Query 003263
Match_columns 835
No_of_seqs 230 out of 420
Neff 4.9
Searched_HMMs 46136
Date Thu Mar 28 20:10:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003263.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003263hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1038 Mitochondrial/chloropl 100.0 2E-183 4E-188 1553.6 56.6 728 90-834 146-896 (1088)
2 PHA00452 T3/T7-like RNA polyme 100.0 1E-152 3E-157 1344.8 64.0 610 176-834 3-624 (807)
3 COG5108 RPO41 Mitochondrial DN 100.0 9E-144 2E-148 1198.4 44.7 606 180-813 251-873 (1117)
4 PF00940 RNA_pol: DNA-dependen 100.0 5.3E-68 1.1E-72 591.1 12.8 207 620-834 1-211 (405)
5 PF14700 RPOL_N: DNA-directed 100.0 1.1E-48 2.4E-53 420.4 23.8 305 180-498 1-318 (318)
6 PLN03188 kinesin-12 family pro 53.6 6.4E+02 0.014 33.8 18.4 45 222-266 1128-1172(1320)
7 PF14554 VEGF_C: VEGF heparin- 40.2 14 0.0003 31.0 1.0 19 130-148 5-23 (55)
8 PF07739 TipAS: TipAS antibiot 30.1 86 0.0019 29.0 4.7 56 173-228 13-71 (118)
9 cd03316 MR_like Mandelate race 24.5 45 0.00097 37.2 2.0 103 625-739 152-271 (357)
10 smart00482 POLAc DNA polymeras 21.3 28 0.0006 36.4 -0.4 89 691-806 3-91 (206)
No 1
>KOG1038 consensus Mitochondrial/chloroplast DNA-directed RNA polymerase RPO41, provides primers for DNA replication-initiation [Transcription; Replication, recombination and repair]
Probab=100.00 E-value=1.7e-183 Score=1553.60 Aligned_cols=728 Identities=53% Similarity=0.867 Sum_probs=659.8
Q ss_pred hhccccccc-------chhhhhhhhhccccchhhcccccccCCCCCcccccccCCcccceeecCCCchhHHHHh-----h
Q 003263 90 IENSVDFHI-------PTCEQEQNFHQRVENTETCADLVIPRSENSTNHQLMCLEPRRRIFVQDPPWFSSIFLK-----G 157 (835)
Q Consensus 90 ~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~ 157 (835)
+.+.++++. +.+++|.+..+-+-|++++.++ +.++++++.---+..-+...-++....|.++.+.. .
T Consensus 146 ~~~p~~~~~~~~~~~l~~~nsF~~~~~~l~G~~~g~s~-a~e~~~~~~~~~~s~~~~~~~~~~~~m~ke~~~~~~~~~~~ 224 (1088)
T KOG1038|consen 146 LVSPEHVRGIRQLLGLNNINSFPHSSEVLSGLIKGSSL-AGESENPTDQEGDSSNKQEINELVTKMEKEGNSLNQISSKF 224 (1088)
T ss_pred ccCchhhhhhHHhhccchhhcccchhhhhhcccccchH-HHHHhCcccccccccchhhHHHHHhHhhhhhhhhhHHHHHH
Confidence 445555665 6677787777888888999966 78888888733222334566677889998887633 3
Q ss_pred hHhhhh---HHHHhhhhHH-HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHcccCCCChh-HHHHHHHHHHHHHHHH
Q 003263 158 LYKRIK---LQEYREMKKR-KFNLLRRRQVKQETEAWERMVDEYK-ELEAKMIEKRLAPNLPH-IKGLFLGWFGPLSEAI 231 (835)
Q Consensus 158 ~~~~~~---~~~~~~~~~~-~~~~l~~RQ~~LE~~a~~~a~~r~r-~~~~~~~~~g~a~~~~~-~~~ll~~w~~~L~~~I 231 (835)
+...++ +.+-++.+.. +|-.+.+||..+|.++|++|+++|+ +...+|++..+++++|| +++++++||++|.++|
T Consensus 225 ~~~~~~~~lk~v~k~~~~~~d~~~l~~Rq~~~e~~~~e~a~e~~k~el~~~~c~~~l~~~lp~~lk~lf~~W~~~l~~ai 304 (1088)
T KOG1038|consen 225 LEESRDLPLKAVRKGFGDFKDFFNLDRRQVKLETEAWERAAEEWKIELESDMCEGSLAPNLPYNLKSLFLGWFKPLRDAI 304 (1088)
T ss_pred HHHHhcccHHHHHHhccchHhHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhcccccchHHHHHHHHHHHHHHHHH
Confidence 333333 5666667666 8888999999999999999999999 77789999999999999 9999999999999999
Q ss_pred HHHHHHHHhc--cCccchhhhhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 003263 232 EREQKMQRTK--KQKAAYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNY 309 (835)
Q Consensus 232 ~~e~~~~~~~--~~r~~y~p~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~v~~~~la~~IG~aVe~E~~~~~~~~k~kk~ 309 (835)
++|+..++.. +.|..|+|||++||++++|+|||+++|+++++|++.+++++++++.+||++||+|+|++.++++..++
T Consensus 305 ~ee~n~~r~~~~~~r~~Y~p~L~lL~a~k~aviti~el~~ll~tg~~~~~~~v~~aa~~~G~aveqe~ri~~~lq~~~k~ 384 (1088)
T KOG1038|consen 305 KEEINLLRALVRKGRLNYAPFLKLLDADKMAVITIHELMGLLMTGGETGGVRVVQAAKSLGRAVEQEFRIEQFLQRKTKN 384 (1088)
T ss_pred HHHHHHHHHHHhcCccccchHHHhcChhhHHHHHHHHHHhhhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 9999999876 88999999999999999999999999999999999999999999999999999999999998775443
Q ss_pred hhhhhhhhhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHccccCCCCCCCC
Q 003263 310 KRKKIIADTEEVLSKEKELLRKRVNSLIKSKRVMEAQKLLKN-EETKPWGRDTQAKLGSRLVELLIETAYVQHPVNPADY 388 (835)
Q Consensus 310 ~~~~~~~~~~~~~~k~~~~l~k~~~~~~k~~~~~~~~~~~~~-~~~~~W~~~~~~kvG~~Ll~~L~e~~~i~~~~~~~~~ 388 (835)
+... .....++....++.+..++++.+..+....+.. ....+|+..++++||++|+++||++++|+++.++..+
T Consensus 385 ~~~~-----~~~~~ke~~~~~~~v~~l~~~~k~~~~~~~~~~~~~~~pWp~~v~~kvGs~L~~lL~~~aki~~~~~~~~~ 459 (1088)
T KOG1038|consen 385 KAGD-----SYCELKELGKSRKEVRQLVQNLKLSQRLSGPESHLSEKPWPSAVQAKVGSRLIELLMQVAKIQVPADQPDT 459 (1088)
T ss_pred ccch-----HHHHHHHhhcccHHHHHHHHHHHHHHHhcccccccccCCccHHHHHHHHHHHHHHHHHHhcCCCcccCcCc
Confidence 3221 111234556667778888877776666665555 5678999999999999999999999999999998777
Q ss_pred CCCCccCceeEEeEeeecCCCCccceeEEEEEcCHHHHHHHHhhhhcccCCCCceeeCCCCCcCCCCcccccCCccceec
Q 003263 389 SPPDVRPAFRHRFKTILKHPGQKTTKRYGVVECDPLVLEGLDRSAKHMLIPYVPMLVPPKKWKGYNKGGYLFLPSYVMRT 468 (835)
Q Consensus 389 ~~~~~~paF~h~~~~~~~~~g~~~~k~~gvi~~~~~~~~~l~~~~~~~~~~~LPMlvPPkpW~~~~~GGYL~~~~~~~R~ 468 (835)
+.++.+|||.|.|++. +|++.+++||+|+|||.+..+|++.+.++.++++||||||+||+++++||||++|+++||+
T Consensus 460 ~~~~~~paf~h~f~~~---n~~~~~~~~g~ie~~pll~r~leks~~~~~~~~vPMLvpPkpWt~~~~Ggyl~~~s~lmRt 536 (1088)
T KOG1038|consen 460 KLPDERPAFVHTFQVT---NGQKGGRKYGVIECHPLLSRGLEKSALHFVPPLVPMLVPPKPWTGYDSGGYLFLPSYLMRT 536 (1088)
T ss_pred Cccccchhhhhheeee---cccccceeeeeeecCHHHHHHhhhhhccccccccccccCCCCCCCCCCCceEecchhhhhc
Confidence 7789999999999965 4554578999999999999999998888899999999999999999999999999999999
Q ss_pred CCcHHHHHHH-HhccccchHHHHHHHHhhcCcceEEcHHHHHHHHHHHHcCCCCCCCCCCCCCCCCCCC-CCCCHHHHHH
Q 003263 469 HGSRKQQEAL-KSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRNDVLIPEKP-LSEDMTEVQK 546 (835)
Q Consensus 469 ~~~~~q~~~l-k~~~~~~l~~v~~aLN~Lqst~WrIN~~VL~vi~~~w~~g~~i~~l~~~~~~p~P~~p-~~~d~~~~~~ 546 (835)
+++++|..++ ++.+.+++++||+|||.||+||||||++||||+.++|++|+.+.+++++.+.++|++| ..+|+++++.
T Consensus 537 ~g~~~Q~~~llkas~~~~l~~v~daL~~LG~t~WrVN~rvldvV~riw~~Gg~~~~~v~r~~~~lP~~P~~s~dp~~~~~ 616 (1088)
T KOG1038|consen 537 HGAKEQVDYLLKASPPGQLDPVFDALDTLGNTKWRVNRRVLDVVIRIWQNGGCFLLIVPREDVPLPPKPTLSEDPAELKA 616 (1088)
T ss_pred CCcHHHHHHHHhcCChhhhHHHHHHHHHhcCCCeeecchHHHHHHHHHhcCCCccCCCCCCCCCCCCCCCCCcChHHHHH
Confidence 9999999855 5557789999999999999999999999999999999999999999999999999999 6789999999
Q ss_pred HHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHhcCCCceeeccccCCCCccccCCCCCCCCCchhhhhhhhcccCccCCcc
Q 003263 547 WKWSVRKAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKS 626 (835)
Q Consensus 547 wk~~~~~~~~~~~~~~S~R~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~YP~~~~Ln~qGsDl~RsLL~FaegkpLG~~ 626 (835)
|+++.+++.+.++++||+|||++|+|+||++|+|+ .||||||||||||+||+||||||.|||+|||||+|++|+|||.+
T Consensus 617 wk~e~k~~~k~~~e~HS~RCD~~ykLsvAr~~~de-~Fy~PHNmDFRGRaYP~~PHlNHLgsDlcRglLeF~~GkPLG~s 695 (1088)
T KOG1038|consen 617 WKWEVKKAQKVNRERHSLRCDAEYKLSVARKMKDE-EFYYPHNMDFRGRAYPLPPHLNHLGSDLCRGLLEFAEGKPLGPS 695 (1088)
T ss_pred hHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhccC-eeecCcccCcCCccCCCCchhcccchHHHHHHHHHhcCCcCCcc
Confidence 99999999999999999999999999999999997 59999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhhhhcCCCCCCCHHHHHHHHHHHHHHHHHhccCCCCCchhHhhCCChHHHHHHHHHHHHHHhcCCCCcccc
Q 003263 627 GLRWLKIHLANLFSGGVEKLSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVIS 706 (835)
Q Consensus 627 Gl~WLKIhlANlyG~G~DK~S~deRi~wv~~n~~~I~dsA~dPL~g~~wW~~AD~PwQfLAaC~El~~al~s~dP~~y~S 706 (835)
||+|||||+||+|| |+||+|+++|++|+++|+++|+|||++||+|++||++|||||||||+||||++|++++||+.|+|
T Consensus 696 GL~WLKIHlaNL~~-g~~kl~~~~RlAF~E~hl~DI~DSAd~PLtG~rWW~~AedPfQ~LA~C~elaea~RspdPeayiS 774 (1088)
T KOG1038|consen 696 GLRWLKIHLANLYA-GVDKLSLRDRLAFTEEHLDDIFDSADRPLTGRRWWLKAEDPFQCLAACMELAEALRSPDPEAYIS 774 (1088)
T ss_pred chhHHHHHHHHHhc-ccccccHHHHHHHHHHHHHHHhhcccCCCcccchhhcCCChHHHHHHHHHHHHHHcCCCHHHHHh
Confidence 99999999999997 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCchhhHHHHHhhCChhhhcccccCCCCCcccchhHHHHHHHHHHHhhcCCCCCCCcHHHHHHHcccCCCccc
Q 003263 707 HLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKL 786 (835)
Q Consensus 707 ~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLipsd~PqDVYs~Va~~V~~~i~~da~~d~~~~~~~~~ak~l~~~I~RKv 786 (835)
|+||||||||||||||||||||..||++|||+|||+|||||++||..|.+.+++||++|+ .+|++|.+.|||||
T Consensus 775 H~PIHQDGSCNGLQHYAALGrD~~GA~~VNLvpsdkPqDVYs~VA~~V~~~~k~DAe~g~------e~Ak~L~~~V~RKv 848 (1088)
T KOG1038|consen 775 HIPIHQDGSCNGLQHYAALGRDSEGAAAVNLVPSDKPQDVYSAVAARVEKIMKQDAEKGP------EVAKILKDQVTRKV 848 (1088)
T ss_pred cCCcccCCCcchHHHHHHhcCccccchhccccCCCCchhHHHHHHHHHHHHHHHhhhcCh------HHHHHHHHHHhHHH
Confidence 999999999999999999999999999999999999999999999999999999999985 58999999999999
Q ss_pred ccccccccccccchhhHHHHHHHHHhhCCCCCChHHHHHhhhhhhhcc
Q 003263 787 VKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVS 834 (835)
Q Consensus 787 VKqtVMT~vYGvT~~Gar~QI~~~L~e~g~i~d~~~~~~aa~Ylak~t 834 (835)
|||||||+|||||++|||+||.++|+++|.++|+.++|+|||||+|+|
T Consensus 849 VKQTVMT~VYGVTyvGAR~QI~krL~e~~~f~d~~~v~~as~Yltk~t 896 (1088)
T KOG1038|consen 849 VKQTVMTSVYGVTYVGARLQIKKRLKEIDDFPDEKEVFDASCYLTKKT 896 (1088)
T ss_pred hhhheeeeeeeeeEecHHHHHHHHhhhccCcchhHhhhhHHHHHHHHH
Confidence 999999999999999999999999999999999989999999999987
No 2
>PHA00452 T3/T7-like RNA polymerase
Probab=100.00 E-value=1.4e-152 Score=1344.78 Aligned_cols=610 Identities=31% Similarity=0.491 Sum_probs=532.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHHHhccCccchhhhhccCC
Q 003263 176 NLLRRRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQRTKKQKAAYAPHIELLP 255 (835)
Q Consensus 176 ~~l~~RQ~~LE~~a~~~a~~r~r~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~~~~~~r~~y~p~L~~l~ 255 (835)
..|.+||++||++++++|++||++++++++++|+++++|++++++.+||++|+++|+++++.++++|.++.|+|||+++|
T Consensus 3 ~~l~~rQ~~lE~~~~~~a~~r~~~~~~~~~~~g~~~~~~~~~~l~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~L~~~~ 82 (807)
T PHA00452 3 EDLAAEQLQLEEEAYGEGEERFRKALERQLEAGEADDNPVARRLLATLLPPVAEAIDAWKEEYKKRGRAAKARGLLRLVD 82 (807)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCchhhHHHHHcCC
Confidence 46889999999999999999999999999999999999999999999999999999999999877889999999999999
Q ss_pred hhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHHHH
Q 003263 256 ADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVNS 335 (835)
Q Consensus 256 ~e~lA~Iti~~~l~~~~~~~~~~~v~~~~la~~IG~aVe~E~~~~~~~~k~kk~~~~~~~~~~~~~~~k~~~~l~k~~~~ 335 (835)
||+||+|||+++|++++++ ++.++++++++||++||+|++++.+++++++...+.. ....+++.+.
T Consensus 83 ~d~lA~Iti~~~l~~l~~~---~~~~~~~~~~~iG~aie~E~r~~~~~~~~~~~~~~~~-----------~~~~~~~~~~ 148 (807)
T PHA00452 83 PEVLAVITLKVTLDMLLSK---ETPTAQAVATAIGRAIEDEIRFGRIEDLNPKYFKKVV-----------EYLKRSRTGS 148 (807)
T ss_pred HHHHHHHHHHHHHHHHhcC---CCchHHHHHHHHHHHHHHHHHHHHHHHhChHHHHHHH-----------HHHHhcccch
Confidence 9999999999999999873 4568999999999999999999999876655432211 0112222333
Q ss_pred HHHhHH-HHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHc-cccCCCCCCCCCCCCccCceeEEeEeeecCCCCccc
Q 003263 336 LIKSKR-VMEAQKLLKNEETKPWGRDTQAKLGSRLVELLIETA-YVQHPVNPADYSPPDVRPAFRHRFKTILKHPGQKTT 413 (835)
Q Consensus 336 ~~k~~~-~~~~~~~~~~~~~~~W~~~~~~kvG~~Ll~~L~e~~-~i~~~~~~~~~~~~~~~paF~h~~~~~~~~~g~~~~ 413 (835)
..++.+ .+.++..+...++.+|+.+++++||++|+++|++++ .|+++... . .++ +
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~W~~~~~~kvG~~Ll~~l~~~a~~~~~~~~~-------------------~-~~~---~ 205 (807)
T PHA00452 149 VYHIAFMMVVEADMVLLGEWDPWPKEDYIHVGKWLLEALIESTGLVELVRHT-------------------G-GNG---G 205 (807)
T ss_pred HHHHHHHHHHHHHhhhccCCCCCCHHHHHHHHHHHHHHHHHhhCceeeeecc-------------------c-CCC---C
Confidence 332222 122333333334889999999999999999999996 55443111 0 011 3
Q ss_pred eeEEEEEcCHHHHHHHHhhhhc---ccCCCCceeeCCCCCcCCCCcccccCC---ccceecCCcHHHHHHHHhccccchH
Q 003263 414 KRYGVVECDPLVLEGLDRSAKH---MLIPYVPMLVPPKKWKGYNKGGYLFLP---SYVMRTHGSRKQQEALKSVTGNCMK 487 (835)
Q Consensus 414 k~~gvi~~~~~~~~~l~~~~~~---~~~~~LPMlvPPkpW~~~~~GGYL~~~---~~~~R~~~~~~q~~~lk~~~~~~l~ 487 (835)
+++|+|.+||.+++.+++.... +.+.+|||||||+||+++.+||||+.+ ...+|+++...+..+ .+++|+
T Consensus 206 ~~~g~i~~~~~~~~~l~~~~~~~~~~~p~~lPMlvpP~pW~~~~~GGyl~~~~~~~~~~~~~~~~~~~~~----~~~~l~ 281 (807)
T PHA00452 206 KDHEYLELSEEAVELLQDIAAAAAGISPMYQPMVVPPKPWTSIVGGGYHTEGRRPLAPLVRKTKKALRRY----RQKQMP 281 (807)
T ss_pred ceeeEEEeCHHHHHHHHhhhhhhhhcCcccCceeccCcccCCCCCCCceeccccccceeEecCHHHHHHH----HhhhhH
Confidence 5689999999999999886533 233499999999999999999999853 567888776555433 347999
Q ss_pred HHHHHHHhhcCcceEEcHHHHHHHHHHHHcCCCCCCCCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHHHhhhhh
Q 003263 488 KVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRNDVLIPEKPLS--EDMTEVQKWKWSVRKAKKINQERHSQR 565 (835)
Q Consensus 488 ~v~~aLN~Lqst~WrIN~~VL~vi~~~w~~g~~i~~l~~~~~~p~P~~p~~--~d~~~~~~wk~~~~~~~~~~~~~~S~R 565 (835)
.||++||+||+|||+||++||+||+++|++| .++++++..+.|.|++|+. ++++++++|++++++++++++++||+|
T Consensus 282 ~v~~aLN~Lg~t~w~IN~~vl~v~~~~~~~~-~~~~~~~~~~~~~P~~P~~~~~~~~~~~~wk~~~~~~~~~~~~~~S~r 360 (807)
T PHA00452 282 EVYKAVNALQNTAWRINKDVLAVVNEVVNWG-PVGDVLGIPRRPLPPKPEFLDENEEAFKAWKRAAAAWYTKEKERVSKR 360 (807)
T ss_pred HHHHHHHHHhcCCceecHHHHHHHHHHHhcC-CcccCCCCCCCCCCCCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999 8888888878888888864 456899999999999999999999999
Q ss_pred hhhhHHHHHHHHhcCCCceeeccccCCCCccccCCCCCCCCCchhhhhhhhcccCccCCcchhHHHHHHHhhhhcCCCCC
Q 003263 566 CDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANLFSGGVEK 645 (835)
Q Consensus 566 ~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~YP~~~~Ln~qGsDl~RsLL~FaegkpLG~~Gl~WLKIhlANlyG~G~DK 645 (835)
|+++++|++|++|+|++.||||||+|||||+|| +|||||||+|+|||||+||+|+|||++|++|||||+||+| |+||
T Consensus 361 ~~~~~~l~iA~~f~~~~~fYfP~n~DfRGR~Yp-~~~ln~qg~Dl~RsLL~Fa~gkpLG~~Gl~WLkih~AN~~--G~dK 437 (807)
T PHA00452 361 RRLEFMLRVANKFADYKAIYFPYNMDWRGRVYA-VSMLNPQGSDLQKALLRFAEGKPLGKRGLYWLKVHGANCY--GVDK 437 (807)
T ss_pred HHHHHHHHHHHHhcCCCceeccccccCCCCCCC-CCCCCCCCchHHHHHHHhcCCCCCChhHHHHHHHHHHHHh--CCCc
Confidence 999999999999999889999999999999999 9999999999999999999999999999999999999999 8999
Q ss_pred CCHHHHHHHHHHHHHHHHHhccCCCCCchhHhhCCChHHHHHHHHHHHHHHhcCCCCcccccccccccCCchhhHHHHHh
Q 003263 646 LSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAAL 725 (835)
Q Consensus 646 ~S~deRi~wv~~n~~~I~dsA~dPL~g~~wW~~AD~PwQfLAaC~El~~al~s~dP~~y~S~lPVhqDGSCNGLQHyAAL 725 (835)
+||+||++||++|+++|+++|+|||+|. ||++||+||||||+|+||++|+++|+ +|+||||||||||||||||||||
T Consensus 438 ~s~~eR~~wv~~n~~~I~~~A~dPl~~~-ww~~Ad~P~qfLA~c~El~~a~~~~~--~~~s~lPI~qDgSCnGlQHyAAL 514 (807)
T PHA00452 438 VTFDERAAWVDENHDNILAAAEDPLNNT-WWAEADSPLCFLAACFEYAAAVHSGT--SYVSGLPVAMDGTCSGLQHFSAM 514 (807)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhCcCCch-hhhcCCCHHHHHHHHHHHHHHHhCCC--ccccccccccCCcccHHHHHHHH
Confidence 9999999999999999999999999987 99999999999999999999999887 99999999999999999999999
Q ss_pred hCChhhhcccccCCCCCcccchhHHHHHHHHHHHhhcCCCCCCCcHHHHHHHcccCCCcccccccccccccccchhhHHH
Q 003263 726 GRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGARE 805 (835)
Q Consensus 726 grD~~Ga~~VNLipsd~PqDVYs~Va~~V~~~i~~da~~d~~~~~~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~Gar~ 805 (835)
|||.+||++|||+|+|+|||||+.||+.|.+.+++|+.++.+ ......+++|..+|+||+|||||||+|||||++|+++
T Consensus 515 ~rD~~ga~~VNL~p~d~p~DvY~~Va~~v~~~i~~d~~~~~~-~~~~~~~~~l~~~i~RkvvKqtVMT~vYGvT~~g~~~ 593 (807)
T PHA00452 515 LRDEVGGRAVNLLPSDKPQDIYGIVAEVVNEKLERDAINGTD-NTRALARLWLAYGITRSLTKRPVMTLPYGSTRFSCRD 593 (807)
T ss_pred hCCHHhHHHhCCCCCCCCccHHHHHHHHHHHHHHHHHhCCCc-chHHHHHHHHhCCCChhhcccccccceeCCchhhhHH
Confidence 999999999999999999999999999999999999876432 1233445678889999999999999999999999999
Q ss_pred HHHHHHhhCCCCCChHHH--HHhhhhhhhcc
Q 003263 806 QIKRRLEEKGHITDDRQL--FAAACYAAKVS 834 (835)
Q Consensus 806 QI~~~L~e~g~i~d~~~~--~~aa~Ylak~t 834 (835)
||.++|+++|...++... +.+|+|||+++
T Consensus 594 qI~~~l~~~~~~~~~~~~~~~~~~~yla~~i 624 (807)
T PHA00452 594 YILEDLLQPGIDEGDGAMFTNQAASYMAKLI 624 (807)
T ss_pred HHHHHHHhcCCCcccchhhhHHHHHHHHHHH
Confidence 999999999987655443 89999999976
No 3
>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]
Probab=100.00 E-value=8.5e-144 Score=1198.42 Aligned_cols=606 Identities=36% Similarity=0.585 Sum_probs=535.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHH-HH---------hccCccchhh
Q 003263 180 RRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKM-QR---------TKKQKAAYAP 249 (835)
Q Consensus 180 ~RQ~~LE~~a~~~a~~r~r~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~-~~---------~~~~r~~y~p 249 (835)
+||..||..++..|.|+|+..+++..++|--.--.-+.+.++.||..+..+.++|+.. .+ +.+.|..|+|
T Consensus 251 ~rqk~le~~ai~~a~E~wk~~~e~~~~rg~~~~eKN~~~~~~swy~~i~~l~keeI~~l~e~l~~~~sl~K~~~rl~ygp 330 (1117)
T COG5108 251 ERQKWLEKSAIALAEEMWKAGIERFEKRGEKNREKNAEASNLSWYRMIIHLHKEEIAGLLEALLAEASLGKAGKRLTYGP 330 (1117)
T ss_pred HHHHHHHHhHHHHHHHHHHhhHHHHHhccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHHHhhhhcccccCeecccc
Confidence 6899999999999999999999999998865444457889999999999999998874 22 2467999999
Q ss_pred hhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHH
Q 003263 250 HIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELL 329 (835)
Q Consensus 250 ~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~v~~~~la~~IG~aVe~E~~~~~~~~k~kk~~~~~~~~~~~~~~~k~~~~l 329 (835)
||++++++++|+|||+++++++.+++.+.||+++.+...+|++||+|++.++|...+++.+....+ +.-+.+
T Consensus 331 yLkl~d~~k~a~lTi~el~~l~s~~~~~~gmr~t~l~i~lg~~vE~Ef~seq~~~~e~~ay~d~~k--------k~p~~f 402 (1117)
T COG5108 331 YLKLADLDKVAHLTIRELFDLVSMRRYDRGMRLTPLSIRLGAMVEDEFFSEQFKGHEKDAYEDARK--------KIPEQF 402 (1117)
T ss_pred ceeccCcccchhhhHHHHHHhhccccccccceeehhHHHHHHHHHHHHHHHHHhhhhhHHHHHHhh--------cChHHH
Confidence 999999999999999999999998888889999999999999999999999887655432211000 011112
Q ss_pred HHHHHHHHHhHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCC--CCCccCceeEEeEeeecC
Q 003263 330 RKRVNSLIKSKRVMEAQKLLKNEETKPWGRDTQAKLGSRLVELLIETAYVQHPVNPADYS--PPDVRPAFRHRFKTILKH 407 (835)
Q Consensus 330 ~k~~~~~~k~~~~~~~~~~~~~~~~~~W~~~~~~kvG~~Ll~~L~e~~~i~~~~~~~~~~--~~~~~paF~h~~~~~~~~ 407 (835)
++ .++..+...-.+..++.+|.+||++++++||++++.+|+++++|.+...+...+ .....|||.|+|++.
T Consensus 403 ~~----aV~n~rs~tr~~~~~~~~~~~Wpq~i~akvGsv~l~lll~vaki~v~~id~~t~~~l~ge~~af~h~yqyh--- 475 (1117)
T COG5108 403 HN----AVHNKRSMTRHAKHKGAEWQDWPQDIKAKVGSVALCLLLSVAKIEVKLIDIATEQTLKGEFEAFRHSYQYH--- 475 (1117)
T ss_pred HH----HHHHHHhhhhhhhhcCcchhcChHHHHHHhhHHHHHHHHHhhhheeEeeechhhchhhhhHHHHHHhhhhc---
Confidence 22 222112111223455678999999999999999999999999999876553322 235679999999985
Q ss_pred CCCccceeEEEEEcCHHHHHHHHhhhh--cccCCCCceeeCCCCCcCCCCcccccCCccceecCCcHHHHHHHHhc-ccc
Q 003263 408 PGQKTTKRYGVVECDPLVLEGLDRSAK--HMLIPYVPMLVPPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEALKSV-TGN 484 (835)
Q Consensus 408 ~g~~~~k~~gvi~~~~~~~~~l~~~~~--~~~~~~LPMlvPPkpW~~~~~GGYL~~~~~~~R~~~~~~q~~~lk~~-~~~ 484 (835)
+| +++|||.+|..+...+.+... .+.+.+|||||||+||+++..|||++....++|..++.+|-+|+..+ ..+
T Consensus 476 Ng----~kigvv~~h~tl~~ll~~~~~~a~l~PqlLPmLV~PkPWtsw~~GGY~y~r~~llRlk~t~eqv~yl~~aseng 551 (1117)
T COG5108 476 NG----TKIGVVATHETLDWLLTENSRLAPLSPQLLPMLVPPKPWTSWFRGGYWYGRVRLLRLKKTGEQVRYLLMASENG 551 (1117)
T ss_pred CC----ceeEEEeeHHHHHHHhhcccccCCCChhhhccccCCCCCcCcccCceeeccceeeeecCcHHHHHHHHHhhhcC
Confidence 54 579999999998877765543 23334899999999999999999999999999999999999998766 468
Q ss_pred chHHHHHHHHhhcCcceEEcHHHHHHHHHHHHcCCCCCCCCCCCC-CCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHhh
Q 003263 485 CMKKVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRND-VLIPEK-PLSEDMTEVQKWKWSVRKAKKINQERH 562 (835)
Q Consensus 485 ~l~~v~~aLN~Lqst~WrIN~~VL~vi~~~w~~g~~i~~l~~~~~-~p~P~~-p~~~d~~~~~~wk~~~~~~~~~~~~~~ 562 (835)
+|++||++||.||+|||+||.+|++||.++|++|+.+..||.+.+ .-+|+. +.+.+|+++..|+.+.+.+...+...+
T Consensus 552 d~d~vy~~in~lg~t~W~iN~rvf~V~~~~Wn~ge~fl~IP~a~d~~~~Pp~p~~~~~P~~~~~Wk~~rktia~~~~~a~ 631 (1117)
T COG5108 552 DMDKVYHSINALGNTAWSINHRVFEVMASLWNNGETFLCIPQADDMWLAPPMPREDMSPEEFSRWKSERKTIAEANARAV 631 (1117)
T ss_pred ChHHHHHHHHHhccCchhhhHHHHHHHHHHHhCCCceeccCchhccccCCCCCcccCCHHHHHHHHHHHHHHHHhhhhhh
Confidence 999999999999999999999999999999999999999998764 344554 456789999999999999999999999
Q ss_pred hhhhhhhHHHHHHHHhcCCCceeeccccCCCCccccCCCCCCCCCchhhhhhhhcccCccCCcchhHHHHHHHhhhhcCC
Q 003263 563 SQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANLFSGG 642 (835)
Q Consensus 563 S~R~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~YP~~~~Ln~qGsDl~RsLL~FaegkpLG~~Gl~WLKIhlANlyG~G 642 (835)
|+||+++|+|+||++|.|+ .|||||+||||||+||+++||||||+|.|||||.||.|||||++|++|||||+||+| |
T Consensus 632 S~RcdfnykLeiAraFl~E-kfYFPH~lDFRGRaYpls~hlnh~gnD~srGLL~F~~gkplgp~Gl~WLkiHlanLf--G 708 (1117)
T COG5108 632 SKRCDFNYKLEIARAFLDE-KFYFPHQLDFRGRAYPLSLHLNHQGNDASRGLLQFANGKPLGPEGLDWLKIHLANLF--G 708 (1117)
T ss_pred hhhcchHHHHHHHHHhccC-ccccccccccCcccccCccccccccchhhhhHHHhhcCCcCCcchhhHHHHHhhccc--C
Confidence 9999999999999999995 899999999999999999999999999999999999999999999999999999999 8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhccCCCCCchhHhhCCChHHHHHHHHHHHHHHhcCCCCcccccccccccCCchhhHHH
Q 003263 643 VEKLSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHLPIHQDGSCNGLQHY 722 (835)
Q Consensus 643 ~DK~S~deRi~wv~~n~~~I~dsA~dPL~g~~wW~~AD~PwQfLAaC~El~~al~s~dP~~y~S~lPVhqDGSCNGLQHy 722 (835)
+||+||.+|++||++|+.+|+|||+|||+|++||..||+|||.||+||||.+++++|||++|+||+||||||||||||||
T Consensus 709 vdK~~~~~Rvafv~~n~qei~dSAenPldgnrwW~tAdkPwQALA~CFE~~e~v~~gd~e~fiSH~PvqqDGTCNGLQhy 788 (1117)
T COG5108 709 VDKCSMNERVAFVMANQQEILDSAENPLDGNRWWLTADKPWQALAFCFEWQEYVAEGDHEAFISHLPVQQDGTCNGLQHY 788 (1117)
T ss_pred cccCcHHHHHHHHHhhHHHHHhhccCCCCCCcchhcCCChHHHHHHHHHHHHHHhcCChHHhhhcCcccccCccchHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCChhhhcccccCCCCCcccchhHHHHHHHHHHHhhcCCCCCCCcHHHHHHHcccCCCcccccccccccccccchhh
Q 003263 723 AALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVG 802 (835)
Q Consensus 723 AALgrD~~Ga~~VNLipsd~PqDVYs~Va~~V~~~i~~da~~d~~~~~~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~G 802 (835)
||||+|++||.+|||+|||+|+|||..||..|...++.+|++++ +.|+.|++++||+|||+||||+|||||++|
T Consensus 789 aAlggD~eGa~qVNLvPSDkP~DvYa~VA~vv~~~L~~~AeagD------e~ak~lKDK~Tr~vVk~tvmtnvygvtyvG 862 (1117)
T COG5108 789 AALGGDEEGAAQVNLVPSDKPNDVYATVASVVIAKLRDIAEAGD------ETAKELKDKETRTVVKETVMTNVYGVTYVG 862 (1117)
T ss_pred HHhcCccccceeeeccCCCCchhHHHHHHHHHHHHHHHHHHhhh------hHHHHHhhhhhhhhhhhccccceeeeEEee
Confidence 99999999999999999999999999999999999999998883 679999999999999999999999999999
Q ss_pred HHHHHHHHHhh
Q 003263 803 AREQIKRRLEE 813 (835)
Q Consensus 803 ar~QI~~~L~e 813 (835)
++.||-++|.-
T Consensus 863 at~qitk~l~~ 873 (1117)
T COG5108 863 ATRQITKRLTL 873 (1117)
T ss_pred hHHHHHHhccc
Confidence 99999999864
No 4
>PF00940 RNA_pol: DNA-dependent RNA polymerase; InterPro: IPR002092 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The phage-type enzymes are family of single chain polymerases found in bacteriophages and mitochondria [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3SPA_A 1CEZ_A 1H38_B 1S77_D 1QLN_A 1S0V_D 3E2E_A 2PI4_A 3E3J_B 1S76_D ....
Probab=100.00 E-value=5.3e-68 Score=591.13 Aligned_cols=207 Identities=54% Similarity=0.943 Sum_probs=186.0
Q ss_pred CccCCcchhHHHHHHHhhhhcCCCCCCCHHHHHHHHHHHHHHHHHhccCCCCCchhHhhCCChHHHHHHHHHHHHHHhcC
Q 003263 620 GRPLGKSGLRWLKIHLANLFSGGVEKLSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALKSS 699 (835)
Q Consensus 620 gkpLG~~Gl~WLKIhlANlyG~G~DK~S~deRi~wv~~n~~~I~dsA~dPL~g~~wW~~AD~PwQfLAaC~El~~al~s~ 699 (835)
|||||++|++|||||+||+| |+||+||+||++||++|+++|+++|+||+++.+||.+||+||||||+|+||+++++++
T Consensus 1 ~kpLg~~gl~wLki~~An~~--G~dK~s~~eR~~wv~~n~~~I~~~a~~P~~~~~~w~~Ad~P~qfLA~c~e~~~~~~~~ 78 (405)
T PF00940_consen 1 GKPLGERGLDWLKIHGANLF--GLDKLSFDERIKWVDDNLDDILDSAEDPLDGEEWWLKADKPWQFLAACFELAKALRSG 78 (405)
T ss_dssp -EE-CCCHHHHHHHHHHHHC--T-TTSTHHHHHHHHHHCHHHHHHHHHTTTTC-TGGGGSSSHHHHHHHHHHHHHHHCCC
T ss_pred CCCCcHhHHHHHHHHHHHhh--CCCCCCHHHHHHHHHHHHHHHHHHhhCcccchHHHhcCCcHHHHHHHHHHHHHHHhcC
Confidence 79999999999999999999 8999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccccccccccCCchhhHHHHHhhCChhhhcccccCCCCCcccchhHHHHHHHHHHHhhc---CCCCCCCcHHHHHH
Q 003263 700 SPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDS---NKDPSKHPQALLAK 776 (835)
Q Consensus 700 dP~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLipsd~PqDVYs~Va~~V~~~i~~da---~~d~~~~~~~~~ak 776 (835)
||++|+||+||||||||||||||||||||.+||++|||+|+++|+|||+.|++.|.+.+.+++ ..+ ..+++
T Consensus 79 ~~~~~~s~lPV~~DgSCsGlQH~sal~rD~~ga~~vNLip~~~p~DiY~~V~~~v~~~l~~~~~~~~~~------~~~~~ 152 (405)
T PF00940_consen 79 NPEEFVSHLPVHQDGSCSGLQHYSALLRDEVGAKAVNLIPSDKPQDIYSEVAEEVKKRLEEDADDAEED------NSLAK 152 (405)
T ss_dssp SGCCSEE-SEEEEEBSTHHHHHHHHHTT-HHHHHHTTSSSSSS---HHHHHHHHHHHHHHHHHHEHHCC------HHHHH
T ss_pred CchheeecceeeecCcccHHHHHHHHccCHhhChhcCCCCCCCCCchHHHHHHHHHHHHHHhhcccccc------hHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999983 222 68899
Q ss_pred HcccCCCcccccccccccccccchhhHHHHHHHHHhhCCCCC-ChHHHHHhhhhhhhcc
Q 003263 777 ILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHIT-DDRQLFAAACYAAKVS 834 (835)
Q Consensus 777 ~l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~e~g~i~-d~~~~~~aa~Ylak~t 834 (835)
++..+|+||+|||+|||+|||||++|+++||+++|++++... +....++++.|||+++
T Consensus 153 ~l~~~i~Rk~vK~~vMT~~YG~T~~g~~~qi~~~l~~~~~~~~~~~~~~~~~~~la~~i 211 (405)
T PF00940_consen 153 WLKGGITRKLVKRPVMTIVYGVTFYGARDQIKEQLKEKGDEEEDKIESYKAAMYLAKII 211 (405)
T ss_dssp HCCCT--HHHHHHHHHHHHHT-TCCHHHHHHHHHCHCHCCCTTTTTTHHHHHHHHHHHH
T ss_pred HhcCCCChhhcccceEEeeeCcchhhHHHHHHHHHHhcccccchhhhHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999998765 5558999999999875
No 5
>PF14700 RPOL_N: DNA-directed RNA polymerase N-terminal; PDB: 3SPA_A 1CEZ_A 1H38_B 1S77_D 1QLN_A 1S0V_D 3E2E_A 2PI4_A 3E3J_B 1S76_D ....
Probab=100.00 E-value=1.1e-48 Score=420.40 Aligned_cols=305 Identities=33% Similarity=0.568 Sum_probs=218.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHHH----hccCccchhhhhccCC
Q 003263 180 RRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQR----TKKQKAAYAPHIELLP 255 (835)
Q Consensus 180 ~RQ~~LE~~a~~~a~~r~r~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~~----~~~~r~~y~p~L~~l~ 255 (835)
|||++||+++++.|++||++..+++.++|.++++++++++|.+|+++|+++|+++++.+. ..++++.|+|||+.||
T Consensus 1 ~rQ~~lE~~~~~~a~~r~~~~~~~~~~~g~~~~~~~~~~l~~~w~~~L~~~i~~~~~~~~~~~~~~~~~~~~~p~L~~l~ 80 (318)
T PF14700_consen 1 ERQLELEEESYEAARERWREEFEKAQKRGRASSLPYLQALMWQWYEPLAEAIQEEQEKLKASSKKRGRRAAYGPFLKLLP 80 (318)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGCCCCCHHHHHHHHHHHHHHHHHHHHHHH--HCCCTT--HCCHHCCTS-
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhccCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCcchHHHHHHcCC
Confidence 689999999999999999999999999999999999999999999999999999999875 3578999999999999
Q ss_pred hhHHHHHHHHHHHHHHhcC-CCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHHH
Q 003263 256 ADKVAVIVMHKMMGLVMAG-HEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVN 334 (835)
Q Consensus 256 ~e~lA~Iti~~~l~~~~~~-~~~~~v~~~~la~~IG~aVe~E~~~~~~~~k~kk~~~~~~~~~~~~~~~k~~~~l~k~~~ 334 (835)
+|++|+|||+++|++++++ +..+++++++++.+||++||+|++++++.+...+...+............. .+..+.
T Consensus 81 ~e~lA~Iti~~~l~~~~~~~~~~~g~~~~~~~~~IG~aVe~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~r~~~ 157 (318)
T PF14700_consen 81 PEKLAVITIREVLNLLSSSEGYSKGMKLTRLAIAIGRAVEQEYRFQQLEKAEPKYYKKLKKNFKKKRSKSQ---QKRHVW 157 (318)
T ss_dssp HHHHHHHHHHHHHHHHTTSSSE----EHHHHHHHHHHHHHHHHHHHHHHHCHCCCCCCHHHHCHCCSTSCH---HCHHHH
T ss_pred HHHHHHHHHHHHHHHhccCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccchh---hHHHHH
Confidence 9999999999999999954 445678999999999999999999998776543322110000000000000 001111
Q ss_pred HHHHhHHHHHHHHhhcCCCCCC--CCHHHHHHHHHHHHHHHHHHccccCCCCCCCCCCCCccCceeEEeEeeecCCCCcc
Q 003263 335 SLIKSKRVMEAQKLLKNEETKP--WGRDTQAKLGSRLVELLIETAYVQHPVNPADYSPPDVRPAFRHRFKTILKHPGQKT 412 (835)
Q Consensus 335 ~~~k~~~~~~~~~~~~~~~~~~--W~~~~~~kvG~~Ll~~L~e~~~i~~~~~~~~~~~~~~~paF~h~~~~~~~~~g~~~ 412 (835)
..++........... +..+.. |+..++++||++|+++|+++++|++...+... ...+|||+|+|++. +|
T Consensus 158 ~~~~~~~~~~~~~~~-~~~~~~~~W~~~~~~~vG~~Ll~~l~~~~~i~~~~~~~~~--~~~~paf~~~~~~~---~~--- 228 (318)
T PF14700_consen 158 QLLKNRKDSSGKPSL-EEEWSDSPWPSDIRAKVGSFLLELLMETAKIPVERKDPET--SEEQPAFYHSYRYR---KG--- 228 (318)
T ss_dssp HHHHHHHSHSS-STT-T-TCCC--SCHHHHHHHHHHHHHHHHHCTCEEEEEESTT-------BSEEEEE------TT---
T ss_pred HHHHHHHHhcccccc-ccccccCCCCHHHHHHHHHHHHHHHHhheeeccccCCccc--cccccchhhhhccc---cC---
Confidence 111110000000000 123444 99999999999999999999999987644221 56899999999875 33
Q ss_pred ceeEEEEEcCHHHHHHHHhhhhc-----ccCCCCceeeCCCCCcCCCCcccccCCccceecCCcHHHHHHHH-hccccch
Q 003263 413 TKRYGVVECDPLVLEGLDRSAKH-----MLIPYVPMLVPPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEALK-SVTGNCM 486 (835)
Q Consensus 413 ~k~~gvi~~~~~~~~~l~~~~~~-----~~~~~LPMlvPPkpW~~~~~GGYL~~~~~~~R~~~~~~q~~~lk-~~~~~~l 486 (835)
+++|+|++||.+.+.++..... .++.+|||||||+||+++++||||..++.+||+++. .|..+++ +...++|
T Consensus 229 -~~~g~i~~~~~~~~~l~~~~~~~~~~~~~~~~lPMlvpP~PW~~~~~GGYl~~~~~l~R~~~~-~~~~~~~~~~~~~~l 306 (318)
T PF14700_consen 229 -KKVGVIKPHPELVKLLSDEPEKSLLQATFPRYLPMLVPPKPWTSPNDGGYLLSPTPLMRTKDS-EQQQYLKKALRRGDL 306 (318)
T ss_dssp -T-EEEEEE-HHHHHHHHHHCH---CCCCCCCCS-BSS--EEECCTCCEESSSSSEBSEE-STT-HHCHHHHHTTTCCGG
T ss_pred -ceEEEEeeCHHHHHHHHhhhhhhhhhhcccccCcCCCCCCCCcCCCcceeeeeCchhhcccch-hhHHHHHHHccccch
Confidence 5689999999999999876541 125599999999999999999999999999999887 5545554 5567899
Q ss_pred HHHHHHHHhhcC
Q 003263 487 KKVFEALDTLGS 498 (835)
Q Consensus 487 ~~v~~aLN~Lqs 498 (835)
+.||+|||+||+
T Consensus 307 ~~v~~~Ln~Lg~ 318 (318)
T PF14700_consen 307 DPVFDALNALGS 318 (318)
T ss_dssp HHHHHHHHHHHT
T ss_pred HHHHHHHHHhcC
Confidence 999999999996
No 6
>PLN03188 kinesin-12 family protein; Provisional
Probab=53.61 E-value=6.4e+02 Score=33.82 Aligned_cols=45 Identities=20% Similarity=0.203 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHhccCccchhhhhccCChhHHHHHHHHH
Q 003263 222 GWFGPLSEAIEREQKMQRTKKQKAAYAPHIELLPADKVAVIVMHK 266 (835)
Q Consensus 222 ~w~~~L~~~I~~e~~~~~~~~~r~~y~p~L~~l~~e~lA~Iti~~ 266 (835)
.-+..+.+.|++-.+...+.|.+..-..|+..|-+|--|+=+=++
T Consensus 1128 ~~hr~i~egi~dvkkaaakag~kg~~~~f~~alaae~s~l~~ere 1172 (1320)
T PLN03188 1128 ARHRRIQEGIDDVKKAAARAGVRGAESKFINALAAEISALKVERE 1172 (1320)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHHHHH
Confidence 334455556665444555567777778898888776555444433
No 7
>PF14554 VEGF_C: VEGF heparin-binding domain; PDB: 2VGH_A 4DEQ_A 1VGH_A 1KMX_A.
Probab=40.23 E-value=14 Score=31.01 Aligned_cols=19 Identities=58% Similarity=0.917 Sum_probs=11.8
Q ss_pred ccccccCCcccceeecCCC
Q 003263 130 NHQLMCLEPRRRIFVQDPP 148 (835)
Q Consensus 130 ~~~~~~~~~~~~~~~~~~~ 148 (835)
+|=..+.|.++++|||||-
T Consensus 5 ~~C~PCSErRk~Lfvqdp~ 23 (55)
T PF14554_consen 5 NHCEPCSERRKRLFVQDPL 23 (55)
T ss_dssp -----SSSSSCTTEEE-TT
T ss_pred ccccccHhHhhhhcccCcc
Confidence 4445568999999999995
No 8
>PF07739 TipAS: TipAS antibiotic-recognition domain; InterPro: IPR012925 TipAL is a bacterial transcriptional regulator of the MerR family. The tipA gene can be expressed as a long form, TipAL, and a short form, TipAS, which constitutes the C-terminal part of TipAL. TipAS forms the antibiotic-recognition domain []. This domain, which has an alpha-helical globin-like fold, is also found at the C terminus of other MerR family transcription factors, including Mta, a central regulator of multidrug resistance in Bacillus subtilis [], and SkgA from Caulobacter crescentus []. ; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1NY9_A 3HH0_A 3QAO_A.
Probab=30.06 E-value=86 Score=29.01 Aligned_cols=56 Identities=21% Similarity=0.483 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HcccCCCChhHHHHHHHHHHHHH
Q 003263 173 RKFNLLRRRQVKQETEAWERMVDEYKELEAKMI---EKRLAPNLPHIKGLFLGWFGPLS 228 (835)
Q Consensus 173 ~~~~~l~~RQ~~LE~~a~~~a~~r~r~~~~~~~---~~g~a~~~~~~~~ll~~w~~~L~ 228 (835)
..|.+..++...|..+.++....+|.+.++++. +.|+.++.+-++.++.+|+.-+.
T Consensus 13 ~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~l~~~~~~g~~p~s~evq~l~~~~~~~~~ 71 (118)
T PF07739_consen 13 EAYAESEERLASLSKEEWQELQKEWDELFAELAALMEEGVDPDSPEVQELAERWMELIN 71 (118)
T ss_dssp --------------------TTHHHHHHHHHHHHHHHHT--TT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHHHH
Confidence 566666666666777777777777877776654 46888999999999999999665
No 9
>cd03316 MR_like Mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. Members of the MR subgroup are mandelate racemase, D-glucarate/L-idarate dehydratase (GlucD), D-altronate/D-mannonate dehydratase , D-galactonate dehydratase (GalD) , D-gluconate dehydratase (GlcD), and L-rhamnonate dehydratase (RhamD).
Probab=24.52 E-value=45 Score=37.17 Aligned_cols=103 Identities=11% Similarity=0.130 Sum_probs=63.7
Q ss_pred cchhHHHHHHHhhhhcCCCCCCCHHHHHHHHHHHHHHHHHhcc-C-CC--CCchhHhhCCChHHHHHHHHHHHHH----H
Q 003263 625 KSGLRWLKIHLANLFSGGVEKLSHDGRLAFVENHLYEIFDSAE-N-PI--NGSRWWLTAEDPFQCLAACINLSEA----L 696 (835)
Q Consensus 625 ~~Gl~WLKIhlANlyG~G~DK~S~deRi~wv~~n~~~I~dsA~-d-PL--~g~~wW~~AD~PwQfLAaC~El~~a----l 696 (835)
+.|++-+|||++.-+ ..+ +|.++..+.+..|.+... + +| +.+..| ++-+++.+|-.+.++ +
T Consensus 152 ~~Gf~~~Kik~g~~~--~~~-----~~~~~d~~~v~~ir~~~g~~~~l~vDaN~~~----~~~~a~~~~~~l~~~~i~~i 220 (357)
T cd03316 152 AEGFTAVKLKVGGPD--SGG-----EDLREDLARVRAVREAVGPDVDLMVDANGRW----DLAEAIRLARALEEYDLFWF 220 (357)
T ss_pred HcCCCEEEEcCCCCC--cch-----HHHHHHHHHHHHHHHhhCCCCEEEEECCCCC----CHHHHHHHHHHhCccCCCeE
Confidence 358888888876433 122 888888888888887653 2 33 123334 455666666555442 2
Q ss_pred hcCCCCcc---------cccccccccCCchhhHHHHHhhCChhhhcccccCC
Q 003263 697 KSSSPHSV---------ISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVA 739 (835)
Q Consensus 697 ~s~dP~~y---------~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip 739 (835)
+.+-|... .+.+||..|.+|.++..+..+.++. .+..||+-+
T Consensus 221 EqP~~~~~~~~~~~l~~~~~ipi~~dE~~~~~~~~~~~i~~~-~~d~v~~k~ 271 (357)
T cd03316 221 EEPVPPDDLEGLARLRQATSVPIAAGENLYTRWEFRDLLEAG-AVDIIQPDV 271 (357)
T ss_pred cCCCCccCHHHHHHHHHhCCCCEEeccccccHHHHHHHHHhC-CCCEEecCc
Confidence 32222110 2568999999999999988887653 456666643
No 10
>smart00482 POLAc DNA polymerase A domain.
Probab=21.32 E-value=28 Score=36.43 Aligned_cols=89 Identities=22% Similarity=0.247 Sum_probs=62.8
Q ss_pred HHHHHHhcCCCCcccccccccccCCchhhHHHHHhhCChhhhcccccCCCCCcccchhHHHHHHHHHHHhhcCCCCCCCc
Q 003263 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (835)
Q Consensus 691 El~~al~s~dP~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLipsd~PqDVYs~Va~~V~~~i~~da~~d~~~~~ 770 (835)
+++.++.. |++| +-|..|-|.==|=.+|.|.+|......-| ...|+|+.+|..+...-.+
T Consensus 3 ~iR~~f~a--~~G~---~lv~~DysqiElRilA~ls~D~~l~~~~~-----~g~D~h~~~A~~~~g~~~~---------- 62 (206)
T smart00482 3 EIRRAFVA--PPGY---VLVSADYSQIELRILAHLSGDENLLEAFN-----NGGDIHSKTAAQVFGVPEE---------- 62 (206)
T ss_pred hhhheeeC--CCCC---EEEEeeHHHHHHHHHHHHcCCHHHHHHHh-----cCCCHHHHHHHHHhCCChh----------
Confidence 34555543 2444 47889999999999999999988777665 3569999988765322110
Q ss_pred HHHHHHHcccCCCcccccccccccccccchhhHHHH
Q 003263 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQ 806 (835)
Q Consensus 771 ~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~Gar~Q 806 (835)
. .....|+..|+.+--..||.+..|..++
T Consensus 63 --~-----v~~~~R~~aK~~~~g~~YG~g~~~la~~ 91 (206)
T smart00482 63 --E-----VTKELRRAAKAINFGIIYGMGAKGLAEQ 91 (206)
T ss_pred --h-----CCHHHHHHHhHHHHHhhhccchhHHHHH
Confidence 0 0123599999999999999987776554
Done!