 2358999999886 44 4455 8999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccceeeEeecchhhhhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccce
Q 000525 1178 LLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHF 1257 (1443)
Q Consensus 1178 l~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~f 1257 (1443)
|+||||+||++|++.||||+|+++++. |||++||||+|+++|++||.+|+.|+|.||||||+||+++|+|| |.|
T Consensus 289 l~LiaD~MT~~G~~~~i~R~Gi~~~~~-----S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GT-G~~ 362 (367)
T TIGR02389 289 LMLVADLMTWDGEVRQIGRHGISGEKA-----SVLARAAFEVTVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGT-GDV 362 (367)
T ss_pred HHHHHHHhcCCceEEeccccccccCCC-----CHHHhcChHhHHHHHHHHhhcCCCCcCCChHHHhhcCCCcCCcC-CeE
Confidence 999999999999999999999987655 99999999999999999999999999999999999999999999 999
Q ss_pred EEEEc
Q 000525 1258 DIIYS 1262 (1443)
Q Consensus 1258 ~ll~~ 1262 (1443)
+|+++
T Consensus 363 ~l~~~ 367 (367)
T TIGR02389 363 DLVMD 367 (367)
T ss_pred EEeeC
Confidence 99974
No 20
>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=8.5e-64 Score=582.42 Aligned_cols=323 Identities=20% Similarity=0.276 Sum_probs=276.1
Q ss_pred CCcccCCceeccccccchhHHHHhcc---cccccc---ccccccccchhhhccCCCCCCCccEeeeehhhhccccccCch
Q 000525 864 PTGEIGDQPVGSLSACAISEAAYSAL---DQPISL---LETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFE 937 (1443)
Q Consensus 864 ~~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~~---l~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e 937 (1443)
.+.+.|||+||++||||||||+|||| +|++++ +.|+|+|||+||+|++++++ +|.|++||.+.+++ ++
T Consensus 34 ~~~~~~Ge~vG~iaAQSiGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEIIna~K~i~--TP~mti~L~~~~~~----~~ 107 (363)
T cd06528 34 RSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKEPS--TPTMTIYLEEEYKY----DR 107 (363)
T ss_pred HHhhccCccccceeeeecCccceecccccccccccccccCccccccHHHHhhcccCCC--CceEEEEecCcchh----hH
Confidence 34678999999999999999999996 788775 56899999999999999665 68999999876542 34
Q ss_pred hhHHHHHhhhcccchhhhhceEEEEEcCCCCcccccCceEEEEEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCC
Q 000525 938 YGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVP 1017 (1443)
Q Consensus 938 ~~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~ 1017 (1443)
+.|+.|+.+||+++|+|++.++++.++ .|.++++||++.|++++|++++|++++.+.++. +
T Consensus 108 ~~a~~v~~~iE~t~l~di~~~~~i~~~----------~~~l~i~ld~~~l~~~~l~~~~i~~~i~~~~~~-----~---- 168 (363)
T cd06528 108 EKAEEVARKIEETTLENLAEDISIDLF----------NMRITIELDEEMLEDRGITVDDVLKAIEKLKKG-----K---- 168 (363)
T ss_pred HHHHHHHHhhceeEHHHhhhheEEecc----------CcEEEEEECHHHHHHcCCCHHHHHHHHHHhcCC-----c----
Confidence 689999999999999999999998642 488999999999999999999999998876421 1
Q ss_pred ceeeecCccccccccccCCCceEEEEEeecccccchhhHHHHHHHhccccccceeeccccceEEEEeecccccccCCCCC
Q 000525 1018 DMLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDD 1097 (1443)
Q Consensus 1018 ~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~~~~~~l~~l~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~ 1097 (1443)
+.+. ++. .+.+. ....+....|+.+++ .|++++|+|+|+|+||+|..
T Consensus 169 -~~~~-------------~~~-~~~~~--~~~~~~~~~l~~l~~----~l~~~~v~Gi~gI~r~~i~~------------ 215 (363)
T cd06528 169 -VGEE-------------GDV-TLIVL--KAEEPSIKELRKLAE----KILNTKIKGIKGIKRVIVRK------------ 215 (363)
T ss_pred -cccc-------------CCc-cEEEE--cCCcchHHHHHHHHH----hhcccEEeCCCCceEEEEec------------
Confidence 1110 010 11111 112344567777776 67799999999999999873
Q ss_pred CCceEEEEEeeccccccchhHHHHhhhhccccccccccccCCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHH
Q 000525 1098 SFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEH 1177 (1443)
Q Consensus 1098 ~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rH 1177 (1443)
.++||+|+|+|++ ||.+ +. +++|||+|++||||+||+++|||||||++|++||++||+.||++||+||
T Consensus 216 ~~~~~~l~teG~n------l~~v-----~~-~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rH 283 (363)
T cd06528 216 EEDEYVIYTEGSN------LKAV-----LK-VEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRH 283 (363)
T ss_pred CCceEEEEecCcC------HHHH-----hc-CCCCcccccccCCHHHHHHhCCHHHHHHHHHHHHHHHHHhcCCeecHHH
Confidence 1248999999876 5554 55 8999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccceeeEeecchhhhhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccce
Q 000525 1178 LLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHF 1257 (1443)
Q Consensus 1178 l~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~f 1257 (1443)
|+||||+||++|++.|+||+|+.+++. |||++||||+|+++|++||.+|+.|+|.||+|||+||+++|+|| |.|
T Consensus 284 l~LiaD~MT~~G~~~~i~R~gi~~~~~-----S~L~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GT-G~~ 357 (363)
T cd06528 284 IMLVADIMTYDGEVRQIGRHGIAGEKP-----SVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGT-GDV 357 (363)
T ss_pred HHHHHHHhccCCceecccchhhcCCCC-----ChhhhCchhhHHHHHHHHHhcCCCCcCCCcHHHeeeCCCCCCcC-Cee
Confidence 999999999999999999999987554 99999999999999999999999999999999999999999999 999
Q ss_pred EEEEc
Q 000525 1258 DIIYS 1262 (1443)
Q Consensus 1258 ~ll~~ 1262 (1443)
+|+++
T Consensus 358 ~l~~d 362 (363)
T cd06528 358 ELTMD 362 (363)
T ss_pred EEEec
Confidence 99986
No 21
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=100.00 E-value=7.9e-63 Score=577.96 Aligned_cols=359 Identities=18% Similarity=0.230 Sum_probs=292.8
Q ss_pred chHHHHHHHhheEeeecceEEccCCceEEEEEeccCCCCCCCcccCCceeccccccchhHHHHhcc---cccccc---cc
Q 000525 824 LTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGTSTPTGEIGDQPVGSLSACAISEAAYSAL---DQPISL---LE 897 (1443)
Q Consensus 824 LqRrLvk~lEdl~v~YD~tVR~s~G~~iiq~~yg~~g~~~~~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~~---l~ 897 (1443)
|..+|.+-+++-...|.-|-.. .. .++..+...+ ..+.+.|||+||++||||||||+|||+ +|.+++ +.
T Consensus 18 ~~~~~~~~~~~~~~~~~l~~~~-~~-~~~~~i~~~y---~~~~v~pGe~VG~iaAQsIGEP~TQMTL~TFH~AGva~~nV 92 (383)
T PRK04309 18 LPQKLKEELREKLEERKLTEEE-VE-EIIEEVVREY---LRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINV 92 (383)
T ss_pred CCHHHHHHHHHHHHHcCCCHHH-HH-HHHHHHHHHH---HHhhcCCCCccchhhhhhccchhhhcccccccccCccccCc
Confidence 5666666666655555433221 11 2334344444 255689999999999999999999996 777764 67
Q ss_pred ccccccchhhhccCCCCCCCccEeeeehhhhccccccCchhhHHHHHhhhcccchhhhhceEEEEEcCCCCcccccCceE
Q 000525 898 TSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWI 977 (1443)
Q Consensus 898 t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e~~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp~v 977 (1443)
|+|+|||+||+|++++++ +|.|+++|.++++ .+++.|+.|+.+||+++|++++.++++.++ .++
T Consensus 93 TlGvPRlkEIina~K~~~--TP~~tv~L~~~~~----~d~~~a~~v~~~iE~t~L~~v~~~i~~~~~----------~~~ 156 (383)
T PRK04309 93 TLGLPRLIEIVDARKEPS--TPMMTIYLKDEYA----YDREKAEEVARKIEATTLENLAKDISVDLA----------NMT 156 (383)
T ss_pred ccCchhHHHHHhcccCCC--CCeEEEEecCccc----ccHHHHHHHHhheeeeEHhhhhhheEeccC----------CcE
Confidence 899999999999998554 6899999987653 235689999999999999999999887542 267
Q ss_pred EEEEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCCceeeecCccccccccccCCCceEEEEEeecccccchhhHH
Q 000525 978 CHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSIDLE 1057 (1443)
Q Consensus 978 ~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~~~~~~l~ 1057 (1443)
++++||++.|.+++|+++.|.+++.+... . .+.+. ++ +|.+.+.. .....|.
T Consensus 157 l~i~ld~~~i~~~~l~~~~I~~~i~~~~~-----~-----~~~~~-------------~~--~i~i~~~~---~~~~~l~ 208 (383)
T PRK04309 157 IIIELDEEMLEDRGLTVDDVKEAIEKKKG-----G-----EVEIE-------------GN--TLIISPKE---PSYRELR 208 (383)
T ss_pred EEEEECHHHHHHcCCCHHHHHHHHHHhcC-----c-----ceecc-------------CC--eEEEEecC---chHHHHH
Confidence 89999999999999999999999886541 1 11110 12 33343321 2345566
Q ss_pred HHHHHhccccccceeeccccceEEEEeecccccccCCCCCCCceEEEEEeeccccccchhHHHHhhhhcccccccccccc
Q 000525 1058 TIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRS 1137 (1443)
Q Consensus 1058 ~l~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt 1137 (1443)
.+++ .|++++|||+|+|+|++|.+ .+++|+|+|+|++ ||. ++. +++|||+||
T Consensus 209 ~l~~----~l~~~~vkGi~gI~r~~i~~------------~~~~~~l~teG~n------l~~-----v~~-~~~VD~~rt 260 (383)
T PRK04309 209 KLAE----KIRNIKIKGIKGIKRVIIRK------------EGDEYVIYTEGSN------LKE-----VLK-VEGVDATRT 260 (383)
T ss_pred HHHH----HhcccEEECCCCceEEEEec------------CCCeEEEEEcccC------HHH-----Hhc-CCCEeeccc
Confidence 6554 67799999999999999874 2358999999876 444 455 799999999
Q ss_pred CCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHHHHHHHhhccceeeEeecchhhhhhhhccCCCcchhhhccc
Q 000525 1138 HPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFF 1217 (1443)
Q Consensus 1138 ~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rHl~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asF 1217 (1443)
+||||++|+++|||||||.+|++||++||+.||++||+|||+||||+||++|++.|+||+|+.+++. |||++|||
T Consensus 261 ~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~R~Gi~~~~~-----S~l~~aSF 335 (383)
T PRK04309 261 TTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKA-----SVLARAAF 335 (383)
T ss_pred cCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhccCceEEeeechhhcCCCC-----CHHHhCch
Confidence 9999999999999999999999999999999999999999999999999999999999999987665 99999999
Q ss_pred cccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccceEEEEccCC
Q 000525 1218 SNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHFDIIYSGEG 1265 (1443)
Q Consensus 1218 e~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~f~ll~~~~~ 1265 (1443)
|+|+++|++||.+|+.|+|.||+|||+||+++|+|| |+|+|+++...
T Consensus 336 E~T~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GT-G~~~l~~~~~~ 382 (383)
T PRK04309 336 EVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGT-GDVELTMDPPL 382 (383)
T ss_pred hhHHHHHHHHHhcCCCCCCCCcHHHhhcCCCcCCCC-ceEEEEcCCCC
Confidence 999999999999999999999999999999999999 99999998763
No 22
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=100.00 E-value=1.3e-62 Score=580.37 Aligned_cols=325 Identities=19% Similarity=0.254 Sum_probs=275.2
Q ss_pred CCcccCCceeccccccchhHHHHhcc---cccccc---ccccccccchhhhccCCCCCCCccEeeeehhhhccccccCch
Q 000525 864 PTGEIGDQPVGSLSACAISEAAYSAL---DQPISL---LETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFE 937 (1443)
Q Consensus 864 ~~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~~---l~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e 937 (1443)
.+.+.|||+||++||||||||+|||| ||++++ +.|+|+|||+||+|++++++ +|.|++||.+.++ .++
T Consensus 176 ~~~v~pGE~VG~IAAQSIGEP~TQMTLnTFH~AGVas~NVTlGVPRLkEIINa~K~is--TP~mtiyL~~~~~----~d~ 249 (509)
T PRK14897 176 RARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARKKPS--TPTMTIYLKKDYR----EDE 249 (509)
T ss_pred HhccCCCCCcchhhhhhhCCccccccccccccccccccccccCcchhHHHhhcccCCC--CceEEEEecCccc----ccH
Confidence 45788999999999999999999996 887764 67899999999999998655 6799999986653 234
Q ss_pred hhHHHHHhhhcccchhhhhceEEEEEcCCCCcccccCceEEEEEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCC
Q 000525 938 YGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVP 1017 (1443)
Q Consensus 938 ~~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~ 1017 (1443)
..|+.|+.+||+++|++++..+.. +..|.++++||++.|.+++|+++.|.+++.+..
T Consensus 250 e~A~~V~~~IE~ttL~dv~~~~~d-----------~~~~~i~i~Ld~~~l~~~~l~~~~I~~~I~~~~------------ 306 (509)
T PRK14897 250 EKVREVAKKIENTTLIDVADIITD-----------IAEMSVVVELDEEKMKERLIEYDDILAAISKLT------------ 306 (509)
T ss_pred HHHHHHHhhheeeEHHHHHHHHHH-----------hccceEEEEECHHHHHHcCCCHHHHHHHHHhcc------------
Confidence 689999999999999999974422 234779999999999999999999998887521
Q ss_pred ceeeecCccccccccccCCCceEEEEEeecccccchhhHHHHHHHhccccccceeeccccceEEEEeecccccccCCCCC
Q 000525 1018 DMLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDD 1097 (1443)
Q Consensus 1018 ~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~~~~~~l~~l~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~ 1097 (1443)
.+.+... ++ .|++.+. .+.+..|..+++ .+.+++|+|+|+|+||+|...+
T Consensus 307 ~~~~~~~-----------~~--~I~i~~~---~~~~~~L~~l~~----~l~~i~I~GipgI~r~~i~~~~---------- 356 (509)
T PRK14897 307 FKTVEID-----------DG--IIRLKPQ---QPSFKKLYLLAE----KVKSLTIKGIKGIKRAIARKEN---------- 356 (509)
T ss_pred ceEEecC-----------CC--EEEEEeC---chHHHHHHHHHH----HhhccEEeCCCCccEEEEecCC----------
Confidence 0112111 12 3444332 133456677666 4569999999999999987421
Q ss_pred CCceEEEEEeeccccccchhHHHHhhhhccccccccccccCCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHH
Q 000525 1098 SFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEH 1177 (1443)
Q Consensus 1098 ~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rH 1177 (1443)
..++|+|.|+|++ |.+++. +++|||+||+||||+||+++|||||||++|++||++||+.||++||+||
T Consensus 357 ~~~~~~L~TeG~N-----------L~~vl~-~~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RH 424 (509)
T PRK14897 357 DERRWVIYTQGSN-----------LKDVLE-IDEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRH 424 (509)
T ss_pred CCceeEEEeeccC-----------HHHHhc-CCCcccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCcccHHH
Confidence 2347999999987 677777 7999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccceeeEeecchhhhhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccce
Q 000525 1178 LLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHF 1257 (1443)
Q Consensus 1178 l~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~f 1257 (1443)
|+||||+||++|++.||||+|++.++. |||++||||+|+++|++||.+|+.|+|.||+||||||+++|+|| |.|
T Consensus 425 L~LIAD~MT~~G~v~~i~R~Gi~~~~~-----SpL~rASFE~T~~~L~~AA~~Ge~D~L~GvsenII~G~~ipvGT-G~f 498 (509)
T PRK14897 425 IMLVADMMTFDGSVKAIGRHGISGEKS-----SVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGT-GAV 498 (509)
T ss_pred HHHHHHHhCcCCcccccccccccccCC-----CHHHhcchHhHHHHHHHHhhcCCCCcCCChHHhhhcCCccCCcC-ceE
Confidence 999999999999999999999977654 99999999999999999999999999999999999999999999 999
Q ss_pred EEEEccCC
Q 000525 1258 DIIYSGEG 1265 (1443)
Q Consensus 1258 ~ll~~~~~ 1265 (1443)
+|+++.++
T Consensus 499 dL~~~~~~ 506 (509)
T PRK14897 499 SLVYKGRK 506 (509)
T ss_pred EEEecCCC
Confidence 99998764
No 23
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=100.00 E-value=5.3e-61 Score=546.02 Aligned_cols=290 Identities=22% Similarity=0.298 Sum_probs=255.1
Q ss_pred CcccCCceeccccccchhHHHHhcc---cccccc---ccccccccchhhhccCCCCCCCccEeeeehhhhccccccCchh
Q 000525 865 TGEIGDQPVGSLSACAISEAAYSAL---DQPISL---LETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFEY 938 (1443)
Q Consensus 865 ~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~~---l~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e~ 938 (1443)
+.+.|||+||++||||||||+|||+ +|.+++ +.|.|+|||+||+|++++++ +|.|++||.+. .+++
T Consensus 5 ~~v~pGe~vG~iaaQsiGEp~TQmTL~TFH~aGv~~~nvtlGvPRlkEIinasK~~~--TP~~ti~l~~~------~~~~ 76 (300)
T cd02736 5 AKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNIS--TPIITAKLEND------RDEK 76 (300)
T ss_pred hccCCCccchhhhhhhcCCccccccccccccccccccccccCchHHHHHHhcccCCC--CCeEEEEecCc------ccHH
Confidence 4678999999999999999999996 777654 56899999999999999655 57999998753 2356
Q ss_pred hHHHHHhhhcccchhhhhceEEEEEcCCCCcccccCceEEEEEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCCc
Q 000525 939 GALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVPD 1018 (1443)
Q Consensus 939 ~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~~ 1018 (1443)
.|+.|+.+||+++|+|++.++++.|+|+..+ +.+++|++.++++++..
T Consensus 77 ~a~~v~~~ie~t~l~di~~~~~~~~~p~~~~--------~~i~~d~~~i~~~~l~~------------------------ 124 (300)
T cd02736 77 SARIVKGRIEKTYLGEVASYIEEVYSPDDCY--------ILIKLDKKIIEKLQLSK------------------------ 124 (300)
T ss_pred HHHHHHHHHhhccHHHhhhheEEEEcCCCce--------EEEEecHHHHHHhcCCc------------------------
Confidence 8999999999999999999999999998754 58999999999887610
Q ss_pred eeeecCccccccccccCCCceEEEEEeecccccchhhHHHHHHHhccccccceeeccccceEEEEeecccccccCCCCCC
Q 000525 1019 MLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDDS 1098 (1443)
Q Consensus 1019 i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~~~~~~l~~l~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~~ 1098 (1443)
++..+.++.+++ .|.+++|+|+|+|+|+.|...+ .
T Consensus 125 -------------------------------~~~~~~~~~l~~----~l~~~~v~Gi~gI~r~~i~~~~----------~ 159 (300)
T cd02736 125 -------------------------------SNLYFLLQSLKR----KLPDVVVSGIPEVKRAVINKDK----------K 159 (300)
T ss_pred -------------------------------ccHHHHHHHHHH----HhccceEeCCCCceEEEEecCC----------C
Confidence 011234555555 4449999999999999987421 1
Q ss_pred CceEEEEEeeccccccchhHHHHhhhhccccccccccccCCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHHH
Q 000525 1099 FGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHL 1178 (1443)
Q Consensus 1099 ~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rHl 1178 (1443)
.++|+|.|+|++ |.+++. +++|||+|++||||++|+++|||||||++|++||++||+.||++||+|||
T Consensus 160 ~~~~~l~teG~n-----------l~~v~~-~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl 227 (300)
T cd02736 160 KGKYKLLVEGYG-----------LRAVMN-TPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHI 227 (300)
T ss_pred CCcEEEEEeccc-----------HHHHhc-CCcEeccCCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCccCHHHH
Confidence 358999999987 667777 79999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccceeeEeecchhhhhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccce
Q 000525 1179 LIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHF 1257 (1443)
Q Consensus 1179 ~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~f 1257 (1443)
+||||+||++|++.||||+|+++++. |||++||||+|+++|++||.+|+.|+|.||||||+||+++|+|| |.|
T Consensus 228 ~LiaD~MT~~G~~~~itR~gi~~~~~-----S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~ii~G~~~~~GT-G~f 300 (300)
T cd02736 228 MLLADLMTFKGEVLGITRFGIAKMKE-----SVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGT-GLF 300 (300)
T ss_pred HHHHHHHhccCceeeeecccccccCC-----CHHHhcchHhHHHHHHHHhhcCCCCcCCCcHHHeeeCCCcCCCC-CCC
Confidence 99999999999999999999998776 99999999999999999999999999999999999999999999 876
No 24
>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=8.4e-58 Score=524.08 Aligned_cols=299 Identities=22% Similarity=0.276 Sum_probs=239.1
Q ss_pred CCcccCCceeccccccchhHHHHhcc---ccccc---cccccccccchhhh-ccCCCCCCCccEeeeehhhhccccccCc
Q 000525 864 PTGEIGDQPVGSLSACAISEAAYSAL---DQPIS---LLETSPLLNLKNVL-ECGSKKSNADQTMSLFLSNKLGKRRHGF 936 (1443)
Q Consensus 864 ~~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~---~l~t~gl~rLkEIl-~~~k~~~~~~~~~~l~Ls~~~~k~~~~~ 936 (1443)
.+.+.|||+||++||||||||+|||| +|.++ .+.|+|+|||+||+ +++++++ +|.|+++|.+...
T Consensus 4 ~slv~PGE~VG~iaAQSIGEPsTQMTLnTFH~AGv~~~nVTlGvPRL~EIi~~Ask~i~--TP~m~v~l~~~~~------ 75 (309)
T cd02735 4 RSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIK--TPSMTLPLKNGKS------ 75 (309)
T ss_pred hccCCCCcccchhhhhccCCcccccccccccccCccccccccccccHHHHHhhhccCCC--CCeEEEEecCchh------
Confidence 35688999999999999999999996 77766 36789999999998 5677555 6799999876643
Q ss_pred hhhHHHHHhhhcccchhhhhceEEEEEcCCCCcccccCceEEEEEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccC
Q 000525 937 EYGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISV 1016 (1443)
Q Consensus 937 e~~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~ 1016 (1443)
...|+.|+.+||+++|+|++.++++.| |...+.+.+. +.+
T Consensus 76 ~~~a~~~~~~ie~~~l~dv~~~~~v~~---------------------------------i~~~~~~~~~---~~~---- 115 (309)
T cd02735 76 AERAETLKKRLSRVTLSDVVEKVEVTE---------------------------------ILKTIERVFK---KLL---- 115 (309)
T ss_pred HHHHHHHHhheeEeEHHHhhhhhehhH---------------------------------HHHHHHHHhh---hhh----
Confidence 236999999999999999998776643 2222322220 000
Q ss_pred CceeeecCccccccccccCCCceEEEEEeecccccchhhHHHHHHHhccccccceeeccccceEEEEeecccccccCCCC
Q 000525 1017 PDMLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHD 1096 (1443)
Q Consensus 1017 ~~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~~~~~~l~~l~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~ 1096 (1443)
.+...+.+.... ..+....+..+++ +++ +++|+|+|+|+|+.|...+.
T Consensus 116 -------------------~~~~~~~i~~~~-~~~~~~~~~~~~~-~l~---~~~i~gi~gI~r~~i~~~~~-------- 163 (309)
T cd02735 116 -------------------GKWCEVTIKLPL-SSPKLLLLSIVEK-LAR---KAVIREIPGITRCFVVEEDK-------- 163 (309)
T ss_pred -------------------CCEEEEEEEecC-CchhHHHHHHHHH-Hhc---ccEEeCCCCccEEEEecCcC--------
Confidence 011122222211 1122223333333 444 99999999999999875321
Q ss_pred CCCceEEEEEeeccccccchhHHHHhhhhccccccccccccCCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHH
Q 000525 1097 DSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPE 1176 (1443)
Q Consensus 1097 ~~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~r 1176 (1443)
....+|++.|+|++ +.+++.+.++|||+|++||||++|+++|||||||++|++||++||+.||++||+|
T Consensus 164 ~~~~~~~l~teG~n-----------l~~v~~~~~~vd~~r~~sNdi~ei~~~lGIEAar~~ii~Ei~~v~~~~Gi~V~~r 232 (309)
T cd02735 164 GGKTKYLVITEGVN-----------LAALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPR 232 (309)
T ss_pred CCceEEEEEecccc-----------HHHHHhccCccccccceeCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCeeCHH
Confidence 12347899999887 5666774599999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhccceeeEeecchhhhhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccc
Q 000525 1177 HLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGH 1256 (1443)
Q Consensus 1177 Hl~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~ 1256 (1443)
||+||||+||++|++.++||+|+ +.. .|||++||||+|.++|++||.+|+.|+|.||+|||+||+++|+|| |.
T Consensus 233 Hl~LiaD~MT~~G~~~~~nr~gi-~~~-----~S~l~~asFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GT-G~ 305 (309)
T cd02735 233 HLSLIADYMTFEGGYRPFNRIGM-ESS-----TSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGT-GL 305 (309)
T ss_pred HHHHHHHHHHhCCcEeecchhhe-ccC-----CCHHHhhhhhhHHHHHHHHhhcCCCCCCCChHHheeeCCccCccc-ee
Confidence 99999999999999999999999 433 599999999999999999999999999999999999999999999 99
Q ss_pred eEEE
Q 000525 1257 FDII 1260 (1443)
Q Consensus 1257 f~ll 1260 (1443)
|||+
T Consensus 306 fdll 309 (309)
T cd02735 306 FDLL 309 (309)
T ss_pred EEeC
Confidence 9985
No 25
>PF00623 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; InterPro: IPR000722 RNA polymerases catalyse the DNA dependent polymerisation of RNA from DNA, using the four ribonucleoside triphosphates as substrates. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Eukaryotic RNA polymerase I is essentially used to transcribe ribosomal RNA units, polymerase II is used for mRNA precursors, and III is used to transcribe 5S and tRNA genes. Each class of RNA polymerase is assembled from nine to fourteen different polypeptides. Members of the family include the largest subunit from eukaryotes; the gamma subunit from Cyanobacteria; the beta' subunit from bacteria; the A' subunit from archaea; and the B'' subunit from chloroplast RNA polymerases.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 2PMZ_Q 3HKZ_I 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N ....
Probab=100.00 E-value=4e-57 Score=475.34 Aligned_cols=159 Identities=43% Similarity=0.716 Sum_probs=138.2
Q ss_pred CCCCCCCCceeEeCCCCCccccccccHHHHhhcCcceeechhhHHHhhhhh-cccccccCcceEee-CCeEEEecc----
Q 000525 319 GKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCI-SFRLLEKGELYVCR-KGGLVRIRR---- 392 (1443)
Q Consensus 319 GKRv~~s~RsVI~pdp~l~~~evgvP~~~a~~Lt~pe~Vt~~Ni~~l~~~~-~~~~~~~g~~~i~~-~g~~~~~~~---- 392 (1443)
||||||||||||||||+|+++|||||.+||++||+||.||+||+++|++++ +.....+|+++++. +|+.+.++.
T Consensus 1 GKRVnfSaRSVItpDP~L~~~EvGiP~~iA~~Lt~Pe~Vt~~N~~~l~~~v~ng~~~~pga~~i~~~~~~~~~l~~~~~~ 80 (166)
T PF00623_consen 1 GKRVNFSARSVITPDPNLKIDEVGIPIEIAKKLTFPERVTPFNIEKLRKLVINGPDKYPGANYIKRSNGNKISLRYKKFK 80 (166)
T ss_dssp CEEESSEEEEEEEEETTSCTTEEEEEHHHHHHCECCHHHHTTTHHHHHHHHHHTTTSSSSEEEEESTTCHCCCTTSSSSC
T ss_pred CCCcccCCCcEEECCCCCccceecccHHHHhhCCCcEEEHHHHHHHHHHHHhcCcccchhhhhhhcccCcceeeeecccc
Confidence 999999999999999999999999999999999999999999999999975 45567889988764 455555543
Q ss_pred -cccccCCCEEeceeccCceEEEeCCCCCCccccccccEEEecCCceEEecccCCCCCCCCCCCCceeeecCCChhHHHH
Q 000525 393 -IDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVE 471 (1443)
Q Consensus 393 -~~~l~~g~iV~Rhl~dgD~vl~NRqPsLHk~Simah~v~v~p~~~t~r~n~~~c~pyNADFDGDeMN~h~PQs~~AraE 471 (1443)
...|+.|++|+||+.|||+|||||||||||+|||||+++++++ +||||||++|+||||||||||||+|+|||++|+||
T Consensus 81 ~~~~l~~~~~v~r~l~~gd~vl~nRqPtLh~~s~~a~~~~~~~~-~t~~~~~~~c~~~NADFDGDem~i~~p~~~~a~~E 159 (166)
T PF00623_consen 81 ISKKLRIGDIVERHLCDGDIVLLNRQPTLHRMSIMAHKVRVLPG-KTIRINPLVCSPFNADFDGDEMNIHLPQSYEARAE 159 (166)
T ss_dssp CCHHHHTT-EEEEEHTTT-EEEEEESS-SSGGGEEEEEEEEESS-SSEEEEGGGHHHHT--TSS-EEEEE--SSHHHHHH
T ss_pred ccceecchhhHHHhhhcCceeEEeccchhccceeeeeeeeeecc-cEEEeeccchhhhhccCCcceEEEEecCCHHHHHH
Confidence 2468899999999999999999999999999999999999997 69999999999999999999999999999999999
Q ss_pred HHHHcCc
Q 000525 472 LTELVAL 478 (1443)
Q Consensus 472 a~~Lm~~ 478 (1443)
|.+||+|
T Consensus 160 ~~~L~~~ 166 (166)
T PF00623_consen 160 AKELMNV 166 (166)
T ss_dssp HHHHCBT
T ss_pred HHHHhcC
Confidence 9999986
No 26
>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=7.2e-51 Score=518.07 Aligned_cols=199 Identities=19% Similarity=0.234 Sum_probs=149.6
Q ss_pred cCcccccCCCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCccccccccchHHHHHHHHHhhHHHHHhhh
Q 000525 576 EGSSWLRDYEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTC 654 (1443)
Q Consensus 576 ~~k~~lg~~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~~~~~~~~~~~~~~~~i~~~~~~a~~~~ 654 (1443)
++|+.+ ++|++.++++||.+ |+.|||.+++|+++|++.+|||+|++|+.++++ ++++++ +|++.+
T Consensus 7 idKk~l----~~LI~~~~~~yG~~~t~~~lD~lk~Lgf~~aT~~G~SigidDl~ip~~---K~~li~-------~a~~~v 72 (1227)
T TIGR02388 7 VDKKAL----KNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPA---KQDLLE-------AAEKEI 72 (1227)
T ss_pred cchHHH----HHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcCeEEeeccCCCCHH---HHHHHH-------HHHHHH
Confidence 355555 47999999999996 899999999999999999999999999999864 344443 343332
Q ss_pred hhhhhHHHhHHhhhhccCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---CCCCCcceeeeccC
Q 000525 655 NFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKY---GSKDNSLLAMFKAG 731 (1443)
Q Consensus 655 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~~~~~~~~~~---~~~~N~~~~M~~sG 731 (1443)
. . ....|..|.+... + .++ ..++.|.+..+++.+.+.++ .++.|++++|+.||
T Consensus 73 ~--~----~~~~y~~G~it~~-------E--r~~---------~ii~~w~~t~e~~~~~~~~~~~~~d~~N~v~mMa~SG 128 (1227)
T TIGR02388 73 R--A----TEERYRRGEITEV-------E--RFQ---------KVIDTWNGTNEELKDEVVNNFRQTDPLNSVYMMAFSG 128 (1227)
T ss_pred H--H----HHHHHHcCCCcch-------h--hHH---------HHHHHHHHHHHHHHHHHHHhhhhcCCCCcHHHHhhcc
Confidence 1 1 1122334433210 1 111 22345666666665555544 56899999999999
Q ss_pred CccchhhHhHhhhcccccccCCCCccccCccccccccccCCCCCCccccCCccccccccccccCCCChhhHHHhcccCCC
Q 000525 732 SKGNLLKLVQHSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRD 811 (1443)
Q Consensus 732 SKGS~~Nl~Qi~~~lGqQ~~~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m~gRe 811 (1443)
||||+.|+.|++|+.|+|...++ .+ ++ -+|.|||++||+|.|||||||||||
T Consensus 129 ARGNisQi~QLvGmrGlma~p~G--~i-------------------------i~-lPI~snFreGLt~~EyF~sa~GaRk 180 (1227)
T TIGR02388 129 ARGNMSQVRQLVGMRGLMANPQG--EI-------------------------ID-LPIKTNFREGLTVTEYVISSYGARK 180 (1227)
T ss_pred CcccHHHHHHHhcchheecCCCC--cE-------------------------ee-ccchhhhhcCCCHHHhheecccccc
Confidence 99988888888888888764321 01 01 3478999999999999999999999
Q ss_pred ccccccc--CCCCcchHHHHHHHhheEeeec
Q 000525 812 SSFSDNA--DLPGTLTRRLMFFMRDLCTAYD 840 (1443)
Q Consensus 812 GliDtav--a~sGYLqRrLvk~lEdl~v~YD 840 (1443)
||+|||+ |+|||||||||+++||++|.++
T Consensus 181 GLvDTAlKTAdSGYLTRRLVdv~qDviV~~~ 211 (1227)
T TIGR02388 181 GLVDTALRTADSGYLTRRLVDVSQDVIVREE 211 (1227)
T ss_pred chhhcceeccccchHHHHHHHhhceEEEEEc
Confidence 9999998 9999999999999999999875
No 27
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=4.2e-50 Score=515.12 Aligned_cols=198 Identities=19% Similarity=0.251 Sum_probs=150.7
Q ss_pred cCcccccCCCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCccccccccchHHHHHHHHHhhHHHHHhhh
Q 000525 576 EGSSWLRDYEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTC 654 (1443)
Q Consensus 576 ~~k~~lg~~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~~~~~~~~~~~~~~~~i~~~~~~a~~~~ 654 (1443)
++|+.+ ++|++.++++||.+ |+.|||.+++|+++|++.+|||+|++|+.++++ +++++++.++.+.+..
T Consensus 8 idKk~l----~~LI~~~~~~yG~~~t~~~lD~lk~LGf~~aT~~G~SigidDl~ip~~---K~~li~~Ae~~v~~~~--- 77 (1331)
T PRK02597 8 VDKKAL----KNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPA---KRDLLEQAEEEITATE--- 77 (1331)
T ss_pred ccHHHH----HHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhCcEEEeecccccCHH---HHHHHHHHHHHHHHHH---
Confidence 456655 47999999999996 899999999999999999999999999998864 4455544332222221
Q ss_pred hhhhhHHHhHHhhhhccCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---CCCCCcceeeeccC
Q 000525 655 NFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKY---GSKDNSLLAMFKAG 731 (1443)
Q Consensus 655 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~~~~~~~~~~---~~~~N~~~~M~~sG 731 (1443)
..|..+.+.. .|. + +..++.|.+..+++.+.+.++ .+|.|++++|+.||
T Consensus 78 ----------~~y~~G~it~------------~Er-----~-~kvi~~w~~t~e~l~~~~~~~~~~~dp~N~v~mMa~SG 129 (1331)
T PRK02597 78 ----------ERYRRGEITE------------VER-----F-QKVIDTWNETNERLKDEVVKNFRQNDPLNSVYMMAFSG 129 (1331)
T ss_pred ----------HHHHcCCCch------------hHH-----H-HHHHHHHHHHHHHHHHHHHHHHhhcCCCCcHHHHhhcc
Confidence 1233333211 111 1 223456766667665555444 46789999999999
Q ss_pred CccchhhHhHhhhcccccccC-CCCccccCccccccccccCCCCCCccccCCccccccccccccCCCChhhHHHhcccCC
Q 000525 732 SKGNLLKLVQHSLCLGLQHSL-APLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSR 810 (1443)
Q Consensus 732 SKGS~~Nl~Qi~~~lGqQ~~~-g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m~gR 810 (1443)
||||+.|+.|++|+.|+|... |+ .++ -+|.|||.+||+|.||||||||||
T Consensus 130 ARGN~sQI~QLvGmRGLma~p~G~----------------------------ii~-lPI~snFrEGLs~~EyFis~~GaR 180 (1331)
T PRK02597 130 ARGNMSQVRQLVGMRGLMANPQGE----------------------------IID-LPIKTNFREGLTVTEYVISSYGAR 180 (1331)
T ss_pred CCccHHHHHHHhcchhhccCCCCc----------------------------EEe-cchhhhhhcCCCHHHhheeccccc
Confidence 999999999999999987643 21 011 347899999999999999999999
Q ss_pred Cccccccc--CCCCcchHHHHHHHhheEeeec
Q 000525 811 DSSFSDNA--DLPGTLTRRLMFFMRDLCTAYD 840 (1443)
Q Consensus 811 eGliDtav--a~sGYLqRrLvk~lEdl~v~YD 840 (1443)
|||+|||+ |+|||||||||+++||++|.++
T Consensus 181 KGLvDTAlKTAdSGYLTRRLVdv~QDviVre~ 212 (1331)
T PRK02597 181 KGLVDTALRTADSGYLTRRLVDVSQDVIVREE 212 (1331)
T ss_pred cchhhcceecccchhHHHHHHHhhcceEEEec
Confidence 99999998 9999999999999999999875
No 28
>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=1e-51 Score=475.40 Aligned_cols=263 Identities=22% Similarity=0.324 Sum_probs=195.6
Q ss_pred CCChhhHHHhcccCCCccccccc--CCCCcchHHHHHHHhheEeeecceEEccCCceEEEEEeccCCCCCCCcccCCcee
Q 000525 796 GLNPLECFIHSVTSRDSSFSDNA--DLPGTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGTSTPTGEIGDQPV 873 (1443)
Q Consensus 796 GL~P~EfFfH~m~gReGliDtav--a~sGYLqRrLvk~lEdl~v~YD~tVR~s~G~~iiq~~yg~~g~~~~~~~~~ge~V 873 (1443)
||+|+|||||||||||||||||+ |+||||||||||+|||++|.||+|||++.+ .|+||.||+|| .+.|||||
T Consensus 1 Gl~~~e~f~~~~~~R~gl~dta~kTa~sGyl~R~lv~~~~~~~v~~~~~~~~~~~-~i~~~~~~~~~-----~v~~Ge~V 74 (277)
T PF04998_consen 1 GLTPTEYFFHCMGGREGLIDTAVKTADSGYLQRRLVKVLEDLIVRYDDCVRNSGG-SIIQFIYGEDG-----LVEPGEAV 74 (277)
T ss_dssp C-THHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHTTHEEETTSEEESTTS-EEEESSCTTTS-----B--TTSBH
T ss_pred CcCHHHHHHHHhcccccccccceeeeccccchhhhhhccceEEEEEcCccccccc-eeeeccccccc-----ccCccccc
Confidence 99999999999999999999998 999999999999999999999999999977 69999999997 67899999
Q ss_pred ccccccchhHHHHhcc---cccccc---ccccccccchhhhccCCCCCCCccEeeeehhhhccccccCchhhHHHHHhhh
Q 000525 874 GSLSACAISEAAYSAL---DQPISL---LETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHL 947 (1443)
Q Consensus 874 G~~aAqSi~Ep~tq~l---~~~~~~---l~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e~~a~~Vk~~L 947 (1443)
|++||||||||+|||+ +|.+++ ..+.|+||++|++++++..++ +.+.++...... .....+..++...
T Consensus 75 GiiaAQSIGEP~TQ~TL~TFH~aG~~~~~vt~giprl~eii~~~~~~~~--~~~~~~~~~~~~----~~~~~~~~~~~~~ 148 (277)
T PF04998_consen 75 GIIAAQSIGEPGTQMTLRTFHTAGVASKNVTQGIPRLKEIINASKKIKT--PIITVYGKKKII----SEKKKIKIIRKKI 148 (277)
T ss_dssp HHHHHHHHHCHGCCSHHSCTSSSCSSTSSCSSSHHHHHHHHTTCSSSSS--EEEEECSCSSEC----SSSHHHHHHHHTC
T ss_pred hhhhhchhcchhHHhhhcccccCceeeecccccceeecccccccccccc--ceEEeeccccee----cccccceEEEEee
Confidence 9999999999999995 777654 356899999999999876554 344444332221 1111222222222
Q ss_pred cccchhhhhceEEEEEcCCCCcccccCceEEEEEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCCceeeecCccc
Q 000525 948 ECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDCS 1027 (1443)
Q Consensus 948 E~~tL~di~~~i~i~y~P~~~~~~~~sp~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~~i~i~~~~c~ 1027 (1443)
+. .. .. ..+...
T Consensus 149 ~~------------------------------------------------------~~-----~~------~~~~~~--- 160 (277)
T PF04998_consen 149 KI------------------------------------------------------IK-----NG------KKVKNG--- 160 (277)
T ss_dssp SS------------------------------------------------------SC-----ST------TCEHTT---
T ss_pred ee------------------------------------------------------ee-----cc------cceecc---
Confidence 11 00 00 000000
Q ss_pred cccccccCCCceEEEEEeecccccchhhHHHHHHHhccccccceeeccccceEEEEeecccccccCCCCCCCceEEEEEe
Q 000525 1028 SINMQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVS 1107 (1443)
Q Consensus 1028 ~~~~~~~~~~~~~i~v~~~~~~~~~~~~l~~l~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~~~~el~l~~~ 1107 (1443)
....++.. +.+.... ....+|++.+.
T Consensus 161 -----------------------------------------~~~~~~~~-~~~~~~~------------~~~~~~~l~~~ 186 (277)
T PF04998_consen 161 -----------------------------------------DKIKKGSI-ISKDILE------------KKSKEYVLQTE 186 (277)
T ss_dssp -----------------------------------------CESSSSCS-EHHHHCE------------ECCCCCEEECC
T ss_pred -----------------------------------------eeeeccee-eeecccc------------chhHHHHHHHH
Confidence 00000000 0000000 12346888888
Q ss_pred eccccccchhHHHHhhhhcccccc-ccccccCCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHHHHHHHhhcc
Q 000525 1108 MSGQCHITSLWSALMNDCHQIMDM-IDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLS 1186 (1443)
Q Consensus 1108 gs~~~~~~~~~~vll~~~l~~~~~-id~~rt~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rHl~LlAd~MT 1186 (1443)
|++ +..++. .++ +|++|+++|||++|.++|||||||++|++|++.++..+|++||+||+.|+||+||
T Consensus 187 g~~-----------l~~v~~-~qgvid~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~~~~g~~vn~rhl~llad~mt 254 (277)
T PF04998_consen 187 GSN-----------LQEVYS-SQGVIDNDKHISNDIRQMLSKLGIEAARNSIIKELKNVFESYGIEVNKRHLSLLADYMT 254 (277)
T ss_dssp SHH-----------HHHHTC-STT-EETCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHHHHCTSCCCHHHHHHHHHHHC
T ss_pred hhh-----------chhhee-cccccCCCEEEeceeEeeeeeEEEEECCCceeecCcEeeHHHHHHHHHHHHHhCCCcCe
Confidence 776 667777 777 9999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeEeecchhhhhhhhc
Q 000525 1187 ATGEFVGLNAKGLALQRK 1204 (1443)
Q Consensus 1187 ~~G~~~gi~r~G~~~~~~ 1204 (1443)
++|.++||||+||+.++.
T Consensus 255 ~~g~~~gitR~gl~~~~~ 272 (277)
T PF04998_consen 255 YKGVLLGITRHGLNSNKS 272 (277)
T ss_dssp CCSS---CCTTTTSSSSS
T ss_pred eeeEEEEEEHHHhccCCC
Confidence 999999999999997664
No 29
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=100.00 E-value=1.8e-47 Score=491.59 Aligned_cols=306 Identities=20% Similarity=0.263 Sum_probs=249.4
Q ss_pred HHhc---cccccc---cccccccccchhhhccCCCCCCCccEeeeehhhhccccccCchhhHHHHHhhhcccchhhhhce
Q 000525 885 AYSA---LDQPIS---LLETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDIVST 958 (1443)
Q Consensus 885 ~tq~---l~~~~~---~l~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e~~a~~Vk~~LE~~tL~di~~~ 958 (1443)
.||| |+|.++ .+.|+|+|||+||++++++++ ||+|+++|.+.... ++..|+.|+.+||+++|+|++..
T Consensus 540 v~~~~LnTFH~AGv~~~nVTlGvPRL~EIinask~i~--TP~m~i~l~~~~~~----~~~~a~~v~~~ie~~~L~dv~~~ 613 (858)
T PRK14898 540 VTHNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPS--TPIMTVHLKGEYAT----DREKAEEVAKKIESLTLGDVATS 613 (858)
T ss_pred eeccccceeeccCccccccccCCchHHHHhcccCCCC--CceEEEEECCCccc----hHHHHHHHHhheeeEEHHHHHHH
Confidence 3455 377765 367899999999999998655 57999999776431 24579999999999999999998
Q ss_pred EEEEEcCCCCcccccCceEEEEEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCCceeeecCccccccccccCCCc
Q 000525 959 SMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDA 1038 (1443)
Q Consensus 959 i~i~y~P~~~~~~~~sp~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~~i~i~~~~c~~~~~~~~~~~~ 1038 (1443)
+++.... ..++++||++.+.+++|+++.|.+.|...++ .+ +.. +.
T Consensus 614 ~~~~~~~----------~~~~i~l~~~~~~~~~l~~~~i~~~i~~~~~-----~~-----~~~---------------~~ 658 (858)
T PRK14898 614 IAIDLWT----------QSIKVELDEETLADRGLTIESVEEAIEKKLG-----VK-----IDR---------------KG 658 (858)
T ss_pred hhhhccc----------cEEEEEECHHHHHHcCCCHHHHHHHHHHhcc-----cc-----ccC---------------CC
Confidence 7753210 1368889999999999999999988776541 11 000 11
Q ss_pred eEEEEEeecccccchhhHHHHHHHhccccccceeeccccceEEEEeecccccccCCCCCCCceEEEEEeeccccccchhH
Q 000525 1039 FCVTVMIVENFKRTSIDLETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLW 1118 (1443)
Q Consensus 1039 ~~i~v~~~~~~~~~~~~l~~l~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~~~~el~l~~~gs~~~~~~~~~ 1118 (1443)
..+.+.+.. .....+..++. .|++++|+|+|+|+||.|...+. .+.++|+|.|+|++ |
T Consensus 659 ~~~~~~~~~---~~~~~~~~~~~----~l~~~~i~gi~gI~~~~i~~~~~--------~~~~~~~l~teG~n------l- 716 (858)
T PRK14898 659 TVLYLKPKT---PSYKALRKRIP----KIKNIVLKGIPGIERVLVKKEEH--------ENDEEYVLYTQGSN------L- 716 (858)
T ss_pred CEEEEEecC---chHHHHHHHHH----HhcCcEEECCCCccEEEEecCCC--------CCCceEEEEecCcC------H-
Confidence 234443321 22233444443 57799999999999999884321 12358999999886 4
Q ss_pred HHHhhhhccccccccccccCCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHHHHHHHhhccceeeEeecchhh
Q 000525 1119 SALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKG 1198 (1443)
Q Consensus 1119 ~vll~~~l~~~~~id~~rt~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rHl~LlAd~MT~~G~~~gi~r~G 1198 (1443)
.++|. +++|||+||+||||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|++.||||+|
T Consensus 717 ----~~~~~-~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~gi~V~~rHl~liad~MT~~G~~~~~~r~g 791 (858)
T PRK14898 717 ----REVFK-IEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHG 791 (858)
T ss_pred ----HHHhc-CCCCcccccccCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHccCCcEEEeccCC
Confidence 44455 8899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccceEEEEccC
Q 000525 1199 LALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHFDIIYSGE 1264 (1443)
Q Consensus 1199 ~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~f~ll~~~~ 1264 (1443)
++.++ .|||++||||+|+++|++||.+|+.|+|.|||||||||+++|+|| |+|+|+++.+
T Consensus 792 i~~~~-----~s~l~~asFe~t~~~l~~Aa~~g~~D~l~g~s~~ii~G~~~~~GT-G~~~l~~~~~ 851 (858)
T PRK14898 792 VAGEK-----GSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGT-GCVDLRIDRE 851 (858)
T ss_pred ccCCC-----CCHHHhcChHhHHHHHHHHhhcCCCCcCCCchHHeeeCCccCCcC-ceEEEEecCc
Confidence 97654 499999999999999999999999999999999999999999999 9999999976
No 30
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=100.00 E-value=2e-45 Score=477.58 Aligned_cols=198 Identities=17% Similarity=0.223 Sum_probs=142.0
Q ss_pred cCcccccCCCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCccccccccchHHHHHHHHHhhHHHHHhhh
Q 000525 576 EGSSWLRDYEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTC 654 (1443)
Q Consensus 576 ~~k~~lg~~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~~~~~~~~~~~~~~~~i~~~~~~a~~~~ 654 (1443)
++|+.+ ++|++.++++||.+ |++|||.+++|+++|++.+|||+|++|+.++++ +.++++ +|++.+
T Consensus 14 ~~k~~l----~~li~~~~~~~G~~~t~~~lD~lk~lgf~~at~~G~Sigi~Dl~ip~~---K~~li~-------~a~~~v 79 (1364)
T CHL00117 14 IDKTAL----KRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPS---KGWLVQ-------DAEQQS 79 (1364)
T ss_pred ccHHHH----HHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHhcceEEecCcccCCHH---HHHHHH-------HHHHHH
Confidence 355544 56999999999996 899999999999999999999999999999864 334443 333322
Q ss_pred hhhhhHHHhHHhhhhccCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHhhCCCCCcceeeeccC
Q 000525 655 NFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQN---LAYKYGSKDNSLLAMFKAG 731 (1443)
Q Consensus 655 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~L~~~~~~~~~~~~~~~~~---~~~~~~~~~N~~~~M~~sG 731 (1443)
. . ....|..|.+.. ...++ ..++.|..+.+.+.+ ...+..++.|++++|+.||
T Consensus 80 ~--~----~~~~y~~G~it~---------~er~~---------~~i~~w~~~~~~l~~~~~~~~~~~d~~N~v~mMa~SG 135 (1364)
T CHL00117 80 L--I----LEKHYHYGNVHA---------VEKLR---------QSIEIWYATSEYLKQEMNPNFRMTDPLNPVYMMSFSG 135 (1364)
T ss_pred H--H----HHHHHHcCCCCH---------HHHHH---------HHHHHHHHHHHHHHHHHHHhhccCCCCCcHhhhhhcc
Confidence 1 1 111233343321 01111 234455444444432 2334567899999999999
Q ss_pred CccchhhHhHhhhcccccccCCCCccccCccccccccccCCCCCCccccCCccccccccccccCCCChhhHHHhcccCCC
Q 000525 732 SKGNLLKLVQHSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRD 811 (1443)
Q Consensus 732 SKGS~~Nl~Qi~~~lGqQ~~~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~i~~GfV~~sf~~GL~P~EfFfH~m~gRe 811 (1443)
||||+.++.|++||.|++.. |. |..++ -+|.+||.+||+|.|||||||||||
T Consensus 136 ARGn~sQi~qLvGmRGlma~--------p~-------------------G~iI~-~PI~snFreGLs~~EyFis~~GaRk 187 (1364)
T CHL00117 136 ARGNASQVHQLVGMRGLMSD--------PQ-------------------GQIID-LPIQSNFREGLSLTEYIISCYGARK 187 (1364)
T ss_pred CcccHHHHHHHhcccceeeC--------CC-------------------CcEee-cchhhhhhcCCCHHHhheecccccc
Confidence 99977666666666665432 11 11122 4589999999999999999999999
Q ss_pred ccccccc--CCCCcchHHHHHHHhheEeee
Q 000525 812 SSFSDNA--DLPGTLTRRLMFFMRDLCTAY 839 (1443)
Q Consensus 812 GliDtav--a~sGYLqRrLvk~lEdl~v~Y 839 (1443)
||+|||+ |+|||||||||+++||++|.-
T Consensus 188 GLvDTAlkTAdSGYLtRRLVdv~qdviV~~ 217 (1364)
T CHL00117 188 GVVDTAVRTADAGYLTRRLVEVVQHIVVRE 217 (1364)
T ss_pred chhhcceecccccchhhHHHhhhccEEEEe
Confidence 9999998 999999999999999999964
No 31
>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_W 3QQC_A 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2AUJ_D 1ZYR_D 1SMY_D ....
Probab=100.00 E-value=8.5e-44 Score=419.05 Aligned_cols=229 Identities=26% Similarity=0.433 Sum_probs=154.9
Q ss_pred eeeeeEEEEcCChHHHHhccceEEecC------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccceeecCccc
Q 000525 15 GILTGISLGISTDTEKEKLSVMEIGAV------------SEVTNPRLGLPNPTNECSSCGAKDRKACEGHFGFIKFPFTI 82 (1443)
Q Consensus 15 ~~I~~I~F~~~S~eEI~~~Sv~~I~~~------------~Gl~D~rLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~PV 82 (1443)
.+|.+|+||++|++||+++||+||+++ |||||||||+.++...|+|||. +..+||||||||||+.||
T Consensus 2 ~~i~~i~f~~~s~~eI~~~Sv~~i~~~~~~~~~~~~p~~~Gl~d~rlG~~~~~~~C~tC~~-~~~~CpGHfGhI~L~~PV 80 (337)
T PF04997_consen 2 KKIKSIQFGIYSPEEIRKLSVKEITNPETFDNLTGKPIKGGLYDPRLGPIDKKQICSTCGL-NYTECPGHFGHIELALPV 80 (337)
T ss_dssp EEEEEEEEEE--HHHHHHHEEEB--SSTSBCTSSSSCBSSSSSSSSSS-SSSSSTSSSSSS-SSSSCCCSEEEEEEEEEE
T ss_pred CeeeEEEEEeCCHHHHHHhCcEEEechhhccCCCCCCccccccChhhcCCCcccccccccc-cccccCCceeEEEeCHHH
Confidence 589999999999999999999999864 7999999999999999999995 789999999999999999
Q ss_pred cccccHHHHHHHHhccccccccccCcchhhh-----cc---------------ccccccccccccccCCCCCCccccccc
Q 000525 83 LHPYFLSDIAKLLNSICPKCKTIRKERQKGA-----GS---------------SRKEQPRVCKYCVRNPAQWYPRMRFKL 142 (1443)
Q Consensus 83 fHpgf~~~i~kIL~~iC~~C~rlll~~~~k~-----l~---------------~~~~~~~~C~~C~~~~~~~~p~i~~~~ 142 (1443)
|||+||+.+++||+|+|++|++++++..... +. ..+.....|..|.... ..++ .
T Consensus 81 ~h~~f~~~i~~iL~~~C~~C~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~----~~~~-~- 154 (337)
T PF04997_consen 81 YHPGFFKEIPKILRCICKKCSRLLLSEKEKYFYLKILLKLKKKKKKERLKIISKECKKKSICSHCKAIN----GKIK-K- 154 (337)
T ss_dssp ETCCCHHHHHHHHTTSCTTTSCTSTCCCCHTSCHHHCHCSHSSSHHHHHHHHHHHHHHTCSSTSTCC-S----SS-----
T ss_pred HhhcccccceeeecccccccccccccccccccccccccccccccchhHHHHHHHhhhhhhhhccccccc----cccc-c-
Confidence 9999999999999999999999998754320 00 0112234555554311 0000 0
Q ss_pred ccccccCccceeehhhhhhhccCCCCc----cccccccCccccccccccCCCccccCHHHHHHHhccCChhhHhhc----
Q 000525 143 SSKDLSGKTAIIVEIDEKLSKKNKKLP----DDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPSIREEF---- 214 (1443)
Q Consensus 143 ~~~~~~~k~~ii~e~~~~~~~k~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~LsP~eV~~iLkkI~~ed~~~~---- 214 (1443)
..+. +....+.+..+... ..++..+.+. ......+...+.|+|.+|+++|++|+++++..+
T Consensus 155 -----~~~~----~~~~~~~~~~~~~~~~~~~~i~~~i~~~--~~~~~~~~~~~~l~~~~v~~ilk~l~~~~~~~l~~~~ 223 (337)
T PF04997_consen 155 -----VEKS----KKCEGCGKKNPKIRKEGAEKIQEEIKKK--ESNKEIKEELRILTPEEVRQILKKLSKEDKELLGFDP 223 (337)
T ss_dssp -----SSSE----ETSSSSSSBSCEEEEESHCCCCCHHHSC--CHHHHHHCHCECESHHHHHHHHHHSHHHHHHHHHHHT
T ss_pred -----cccc----hhcccccccCcccccchhhhcccccccc--cccccchhhhhhhhhhhhhhcchhhhhhheeeeeccc
Confidence 0000 00001111111000 1122222111 011111123347999999999999999887653
Q ss_pred -cCCCCcceeeccccCCCCCCccccccccccccccccchhHHHHHHHHHhhC
Q 000525 215 -ILSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRG 265 (1443)
Q Consensus 215 -~~rPE~ffLt~LPVPP~~iRPS~~~~~~~ng~~~~eDDLT~~l~~iv~~~~ 265 (1443)
..+||||||++|||||+++||++.+++ +..++||+|.+|++|+..|.
T Consensus 224 ~~~~P~~~~l~~lpVpP~~~RP~v~~~~----~~~~eddlt~~~~~Ii~~N~ 271 (337)
T PF04997_consen 224 SGSRPEWFFLTVLPVPPPRFRPSVQLGG----GRFSEDDLTSLYRKIIKRNN 271 (337)
T ss_dssp TTBSGGGSEEEEEEE-TGGGS-EEEESS----SEEEE-HHHHHHHHHHHHHH
T ss_pred cccccceeEEeeeecCCceeeeeeeeec----ccccCchHHHHHHHHHHHHH
Confidence 368999999999999999999988753 34689999999999998753
No 32
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=99.97 E-value=2.1e-31 Score=276.86 Aligned_cols=109 Identities=24% Similarity=0.496 Sum_probs=106.0
Q ss_pred cHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHHHHHHHhhccceeeEeecchhhhhhhhccCCCcchhhhcccccc
Q 000525 1141 NIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNP 1220 (1443)
Q Consensus 1141 ~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rHl~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asFe~t 1220 (1443)
||++|+++|||||||++|++||+++|+.||++||+|||+||||+||++|.+.|+||+|++... .|||++||||+|
T Consensus 49 dI~~i~~~lGIEAaR~~iv~El~~v~~~~Gi~V~~rHl~LIAD~MT~~G~~~ginr~g~~~~~-----~Spl~~aSFE~t 123 (158)
T cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASK-----TSPLMRASFEKT 123 (158)
T ss_pred cHHHHHHHhCHHHHHHHHHHHHHHHHHhcCceecHHHHHHHHHHHhcCCcccccccccccccC-----CCHHHHcCHHHH
Confidence 899999999999999999999999999999999999999999999999999999999997544 499999999999
Q ss_pred HHHHHHHHhhCCCcCCCCccceeccCCCCCccCcc
Q 000525 1221 GASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGG 1255 (1443)
Q Consensus 1221 ~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg 1255 (1443)
.++|++||.+|+.|+|.|++|||+||+++|+|| |
T Consensus 124 ~~~L~~AA~~g~~D~l~g~s~~ii~Gk~~~~GT-G 157 (158)
T cd00630 124 TKHLLDAAAAGEKDELEGVSENIILGRPAPLGT-G 157 (158)
T ss_pred HHHHHHHhhcCCCCCCCCcHHhhhccCCCCCCC-C
Confidence 999999999999999999999999999999999 5
No 33
>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=99.95 E-value=1e-28 Score=261.55 Aligned_cols=145 Identities=26% Similarity=0.411 Sum_probs=130.7
Q ss_pred CcccCCCCCcccccchhHHHHHHhhccCccccCHHHHHHHHhhCC-----CccCCCceecccCCccchHHHHHhhcCCCC
Q 000525 481 QLINQQSGRNLLSLGQDSLTAAHLLMEDSVLLSHLQMQQLQMFCP-----HRFLSPDIFKISKDSVWSGKQLFSMLLPPD 555 (1443)
Q Consensus 481 ~~~sp~~g~pl~gl~QD~l~g~~llt~~d~fl~~~~~~~l~~~~~-----~~l~~pai~Kp~~~~lwTGKql~s~~lp~~ 555 (1443)
||+||++|+|+++++||+|+|+|+||.+++|++++|+++++++.. ...+.|+|+|| .++|||||+||++||.+
T Consensus 1 NilSP~~G~Pii~~~QD~vlG~y~LT~~~~f~~~~e~~~~~~~~~~~~~~~~~~~~~I~~~--~~~~tgk~~~s~il~~~ 78 (158)
T PF04983_consen 1 NILSPANGKPIIGPTQDMVLGAYYLTSEDTFLSRDEAQQALMNGLIDDKKIVLLHPAILKP--KELWTGKQTFSRILPNE 78 (158)
T ss_dssp GSEETTTTEESSS--SHHHHHHHHHSSTTTEESHHHHHHHHHCSST----CHCSSSSBSSS--SSCEECHHHHHTTSHTT
T ss_pred CccCCCCCCceEEeccceEeEEEEEEecccccchHHHHHHHHcccccccceeccchhhhcc--ccceeeccHHHHhcccc
Confidence 799999999999999999999999999999999999999999874 45789999999 68999999999999998
Q ss_pred CccccC-----CCcEEEeCCeeccc-cCccccc-CCCccHHHHHHHHhcHH-HHHHHHHHHHHHHHHHhcccceeecCcc
Q 000525 556 FEYTFP-----SKDVYISGGKLISA-EGSSWLR-DYEGNLFQYLIKRYRDK-VLDFLYAAQEVLCEWLSVRGMTVSLSDL 627 (1443)
Q Consensus 556 ~~~~~~-----~~~v~i~~gell~~-~~k~~lg-~~~~~l~~~l~~~~g~~-a~~~l~~~q~l~~~~L~~~GfSigi~D~ 627 (1443)
+++... ++.++|+||+++.+ ++|+++| ++.++|+|.++++||.+ |++|||++|+++++|++.+|||||++|+
T Consensus 79 i~~~~~~~~~~~~~~~i~~g~~l~g~l~k~~lgk~~~~~li~~i~~~yG~~~~~~~ld~i~~lg~~~~t~~GfSvgi~D~ 158 (158)
T PF04983_consen 79 INPEGFSNDPDDGYVVINNGELLSGVLDKKTLGKKSLGSLIHQIYREYGPEATVQFLDAIKRLGFRYLTRSGFSVGIDDM 158 (158)
T ss_dssp HHEEESTSCHSSHSEEECTSSEEEC--SHHHHSCSHTTCHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHTBB-SGGGC
T ss_pred cccccccccccccceeecCCccchhheehheecccchhhHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHcCeeEecccC
Confidence 888753 35799999999975 8999999 67899999999999996 7899999999999999999999999996
No 34
>PF11523 DUF3223: Protein of unknown function (DUF3223); InterPro: IPR021602 This family of proteins has no known function. ; PDB: 2K0M_A.
Probab=99.95 E-value=5.1e-29 Score=228.44 Aligned_cols=75 Identities=52% Similarity=0.903 Sum_probs=61.9
Q ss_pred HHHHHhcCCCCCCCChhh-HHHHHHHhhcCCCccccccCCCCcEEEeecCCCCCcceEEEEEeCCCcccccHHHHH
Q 000525 1344 LKKILHKYSIGQRLSEKD-KTTVIRALYFHPRRNEKLGIEPPDIEVTYHPEHQNSRCFSLVREDGSIEDFSYHKCV 1418 (1443)
Q Consensus 1344 ~~~il~~~~~~~~l~~~d-~~~~~~ll~~Hp~~~~Kig~gi~~~~v~~~~~~~~srcf~vvr~Dg~~~dFSy~kc~ 1418 (1443)
||+|||+|++|++|+++| +.+|.+||+|||++++||||||++|+|+.||.|.+||||||||+|||++||||+|||
T Consensus 1 ~k~iL~~y~~g~~l~~~d~~~~l~~ll~~HP~~~~KiG~Gi~~i~V~~hp~~~~srCF~vvR~DGs~~DFSy~KCi 76 (76)
T PF11523_consen 1 FKRILHRYPDGERLSEEDEKSVLEALLKYHPEAEEKIGCGIDHIMVRKHPEFKDSRCFFVVRTDGSEEDFSYRKCI 76 (76)
T ss_dssp HHHHHHHS-TTEE--HHH-HHHHHHHHHTSTTHHHHHTT-EEEEEEEESSSS---EEEEEEETTS-EEE--GGGSS
T ss_pred ChhHHhhCCCcCCcCHHHHHHHHHHHHHhCCcHHHhhcCCeeeEEEeecCCCCcceEEEEEEeCCCeeeeEhhhhC
Confidence 689999999999999998 666678999999999999999999999999999889999999999999999999996
No 35
>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain. Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Probab=99.90 E-value=2.6e-24 Score=231.98 Aligned_cols=113 Identities=20% Similarity=0.325 Sum_probs=101.3
Q ss_pred CcHHHHHHHH--cHHHHHHHHHHHHHHHhcccCCccCHHHHHHHHhhccceeeEe-------------------ecchh-
Q 000525 1140 DNIRSFCLAY--GIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFV-------------------GLNAK- 1197 (1443)
Q Consensus 1140 n~I~ei~~~l--GIEAar~~ii~el~~~~~~~G~~V~~rHl~LlAd~MT~~G~~~-------------------gi~r~- 1197 (1443)
||++++.+++ ||||||.+|++||++||..||++||+||++||||+||++|.+. .+||.
T Consensus 54 ~~~~~il~~~~~Giea~r~~iv~EIq~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~ 133 (204)
T cd02655 54 INPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRL 133 (204)
T ss_pred CCHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHH
Confidence 7899999999 9999999999999999999999999999999999999996543 22222
Q ss_pred ---------------hhhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCcc
Q 000525 1198 ---------------GLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGG 1255 (1443)
Q Consensus 1198 ---------------G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg 1255 (1443)
|+. |.+|.+.|+|+.||||+|+++|.+||.+|+.|+|.|++||||+|+++|+|| |
T Consensus 134 ~~~~~~~~~y~p~llGIt--k~~l~~~Sfls~ASFqeT~kvL~~AAi~gk~D~L~GlkeNVI~G~liPaGT-G 203 (204)
T cd02655 134 LLLGKKPAKYEPVLLGIT--KASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGT-G 203 (204)
T ss_pred HhCCCCcccccceeeeee--eccccCCCccccCChHHHHHHHHHHHhcCCCCCCCCchhheEECCccCCCC-C
Confidence 343 345567899999999999999999999999999999999999999999999 6
No 36
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=99.64 E-value=2.6e-17 Score=203.30 Aligned_cols=532 Identities=18% Similarity=0.096 Sum_probs=381.8
Q ss_pred CceeccccccchhHHHHhccccccccc------cccccccchhhhccCCCCCCCccEeeeehhhhccccccCchhhHHHH
Q 000525 870 DQPVGSLSACAISEAAYSALDQPISLL------ETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEV 943 (1443)
Q Consensus 870 ge~VG~~aAqSi~Ep~tq~l~~~~~~l------~t~gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e~~a~~V 943 (1443)
|+++|..+|+...+++|.+++.+++.. +.+++..++.++++..+.-..++.+..++..+..+....+++..+.|
T Consensus 881 ~~~l~~~~a~f~~~~~~d~ld~~~~~~~~~~~~e~~~~~~l~~lle~e~~~l~~dr~~l~~i~~~g~~k~~lp~n~~r~I 960 (1605)
T KOG0260|consen 881 GETLGSLNACFESEFAYDALDEPISLSSEEVVNEISELLKLQNLLECEYKKLVRDRRVLLYIFEYGDAKWPLPENLQRII 960 (1605)
T ss_pred cccccchHHHHHhhhhhhhhcCcccchhhhHhhhhhhhHHHHHHHHHHHHhhhhhhhhhhhhcccCCcccccchhHHHHH
Confidence 367788999999999999998776543 66888889999988765566688888888777666666778899999
Q ss_pred HhhhcccchhhhhceEEEEEcCCCCcccccCceEEEEEeeHHHHHHcCCCHHHHHHHHHHhhhhhhhhhcccCCceeeec
Q 000525 944 KNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVPDMLISN 1023 (1443)
Q Consensus 944 k~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~~~~~~~l~~~~~~i~i~~ 1023 (1443)
++.++...+.+...+..+.+.=-...+ .+.-.++.+.-+..+-+..+ +.+.+.+..=..++.+. .
T Consensus 961 ~Na~~~f~~~~r~~t~l~~~~v~~g~~-~l~e~l~iv~g~~~~sraqr-----l~~~lLrs~l~~krv~~---------e 1025 (1605)
T KOG0260|consen 961 WNALKKFSIDERKPTDLIPFKVVKGVK-ELAEKLVIVRGEDYISRAQR-----LFNILLRSTLATKRVLE---------E 1025 (1605)
T ss_pred HHHHhhcccccccccccchhhhhhhhh-hhhheeEEeeCchhHHHHHH-----HHHHHHHhhHHHHHHHH---------H
Confidence 999999999887665444331000000 00001122222222211011 11111111000000000 0
Q ss_pred CccccccccccCCCceEEEEEeecccccchhhHHHHHHHhccccccce-eeccccceEEEEeeccccccc-CCCCCCCce
Q 000525 1024 KDCSSINMQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMPFLLKTV-VKGFREIKKVDILWKDKQKAS-KSHDDSFGE 1101 (1443)
Q Consensus 1024 ~~c~~~~~~~~~~~~~~i~v~~~~~~~~~~~~l~~l~~~iip~ll~~v-VkG~~~I~rv~I~~~d~~~~~-~~~~~~~~e 1101 (1443)
..|+. ++.+-....+|++|........+.......+....|....+. +.+..||+.++|.|-...... ....+.-++
T Consensus 1026 ~rls~-eaf~w~~~~Ie~~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aGVssknVt~gvprlkei~Nv~k~~kt 1104 (1605)
T KOG0260|consen 1026 YRLSS-EAFEWVLGEIEARFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIINVAKNAKT 1104 (1605)
T ss_pred hcccH-HHHHHHhhhhhhheeeeecCccchHhHHHHHHhCCchhhcccchhcccceeeeeeeccCcchhhhhhhhccCCC
Confidence 01111 111111123344554333344555555555655567766666 899999999999986543211 122234456
Q ss_pred EEEEEeeccccccchhHHHHhhhhccccccccccccCCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCccCHHHHHHH
Q 000525 1102 LYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIV 1181 (1443)
Q Consensus 1102 l~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~rt~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~V~~rHl~Ll 1181 (1443)
..|.|...++....+-|.-++.-|++++.+.||++.++-.+..-.+.++|++-+..+.--....-++.| .|.+.||.|.
T Consensus 1105 psLtV~l~g~~~k~~e~ak~v~~~le~ttl~~vt~~t~i~ydpdp~~tvI~ed~e~v~a~~e~pd~D~~-~ispwlLrle 1183 (1605)
T KOG0260|consen 1105 PSLTVYLTGEAAKDNEWAKLVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDEDREFVVAYYEMPDEDVG-RISPWLLRLE 1183 (1605)
T ss_pred ceEEEEecchhhcchHHHHHHhhhcccccHHhhhccCcceecCCCcceeeccchhhHHhhhcCcccchh-hcChHHHHhh
Confidence 777777777555667888889999999999999999999999999999999999999888887777778 9999999999
Q ss_pred HhhccceeeEeecchhhhhhhhccCCCcchhhhccccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccceEEEE
Q 000525 1182 ANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHFDIIY 1261 (1443)
Q Consensus 1182 Ad~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~asFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~f~ll~ 1261 (1443)
+|.-..+|+.+.++..|.++.+.--+...++..++|.+...++.++|..++.|.+.+-.|+.+||+..--|++..+++++
T Consensus 1184 lDr~~m~dk~ltm~~ia~~i~~~f~~d~~~i~~ddna~klv~r~ri~~~~e~D~~l~~Ie~~ml~~~~l~G~~~i~kV~m 1263 (1605)
T KOG0260|consen 1184 LDRASMTDKKLTMEQIAEKINRGFGSDLACIFSDDNAEKLVLRLRIAKEEEDDVFLKCIEANMLGDMTLRGIPDIFKVYM 1263 (1605)
T ss_pred hhhhhcccccccHHHHHHHHHhhccCCCceeecccCCcceEEEEEecCccchhHHHHHHHHhhhhhcccCCccccceEEE
Confidence 99999999999999999988877667778999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCcccccccCcccccc-ccccccceeeecccccccccccc--CC-CcccCCccccccccccccccccceeeccH
Q 000525 1262 SGEGRTLSKPVDVYNLLSTPVS-SKQNEKLKVCKAQGLISDKCGAK--FG-DFAFKGLGNLDFETISRGVLRKSWTYNDV 1337 (1443)
Q Consensus 1262 ~~~~~~~~~~~~~y~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~i 1337 (1443)
..+.+..-++++.|+++-..++ .+-+..-++..++++..+.|-.- .| ...++-+ +....++-.|+|.-|
T Consensus 1264 ~~~~~G~f~~~~ew~LeTdg~~l~~v~s~~~vD~~rt~sn~l~ei~~vlgIea~r~a~-------~~e~~~vi~f~gsyV 1336 (1605)
T KOG0260|consen 1264 SPTEDGEFKPVDEWDLETDGVNLRRVLSEPDVDPARTTSNDLVEIAEVLGIEAVRKAL-------LRELLNVISFDGSYV 1336 (1605)
T ss_pred eecCCCceeecceeEEecCchhHHhhhccCCCCcccccccchhhhhhhhcHHHHHhhh-------hhhhhheEeecccch
Confidence 9988888889999998887655 45566667777777777766541 01 0011111 111123445889999
Q ss_pred HHHHHHHHHHHhcCCCCCCCChhhHHHHHHHhhcCCCccccccCCCCcEEEeecCCCCCcceEEEEEeCCCcccccHHHH
Q 000525 1338 LRLSNALKKILHKYSIGQRLSEKDKTTVIRALYFHPRRNEKLGIEPPDIEVTYHPEHQNSRCFSLVREDGSIEDFSYHKC 1417 (1443)
Q Consensus 1338 ~~~~~~~~~il~~~~~~~~l~~~d~~~~~~ll~~Hp~~~~Kig~gi~~~~v~~~~~~~~srcf~vvr~Dg~~~dFSy~kc 1417 (1443)
.-.-..+...++.|+-+.-....+.--..+.++.||..-++++.++-.+-+-- ..+..+-||-.|+-|+...+|+|.+|
T Consensus 1337 nyrhlaLl~dvmT~~g~lm~itRhg~nr~~tgaLmrcSfEetv~il~~aa~~~-ekd~~rgvsEnImlgqlap~gTg~~d 1415 (1605)
T KOG0260|consen 1337 NYRHLALLCDVMTARGHLMAITRHGINRQDTGALMRCSFEETVDILMDAAAHA-EKDPCRGVSENIMLGQLAPMGTGCFD 1415 (1605)
T ss_pred hHHHHHHHHHHHhcccceeeeeccccchhhccccccccHHHHHHHHHHHHhhh-ccCCCccceeeeeecccccCCCccee
Confidence 99999999999999988888777666666899999999999999887666643 23345778999999999999999999
Q ss_pred Hhhhhhhhc
Q 000525 1418 VIGALEIIA 1426 (1443)
Q Consensus 1418 ~~~~~~~~~ 1426 (1443)
+..-.+...
T Consensus 1416 ~~ld~e~l~ 1424 (1605)
T KOG0260|consen 1416 LMLDAEKLK 1424 (1605)
T ss_pred eeccHHhhh
Confidence 987666543
No 37
>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=99.57 E-value=1.7e-15 Score=150.06 Aligned_cols=78 Identities=27% Similarity=0.349 Sum_probs=62.7
Q ss_pred HHHHHHHHHHHHhhCCCCCcceeeeccCCccchhhHhHhhhcccccccCCCCccccCccccccccccCCCCCCccccCCc
Q 000525 704 KHVFWDIQNLAYKYGSKDNSLLAMFKAGSKGNLLKLVQHSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTECAKSY 783 (1443)
Q Consensus 704 ~~~~~~~~~~~~~~~~~~N~~~~M~~sGSKGS~~Nl~Qi~~~lGqQ~~~g~~~~r~p~~~~~~~l~~~~~~~~~~~~~~~ 783 (1443)
..+.+++++++.+++..+|++++|+.||||||++|++||+||+|||.++|+ |+|.++++|+||+|++.+..|.+
T Consensus 31 ~~~~~~~~~~~~~~~~~~N~l~~M~~SGaKGs~~ni~Qi~g~lGqq~~~g~---ri~~~~~~Rtlp~f~~~~~~~~~--- 104 (108)
T PF05000_consen 31 NKVRDEIGKIIKKNLPFNNSLLIMINSGAKGSMSNISQISGCLGQQSVEGK---RIPRGFSGRTLPHFKPFDESPES--- 104 (108)
T ss_dssp HHCCHHHHHHHHHCSTTTSHHHHHHHSSSS--HHHHHHHHST-EEEEETTS---ES--SSTTCSSTTS-SS-SSTTT---
T ss_pred HHHHHHHHHHHHHhCCCCCcHHhhhhccCCCCHHHHHHHHHHHHHhhcccc---ccccCCCCCcCCCcCCCCCCccc---
Confidence 346677899999998878999999999999999999999999999999996 89999999999999988876654
Q ss_pred cccccc
Q 000525 784 IPSAVV 789 (1443)
Q Consensus 784 i~~GfV 789 (1443)
+|||
T Consensus 105 --~GFI 108 (108)
T PF05000_consen 105 --RGFI 108 (108)
T ss_dssp --TTEE
T ss_pred --CCCC
Confidence 5776
No 38
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=99.25 E-value=1.6e-13 Score=175.90 Aligned_cols=359 Identities=15% Similarity=0.109 Sum_probs=240.7
Q ss_pred HHHHHhheEeeecceEEccCCceEEEEEeccCCCCCCCcccCCceeccccccchhHHHHhcc---ccccc-----ccccc
Q 000525 828 LMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGTSTPTGEIGDQPVGSLSACAISEAAYSAL---DQPIS-----LLETS 899 (1443)
Q Consensus 828 Lvk~lEdl~v~YD~tVR~s~G~~iiq~~yg~~g~~~~~~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~-----~l~t~ 899 (1443)
+|.|.|.+-+.+. |.|-. .++=-.|..|-+. ....+++..+|..+|||.+++.+|+. .++.. ...+.
T Consensus 377 Imq~~e~vl~~gk-t~rLh---~lVc~~yNADFDG-DeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v 451 (808)
T COG0086 377 IMQAFEPVLPEGK-AIRLH---PLVCEAYNADFDG-DEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTV 451 (808)
T ss_pred HHhhceeeccccc-eeecc---hhhccccccccCc-hhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEE
Confidence 3366666554332 22221 1222345544321 22456778888999999999999983 44332 22345
Q ss_pred ccccchhhhccCCCCCCCccEeeeehhhhccccccCchhhHHHHHhhhcccchhhhhceEEEEEcCCCCcccccCceEEE
Q 000525 900 PLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICH 979 (1443)
Q Consensus 900 gl~rLkEIl~~~k~~~~~~~~~~l~Ls~~~~k~~~~~e~~a~~Vk~~LE~~tL~di~~~i~i~y~P~~~~~~~~sp~v~~ 979 (1443)
+.+++-++.++ + .++++.+++++...+. ...+.+..+.+.++.++.+++++++..... ...+.
T Consensus 452 ~g~ylLt~~d~-~--~~~~~~~ei~l~~~~~----~~~e~~~ai~~~~~~~~~k~i~~~i~~~~~----------~~~i~ 514 (808)
T COG0086 452 GGPYLLTIVDA-K--LPSTPVGEIYLKDEYA----DDREKAEAIAKKIELTTGKVIVSTISPDLA----------ELSII 514 (808)
T ss_pred eccEEEEEecc-c--CCCCcceEEEeccccc----cchhhhHHHhcccceeeeeEEEEEeeccCC----------cceEE
Confidence 56677766666 2 4556788887763332 223578999999999999999886443211 12345
Q ss_pred EEeeHHHHHHcCCCHHH-HHHHHHHhhhhhhhhhcccCCceeeecCccccccccccCCCceEEEEEeeccccc-chh-hH
Q 000525 980 FHVRKEIMKRTGLKEHS-IIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMIVENFKR-TSI-DL 1056 (1443)
Q Consensus 980 ~~Ldke~l~~~~L~i~~-I~~~i~~~~~~~~~~l~~~~~~i~i~~~~c~~~~~~~~~~~~~~i~v~~~~~~~~-~~~-~l 1056 (1443)
+..+.+.+..+.+..+. +...+.+.. ..+ -.+ .. . ...+...... ... .+
T Consensus 515 ~t~~~~~~~~~~~~~~~d~~~~i~~~~-----l~~-----~~i-~k-------------~---~~~i~~~~g~~~~~~~~ 567 (808)
T COG0086 515 VTTDGRRIFNRGLPEDKDVLVKIVNGK-----LIK-----GVI-DK-------------K---IVTIYREYGPEVASKAL 567 (808)
T ss_pred EecchhhhhhccCCcccceeeEEeccc-----cce-----eee-hh-------------h---HHHHHHHhCchhhHHHH
Confidence 66677777766665441 221111110 000 000 00 0 0000000000 000 22
Q ss_pred HHHHHHhccccccceeeccccceEEEEeecccccccCCCCCCCceEEEEEeeccccccchhHHHHhhhhccccccccccc
Q 000525 1057 ETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTR 1136 (1443)
Q Consensus 1057 ~~l~~~iip~ll~~vVkG~~~I~rv~I~~~d~~~~~~~~~~~~~el~l~~~gs~~~~~~~~~~vll~~~l~~~~~id~~r 1136 (1443)
.. .+..|.+.-+++..++..++...... ......|++.+++++. ++..++ .+.+|.++
T Consensus 568 ~~----~~dkl~~~~~~~~~~~~~~i~~~d~~------~~~~~~e~v~~ae~~v-----------~~~i~~-~~~g~lt~ 625 (808)
T COG0086 568 VK----LLDKLKNLGIKGIGGFGIGIGRKDIE------AEDEKDEIVIEAEGSV-----------LKLILQ-YEEGDLTR 625 (808)
T ss_pred HH----HHHHHHHhheeeeccceEEeeccccc------chHHHHHHHHHHHHHH-----------HHHHHH-hhcCCccc
Confidence 22 23355566777777777776553200 0122346776665543 445555 78999999
Q ss_pred cCCCcHHHHHHHHcHHHHHHHHHHHHHHHhcccCCc-cCHHHHHHHHhhccceeeEeecchhhhhhhhccCCCcchhhhc
Q 000525 1137 SHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKN-ILPEHLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQA 1215 (1443)
Q Consensus 1137 t~sn~I~ei~~~lGIEAar~~ii~el~~~~~~~G~~-V~~rHl~LlAd~MT~~G~~~gi~r~G~~~~~~~l~~~Spl~~a 1215 (1443)
+..||+.++..++|+||+++++++++..+...+|.. ++.+|+++.+|.||.+|...-+.++|+...+. |++++|
T Consensus 626 ~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~n~sq~~~~iG~~gv~g~r~-----~~~~~~ 700 (808)
T COG0086 626 TERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKI-----SVLARA 700 (808)
T ss_pred cCCCCeEEEeehHHHHHHHHHHHHHHhhhHHhcCCcchhHHHHhhhhhccCHHHHHHHhhhheeeccCC-----Cccccc
Confidence 999999999999999999999999999999999999 99999999999999999999999999998765 899999
Q ss_pred cccccHHHHHHHHhhCCCcCCCCccceeccCCCCCccCccceEEEEccC
Q 000525 1216 FFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHFDIIYSGE 1264 (1443)
Q Consensus 1216 sFe~t~~~l~~AA~~g~~D~l~gvs~~ii~Gk~~~~GTgg~f~ll~~~~ 1264 (1443)
+||.+..+ ..|+.+++.+.+.|++++.+.|++++.|| |.+|.-++.-
T Consensus 701 ~Fe~~~~~-~~a~~~i~s~f~eGLt~~e~f~~~~ggR~-GlvDTA~KTa 747 (808)
T COG0086 701 AFEVTVKH-LEAEGPGESSFLEGLTENEYFGHPIGGRT-GLVDTALKTA 747 (808)
T ss_pred cccccccc-ceeeeeeecccCCCCCcceEEeecCcccc-chHHHhhhhc
Confidence 99999999 99999999999999999999999999999 9999988754
No 39
>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=97.61 E-value=5.9e-05 Score=77.66 Aligned_cols=56 Identities=20% Similarity=0.429 Sum_probs=45.1
Q ss_pred cchhhhhceEEEEEcCCCC-------------c---------ccccCceEEEEEeeHHHHHHcCCCHHHHHHHHHHhh
Q 000525 950 LMLSDIVSTSMIIYSPQTG-------------S---------MKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQC 1005 (1443)
Q Consensus 950 ~tL~di~~~i~i~y~P~~~-------------~---------~~~~sp~v~~~~Ldke~l~~~~L~i~~I~~~i~~~~ 1005 (1443)
|||++|+...+|.|+|+.. | ...+|||++++.||++.|..++|+++.|.++|.+.+
T Consensus 1 TtL~~vt~~teIyYDPdp~~Tvi~eD~e~V~~y~e~pd~~~~~~~~spWlLRieLdr~~m~dk~l~m~~I~~~I~~~f 78 (135)
T PF04990_consen 1 TTLRDVTASTEIYYDPDPRNTVIEEDREFVESYFEIPDEDDDPSRLSPWLLRIELDRKKMIDKKLTMEDIAEKIKEEF 78 (135)
T ss_dssp ECCHCHECEEEEEE-SSTTSSSSSTTHCHHHHCCCTT-SSTT-SSBESEEEEEEE-CCCCCCTT--HHHHCCCHHHCC
T ss_pred CcHHHhhhheeEEECCCCCCCcchhhHHHHHHHHhCCCcccCcccCCCeEEEEEEcHHHHHhcCCCHHHHHHHHHHhc
Confidence 6899999999999999863 1 235679999999999999999999999999998876
No 40
>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=97.35 E-value=4.1e-05 Score=83.95 Aligned_cols=47 Identities=17% Similarity=0.061 Sum_probs=39.4
Q ss_pred cccCCceeccccccchhHHHHhcc---cccccc--ccccccccchhhhccCC
Q 000525 866 GEIGDQPVGSLSACAISEAAYSAL---DQPISL--LETSPLLNLKNVLECGS 912 (1443)
Q Consensus 866 ~~~~ge~VG~~aAqSi~Ep~tq~l---~~~~~~--l~t~gl~rLkEIl~~~k 912 (1443)
.+.+||+||++||||||||+|||+ +|..++ ..++|+||++|++++++
T Consensus 2 ~~~~g~~vg~~aaqsigep~tq~t~~tfh~~g~~~dIt~Glprv~el~e~r~ 53 (204)
T cd02655 2 LVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVATDITQGLPRVEELFEARK 53 (204)
T ss_pred ccCcccccchhhhhhcCCCccccccchhhhcccccccccccHHHHHHHHhhc
Confidence 357899999999999999999996 555443 34689999999999976
No 41
>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=96.31 E-value=0.00098 Score=70.61 Aligned_cols=42 Identities=29% Similarity=0.283 Sum_probs=33.9
Q ss_pred CceeccccccchhHHHHhcc-ccc-----cccccccccccchhhhccC
Q 000525 870 DQPVGSLSACAISEAAYSAL-DQP-----ISLLETSPLLNLKNVLECG 911 (1443)
Q Consensus 870 ge~VG~~aAqSi~Ep~tq~l-~~~-----~~~l~t~gl~rLkEIl~~~ 911 (1443)
|||||++||||||||+||++ ..+ .+...|+++||+++++++.
T Consensus 1 g~~~g~~a~~~~~~p~~~~tl~t~~~~~~~~~~~t~~~pk~~~~~~~~ 48 (158)
T cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48 (158)
T ss_pred CCcchhhhhhhcCCCccchhhhhhhhccccccccccCCccchhhcccc
Confidence 79999999999999999985 222 2234568999999999886
No 42
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=91.48 E-value=0.057 Score=71.98 Aligned_cols=39 Identities=15% Similarity=-0.035 Sum_probs=31.6
Q ss_pred EEEEEeccCCCCCCCcccCCceeccccccchhHHHHhccccc
Q 000525 851 IVQFSYNIEGTSTPTGEIGDQPVGSLSACAISEAAYSALDQP 892 (1443)
Q Consensus 851 iiq~~yg~~g~~~~~~~~~ge~VG~~aAqSi~Ep~tq~l~~~ 892 (1443)
|++.++..+ ..+.+.|||+||++||||||||+|||+..+
T Consensus 41 Il~~I~~~y---~~a~vepge~vG~~aaqsi~~~~~~~~~~~ 79 (858)
T PRK14898 41 IIDEVVSAY---LNALVEPYEAVGIVAAQSIGEPGTQMSLPY 79 (858)
T ss_pred HHHHHHHHH---hhCCCCCCceeeeeeehhcCCCCccccCCC
Confidence 666666666 356789999999999999999999996443
No 43
>PF05183 RdRP: RNA dependent RNA polymerase; InterPro: IPR007855 This entry represents various eukaryotic RNA-dependent RNA polymerases (RDRP; 2.7.7.48 from EC), such as RCRP-1, RDRP-2 and RDRP-6. These enzymes are involved in the amplification of regulatory microRNAs during post-transcriptional gene silencing []; they are also required for transcriptional gene silencing. Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways []. These enzymes also play a role in the RNA interference (RNAi) pathway, which is important for heterochromatin formation, accurate chromosome segregation, centromere cohesion and telomere function during mitosis and meiosis. RDRP enzymes are highly conserved in most eukaryotes, but are missing in archaea and bacteria. The core catalytic domain of RDRP enzymes is structurally similar to the beta' subunit of DNA-dependent RNA polymerases (DDRP), however the other domains of DDRP show no similarity to those of RDRP.; GO: 0003968 RNA-directed RNA polymerase activity; PDB: 2J7O_A 2J7N_A.
Probab=49.60 E-value=11 Score=48.70 Aligned_cols=55 Identities=29% Similarity=0.404 Sum_probs=28.9
Q ss_pred ceeccCceEEEeCCCCCCccccccccEEEecCCc----eE-------EecccCCCCCCCCCCCCceeee
Q 000525 404 RPLTDGDIVLINRPPSIHPHSLIALTVKVLPISS----VV-------TINPLCCSPFHGDFDGDCLHGY 461 (1443)
Q Consensus 404 Rhl~dgD~vl~NRqPsLHk~Simah~v~v~p~~~----t~-------r~n~~~c~pyNADFDGDeMN~h 461 (1443)
..+..| .||+-|.|++|..-|+-.++.-.|.=+ ++ |=++..|+ ++|+|||+-.+-
T Consensus 364 ~~~~~g-~VlV~R~P~~~pgDir~~~av~~p~L~~l~~vIVF~~~G~r~~~~~ls--GgDlDGD~~~V~ 429 (579)
T PF05183_consen 364 SQVLEG-DVLVTRNPCLHPGDIRKVKAVDKPELRHLKDVIVFSTKGDRPLPSELS--GGDLDGDEYFVC 429 (579)
T ss_dssp EEEEE--EEEEE-SS--SGGGEEEEEE---GGGTT--SEEEE-S-SSS-HHHHTT--T--SSS-EEEEE
T ss_pred cceeee-eEEEecCCccCcCceeEEEeeccHHHcccCCEEEeCCCCCCCchHHhc--CCCCCCceEEEE
Confidence 345677 899999999999999998887665211 11 11122233 479999998865
No 44
>PF05094 LEF-9: Late expression factor 9 (LEF-9); InterPro: IPR007786 The baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) encodes a DNA-dependent RNA polymerase that is required for transcription of viral late genes. This polymerase is composed of four equimolar subunits, LEF-8, LEF-4, LEF-9, and p47. LEF-9 is homologous to the largest beta-subunit of prokaryotic DNA-directed RNA polymerase [].; GO: 0019083 viral transcription
Probab=29.27 E-value=74 Score=38.77 Aligned_cols=66 Identities=21% Similarity=0.187 Sum_probs=50.0
Q ss_pred eEEEeCCCCCCccccccccEEEecC--CceEEecccCCCCCCCCCCCC-ceeeecCCChhHHHHHHHHcC
Q 000525 411 IVLINRPPSIHPHSLIALTVKVLPI--SSVVTINPLCCSPFHGDFDGD-CLHGYIPQAIGARVELTELVA 477 (1443)
Q Consensus 411 ~vl~NRqPsLHk~Simah~v~v~p~--~~t~r~n~~~c~pyNADFDGD-eMN~h~PQs~~AraEa~~Lm~ 477 (1443)
.+.--|+|.+-..|-+--+|+.-.. .-.+++=..+...-|+|-||| |.--++|+. ++-.+++.|+.
T Consensus 212 raw~tRHPniSqlsTq~s~v~~~~~~~~wnvkvGlG~F~Gan~DCDGDKeviT~lP~P-NSLidlE~lLY 280 (487)
T PF05094_consen 212 RAWTTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFVGANRDCDGDKEVITYLPYP-NSLIDLESLLY 280 (487)
T ss_pred eeeecCCCCchhhchhheEeeccccCCCcceeeeeccccCCCCCCCCCceEEEecCCC-cchhhHHHHhc
Confidence 4566799999999999988886421 124777778889999999999 777888883 35666666665
No 45
>PF14754 IFR3_antag: Papain-like auto-proteinase
Probab=27.96 E-value=12 Score=39.01 Aligned_cols=30 Identities=27% Similarity=0.798 Sum_probs=21.2
Q ss_pred CCCCCCCCC--CCCCCCCCCCcc-ceeecCccc
Q 000525 53 NPTNECSSC--GAKDRKACEGHF-GFIKFPFTI 82 (1443)
Q Consensus 53 ~~~~~C~TC--g~~~~~~CpGHF-GhIeL~~PV 82 (1443)
|.+..|..| |-..+.+|||-| |-++|+.||
T Consensus 36 dgstlcaecfrgcegmeqcpglfmgllklaspv 68 (249)
T PF14754_consen 36 DGSTLCAECFRGCEGMEQCPGLFMGLLKLASPV 68 (249)
T ss_pred cCccHHHHHhccCcchhhCcHHHHHHHHhcCCC
Confidence 345667776 223578999976 889998665
No 46
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.66 E-value=50 Score=43.46 Aligned_cols=47 Identities=23% Similarity=0.355 Sum_probs=35.6
Q ss_pred CccceeecCccccccccHHHHHH-HHh-------------ccccccccccCcchhhhcccccccccccccccc
Q 000525 71 GHFGFIKFPFTILHPYFLSDIAK-LLN-------------SICPKCKTIRKERQKGAGSSRKEQPRVCKYCVR 129 (1443)
Q Consensus 71 GHFGhIeL~~PVfHpgf~~~i~k-IL~-------------~iC~~C~rlll~~~~k~l~~~~~~~~~C~~C~~ 129 (1443)
||--||+|+-..-+|-=+..+++ +.. .+|..|+.+- .....||.|+.
T Consensus 587 G~I~hv~l~e~~~n~~a~~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~------------g~~~~CP~CG~ 647 (656)
T PRK08270 587 GTVFHLYLGEAISDAEACKKLVKKALENYRLPYITITPTFSICPKHGYLS------------GEHEFCPKCGE 647 (656)
T ss_pred eEEEEEECCCCCCCHHHHHHHHHHHHHhCCCceEEeCCCCcccCCCCCcC------------CCCCCCcCCcC
Confidence 69999999998888877777766 555 4699999741 11367999985
No 47
>PHA03396 lef-9 late expression factor 9; Provisional
Probab=23.68 E-value=1e+02 Score=37.81 Aligned_cols=66 Identities=20% Similarity=0.136 Sum_probs=47.6
Q ss_pred eEEEeCCCCCCccccccccEEEecCC--ceEEecccCCCCCCCCCCCC-ceeeecCCChhHHHHHHHHcC
Q 000525 411 IVLINRPPSIHPHSLIALTVKVLPIS--SVVTINPLCCSPFHGDFDGD-CLHGYIPQAIGARVELTELVA 477 (1443)
Q Consensus 411 ~vl~NRqPsLHk~Simah~v~v~p~~--~t~r~n~~~c~pyNADFDGD-eMN~h~PQs~~AraEa~~Lm~ 477 (1443)
.+.--|+|.+-..|-+--+|+.-... --++.=..+...-|+|-||| |.--++|+.. +-.+++.|+.
T Consensus 215 raw~tRHPnisqlstq~s~v~~~~~~~~wNvkvGlG~F~GanrDCDGDKeviT~lP~PN-sLidlE~lLY 283 (493)
T PHA03396 215 RAWTTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFPGANRDCDGDKEVITFLPYPN-SLIDLECLLY 283 (493)
T ss_pred EEeecCCCCchhhchhheEeeccccccccceeeeeccccCCCCCCCCCceEEEecCCCc-chhhHHHHhc
Confidence 45667999999999998888763211 12556667788999999999 7888888832 5555555554
No 48
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.40 E-value=55 Score=41.80 Aligned_cols=57 Identities=23% Similarity=0.457 Sum_probs=34.7
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCccceeecCccccccccHHHHHHHHhccccccccccCcchhhhcccccccccccc
Q 000525 46 NPRLGLPNPTNECSSCGAKDRKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKCKTIRKERQKGAGSSRKEQPRVCK 125 (1443)
Q Consensus 46 D~rLG~~~~~~~C~TCg~~~~~~CpGHFGhIeL~~PVfHpgf~~~i~kIL~~iC~~C~rlll~~~~k~l~~~~~~~~~C~ 125 (1443)
=+|-|- .+.-.|..||. ...|| | ..-++ +||-. .+ +..|++|+.-. .....||
T Consensus 205 lnrrGy-a~~~~C~~Cg~--~~~C~-~---C~~~l-~~h~~-----~~--~l~Ch~Cg~~~------------~~~~~Cp 257 (505)
T TIGR00595 205 LNRRGY-SKNLLCRSCGY--ILCCP-N---CDVSL-TYHKK-----EG--KLRCHYCGYQE------------PIPKTCP 257 (505)
T ss_pred EeCCcC-CCeeEhhhCcC--ccCCC-C---CCCce-EEecC-----CC--eEEcCCCcCcC------------CCCCCCC
Confidence 355664 35668999994 67887 2 22222 23311 11 35799999753 2346899
Q ss_pred cccc
Q 000525 126 YCVR 129 (1443)
Q Consensus 126 ~C~~ 129 (1443)
.|++
T Consensus 258 ~C~s 261 (505)
T TIGR00595 258 QCGS 261 (505)
T ss_pred CCCC
Confidence 9986
Done!