HHsearch alignment for GI: 254780143 and conserved domain: CHL00001
>CHL00001 rpoB RNA polymerase beta subunit.
Probab=100.00 E-value=0 Score=2638.78 Aligned_cols=1040 Identities=43% Similarity=0.724 Sum_probs=964.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEE--EEEECCCCCCHHHHHHCCCCE
Q ss_conf 666788708899999999986246652211122589997663780767985899999--789809858899999839975
Q gi|254780143|r 21 PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDPPKFDVDDCLWRDLTY 98 (1386)
Q Consensus 21 ~~~~~~P~Li~iQ~~Sf~~Flq~~~~~~~r~~~GL~~v~~~~fPI~d~~~~~~Lef~--~y~l~~Pk~tp~ECRlR~lTY 98 (1386)
T Consensus 2 ~~~~~~PdLv~~Q~dSFn~Fl----------~~gL~ei~~~~~pI~d~~~~~~l~~~~~~y~l~~P~~t~~Ecr~r~lTY 71 (1065)
T CHL00001 2 EGMSTIPDFLQIQFESFCRFI----------DQGLTEELSKFPKIEDTDQEIEFQLFGETYQLVEPLIKERDAVYESLTY 71 (1065)
T ss_pred CCCCCCCCHHHHHHHHHHHHH----------HHHHHHHHHHCCCEECCCCCEEEEEEECEEEECCCCCCHHHHHHHCCCC
T ss_conf 884679977999999999999----------9748999985598784799889999705799848968999998619931
Q ss_pred EEEEEEEEEEEEECCCCCCCCCCCEEEEEEEEEEEECCEECCCCCEEECCEEEEEEEEECCCCCEEECCCCCCCCCCCCE
Q ss_conf 33589999999931787665520001223678751000026896289868214686651227852120234651577856
Q gi|254780143|r 99 AVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178 (1386)
Q Consensus 99 sapL~V~i~l~v~~~~~~~~~k~~~~ike~~V~lG~IPiMt~~GyFIING~ERVIVsQl~RSPGVyf~~~k~k~~~s~k~ 178 (1386)
T Consensus 72 saplyV~v~l~~~---------~~~~ik~~~V~iG~iPiMt~~GyFIING~ERVIV~Qi~rsPGiyf~~~~d~---~~~~ 139 (1065)
T CHL00001 72 SSELYVPAGLIWK---------KSRDIQEQTIFIGNIPLMTSLGTFIINGIYRVVINQILRSPGIYYRSELDH---NGIS 139 (1065)
T ss_pred CCCEEEEEEEEEC---------CCCEEEEEEEEEEEECEECCCCEEEECCCEEEEEEEEECCCCCEEEEEECC---CCCE
T ss_conf 1018999999987---------774799999999873779999789990852489898614898378766358---9967
Q ss_pred EEEEEEECCCCCEEEEEECCCCEEEEEECCCCCHHHHHHHHHCCCCHHHHHHHHCCCEEEEECCCCCCCCCCHHHHHHHH
Q ss_conf 79999811887236899758982999971878703998998809984799997387405773067310235456664210
Q gi|254780143|r 179 LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258 (1386)
Q Consensus 179 ~ysa~IIP~RGSwLe~e~d~kd~iyvrIdr~rKIPi~ilLrALG~ssdeIl~~f~~~~~~~~~~~~~~~~~~~~~~~~~~ 258 (1386)
T Consensus 140 ~~~a~ii~~rG~wl~~e~~~k~~i~vri~k~~kIPi~ilLrALG~sd~eI~~~i~~~e~-----------------~--- 199 (1065)
T CHL00001 140 VYTGTIISDWGGRLKLEIDKKARIWARVSKKQKISILVLLSAMGLNLREILDNVCYPEI-----------------F--- 199 (1065)
T ss_pred EEEEEEEECCCCEEEEEECCCCEEEEEECCCCCEEHHHHHHHHCCCHHHHHHHHCCHHH-----------------H---
T ss_conf 99999996898649999837986999937988340999998869799999988356688-----------------8---
Q ss_pred HHHHHHCCCCCCCEEECCCCHHHHHHHHHHHHCCCCCCCCCHHHHCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf 12232112445845440221020799887876360001026677347410000136667769996234599899999986
Q gi|254780143|r 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338 (1386)
Q Consensus 259 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~~~~~~~~~d~~~gei~~~~~~~~~~~~l~~~~~ 338 (1386)
T Consensus 200 -------------------------------------------------------------------------------- 199 (1065)
T CHL00001 200 -------------------------------------------------------------------------------- 199 (1065)
T ss_pred --------------------------------------------------------------------------------
T ss_conf --------------------------------------------------------------------------------
Q ss_pred CCCCCEEEEEECCCCCCCCCCHHHHCCCCCCHHHHHHHHHHHH--CCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Q ss_conf 5654102442024445520000011023458899999988760--57763104568888620245302333455557776
Q gi|254780143|r 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416 (1386)
Q Consensus 339 ~~~~~~~~l~~~~~~~~~~i~~~~~~d~~~~~~eAl~~I~k~l--r~~~~~~~~~~~~~~~~~~~~~~~y~l~~vgr~~~ 416 (1386)
T Consensus 200 --------------------~~~~~~~~i~t~e~Al~ei~~~~~~~~~~~~~~~~a~~~l~~~ff~-~rydLg~vGR~kl 258 (1065)
T CHL00001 200 --------------------LSFKEKKKIGSKENAILEFYKQFACVGGDPVFSESLCKELQKKFFQ-QRCELGRIGRRNI 258 (1065)
T ss_pred --------------------HHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH-HHCCCHHHHHHHH
T ss_conf --------------------8776540458889999999986325789862168999999987644-3046113416776
Q ss_pred HHHCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-
Q ss_conf 5420366776770661899888898887630487643440101533233335787898888889999887653113443-
Q gi|254780143|r 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI- 495 (1386)
Q Consensus 417 n~~l~~~~~~~~~~Lt~~d~~~~i~~L~~l~~g~~~~DdiDhlgnkRvr~vgeLl~~~fr~~l~rl~r~i~~~~~~~~~- 495 (1386)
T Consensus 259 n~kl~l~i~~~~~~L~~~dil~~i~~Li~l~~g~~~~DDiDhlgNKRlrlaGeLL~~~fr~~l~rl~r~ik~~m~~~~~~ 338 (1065)
T CHL00001 259 NKKLNLDIPQNNTFLLPQDILAAADYLIGLKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENVVRETICGAIRH 338 (1065)
T ss_pred HHHHCCCCCCCCEEECHHHHHHHHHHHHHHHCCCCCCCCCHHCCCCEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 66306898843117639999999999998650899876501205844355899999999999999999999999776424
Q ss_pred -CCCCCCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCC
Q ss_conf -3435211222023465554202667503541554210232200112234444432234665543221111044430356
Q gi|254780143|r 496 -DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574 (1386)
Q Consensus 496 -~~~~~~~~in~~~i~~~i~~ff~t~~lsq~ld~~n~ls~lth~RR~s~lgpggl~r~~~~~evR~ih~s~~GriCPieT 574 (1386)
T Consensus 339 ~~~~~~~~li~~~~it~~ik~ffgs~~LSQfmdqtNpLseltHkRRlSalGPGGltr~~a~fevR~lHpShwGriCPiET 418 (1065)
T CHL00001 339 KLIPTPQNLVTSTPLTTTYEEFFGSHPLSQFLDQTNPLTEIVHKRKLSYLGPGGLTRRTASFRVRDIHPSHYGRICPIET 418 (1065)
T ss_pred CCCCCHHHHCCCHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCC
T ss_conf 54478888427478999999987566431443425888887766653235887655455676100036654630224558
Q ss_pred CCCCCCEEEECEEEEEEECCCCCCCCEEEEEECCCCCCC--EEECCHHHHCCEEEECCCCEECCCCCCCCCCEEECCCCC
Q ss_conf 676521021000122442468764410698622553481--664296773763796165341146840222000000233
Q gi|254780143|r 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652 (1386)
Q Consensus 575 PEG~n~GLv~~la~~a~in~~g~ie~py~~v~~~~~~~~--i~~l~~~~e~~~~Ia~~~~~l~~~~~~~~~~~~~r~~~~ 652 (1386)
T Consensus 419 PEG~n~GLVknLAl~a~I~~~G~ietP~~~v~~~~~~~~~~~~~l~~~~e~~~~ia~~~~~~~~~~~~~~~~~~~r~~~e 498 (1065)
T CHL00001 419 SEGINAGLIGSLAIHARINHWGFLESPFYKISEGKVSKEERMVYLSPGRDEYYMIAAGNSLALNQGIQEEQVVPARYRQE 498 (1065)
T ss_pred CCCCCCCHHHHHHHEEECCCCCCCCCCCEEEECCEEECCCEEEEECCCCCCCEEEECCCEEECCCCCCCCCEEEEECCCC
T ss_conf 88765421432211220367775578858920570642562898465222763880274345257826354021001465
Q ss_pred CCCCCHHHEEECCCCCCCEEEECCCCCCCHHHCCHHHHHHHHHHHHHHHCCCCCCCCEECCCCCHHHHHHCCCEEECCCC
Q ss_conf 33225787220236721102311233320110100221122234443210136654111266201110106530102124
Q gi|254780143|r 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732 (1386)
Q Consensus 653 ~~~~~~~~v~~~~i~p~~i~sv~aslIPflehdda~R~l~g~nm~rQav~l~~~~~~~v~tg~E~~~~~~s~~~i~a~~~ 732 (1386)
T Consensus 499 ~~~~~~~~v~~~~i~p~q~~sv~aslIPflehnda~R~lmgsnMqrQavpll~~e~p~Vgtg~e~~~a~ds~~~~~a~~~ 578 (1065)
T CHL00001 499 FLTIAWEQVHFRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLLRSEKCIVGTGLERQVALDSGVVAIAEHE 578 (1065)
T ss_pred CEEECCCEEEEEECCCCEEEEEEEEEECCHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHCCCCEEEECCC
T ss_conf 04503222578860566476433224210321873233333320355011013656501267254443204736884268
Q ss_pred CCCCCCCCCCEEEECCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCEEECCCEECCCCCCCCCCCCCCCCCE
Q ss_conf 43433565530252156655644466301114655544547322445304479772078520355223578602223751
Q gi|254780143|r 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812 (1386)
Q Consensus 733 g~v~~vd~~~i~i~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~q~p~V~~g~~~~~~~~l~~~~~~~~~el~~G~N~~ 812 (1386)
T Consensus 579 G~v~y~d~~~i~~~~~~~-------~~~~y~l~~~~rsn~~t~~~q~P~V~~g~~v~~g~ilad~~~t~~~el~~G~N~~ 651 (1065)
T CHL00001 579 GKIIYVDADKIILSGNKG-------DTLSIPLVKYQRSNQNTCMHQKPIVWRGECIKKGQILADGAATVGGELALGKNVL 651 (1065)
T ss_pred CEEEEEECCEEEEECCCC-------CEEEEEECCCCCCCCCCCCCCCEEEECCCEEECCCEECCCCHHHCCEECCCCCEE
T ss_conf 628885076689963788-------5578752566668755542512056248677128374356321078501221037
Q ss_pred EEEEECCCCCCCCCEECCHHHHHCCCCCEEEEEEEEHHHHHCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCEECCCC
Q ss_conf 55531355444442000013442587310346665311211478840024666546867841024137413773313676
Q gi|254780143|r 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892 (1386)
Q Consensus 813 VA~m~~~GYN~EDaiiin~~~v~rg~~~s~h~~~y~~~~~~~~~g~~~~~~~~~~~~~~~~~~ld~~Giv~~G~~V~~gD 892 (1386)
T Consensus 652 VA~m~~~GYN~EDAiiin~~~v~~~~ftSih~~~ye~~~~~~~~g~e~it~~ip~~~~~~~~~LD~dGii~~G~~V~~gD 731 (1065)
T CHL00001 652 VAYMPWEGYNFEDAVLISERLVYEDIYTSIHIEKYEIETRVTSQGPERITKEIPHLEAHLLRNLDENGIVMLGSWVETGD 731 (1065)
T ss_pred EEEECCCCCCHHHHEEECHHHHHCCCEEEEEEEEEEEEEEECCCCCCEECCCCCCCCHHHHHHCCCCCCCCCCCEEECCC
T ss_conf 89834576026681330224543575059999998899984478874313669997778885486567707887884797
Q ss_pred CEEECCCCC--CCCCCCHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 111012467--777677034665430355554432332022788532200121014565420266788889999999872
Q gi|254780143|r 893 ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970 (1386)
Q Consensus 893 ilvgk~tp~--~~~~~~pe~~~l~~i~~~~~~~~~d~~~~~~~g~~g~v~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 970 (1386)
T Consensus 732 ilvgK~tp~~~~~~~~~pe~~ll~~ifg~k~~~~kd~Sl~~~~g~~G~Vidv~~~~~~~~~------------------- 792 (1065)
T CHL00001 732 ILVGKLTPQEAEESSYAPEGKLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGS------------------- 792 (1065)
T ss_pred EEEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCEEECEEECCCCCCEEEEEEEEEECCCCC-------------------
T ss_conf 7999745778775555757766777634666741014275369985689999999757888-------------------
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCHHHHHEEEECCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 88899988788898888862585345665555543211357640148543100141586789999999998999999999
Q gi|254780143|r 971 KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050 (1386)
Q Consensus 971 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1050 (1386)
T Consensus 793 -------------------------------------------------------------------------------- 792 (1065)
T CHL00001 793 -------------------------------------------------------------------------------- 792 (1065)
T ss_pred --------------------------------------------------------------------------------
T ss_conf --------------------------------------------------------------------------------
Q ss_pred HHHHHHHHHHCCCCCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCEEEEEECCCCCCCC
Q ss_conf 99898876312588677472769999998755885523143366787358886300007879358715698668986750
Q gi|254780143|r 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130 (1386)
Q Consensus 1051 ~~~~~k~~ki~~~~~~~~gv~~~vKV~ir~~R~p~iGDKfasRHGqKGVis~i~p~eDMPf~~dG~~pDIIlNPhgvPSR 1130 (1386)
T Consensus 793 --------------~~~---~~~vkv~i~~~R~p~iGDKfasRHGqKGvig~I~p~eDMPf~~dG~~pDiIlNPhgvPSR 855 (1065)
T CHL00001 793 --------------SYN---PETIRVYILQKRKIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSR 855 (1065)
T ss_pred --------------CCC---CEEEEEEEEECCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCEEECCCCCCCC
T ss_conf --------------767---569999997405897553102145777554566043029979899875087888867666
Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEECCCC
Q ss_conf 70899999999999987196224333432222102467778776315432210000135256777665302684002565
Q gi|254780143|r 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210 (1386)
Q Consensus 1131 MtIGqllE~~lGka~~~~G~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~aTP~ 1210 (1386)
T Consensus 856 MtvGqllE~~lG~a~~~~g~~~~~tpF~~~~~~e~s~~li~--------------------------------------- 896 (1065)
T CHL00001 856 MNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVF--------------------------------------- 896 (1065)
T ss_pred CCHHHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHH---------------------------------------
T ss_conf 71999999998888874387044467766420345677889---------------------------------------
Q ss_pred CCCCCHHHHHHHHHHC------CCCCCCCEEEECCCCCCCCCCCEEEEEEEEEECCCHHHHHCCCCCCCCCCCEEECCCC
Q ss_conf 5788999999999986------8689986999868988402685048846454101102110000236873110307998
Q gi|254780143|r 1211 FDGADEEAINSMLRMA------DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284 (1386)
Q Consensus 1211 F~g~~~~~i~~~L~~a------G~~~~Gke~lydG~TGe~~~~~IfvG~~YyqkL~HMV~DKiHARstGP~sllTrQP~e 1284 (1386)
T Consensus 897 ------~~l~~~~~~~~~~~~f~~~~~Gk~~lydG~TGe~~~~~I~vG~~YyqkL~HmV~DKiHaRs~GP~s~lTrQP~~ 970 (1065)
T CHL00001 897 ------SELYEASKQTANPWLFEPEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSTGPYSLVTQQPLR 970 (1065)
T ss_pred ------HHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCC
T ss_conf ------99998665406652246689998798889988814673887277865434452436513663999531028999
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCC-CCCHHHHHHHHHHHHCCCCEEE
Q ss_conf 623317843207899999998698999986111001101599998876387878997-8667789999999854200276
Q gi|254780143|r 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSIDL 1363 (1386)
Q Consensus 1285 GRsr~GGlRfGEMErwaL~AyGAa~~LqE~Lt~kSDdv~gr~~~~~~iv~g~~~~~~-~~pesf~vl~~El~~l~l~~~~ 1363 (1386)
T Consensus 971 Grsr~GG~R~GEME~~aL~ayGAa~~L~E~L~~kSDd~~~r~~~~~~i~~g~~~~~~~g~pesf~vl~~El~~l~l~~~~ 1050 (1065)
T CHL00001 971 GRAKQGGQRVGEMEVWALEGFGAAYILQEMLTYKSDHIRARQEVLGAIIKGGTIPKPEGAPESFRLLVRELRSLALELNH 1050 (1065)
T ss_pred CCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEE
T ss_conf 74467986004788899999889999999844547463426688888766998888899995176899999854205167
Q ss_pred EECCCCCC
Q ss_conf 40665431
Q gi|254780143|r 1364 ENSRTKNS 1371 (1386)
Q Consensus 1364 ~~~~~~~~ 1371 (1386)
T Consensus 1051 ~~~~~~~~ 1058 (1065)
T CHL00001 1051 FLVSEKNF 1058 (1065)
T ss_pred EEECCCCC
T ss_conf 77145455