Query 003002
Match_columns 858
No_of_seqs 244 out of 438
Neff 5.4
Searched_HMMs 46136
Date Thu Mar 28 15:04:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003002.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003002hhsearch_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 4E-206 8E-211 1744.1 63.8 827 1-857 89-951 (1088)
2 PHA00452 T3/T7-like RNA polyme 100.0 7E-169 1E-173 1494.1 69.6 665 139-857 3-680 (807)
3 COG5108 RPO41 Mitochondrial DN 100.0 6E-158 1E-162 1313.6 50.3 677 143-856 251-965 (1117)
4 PF00940 RNA_pol: DNA-dependen 100.0 3.6E-83 7.8E-88 719.3 17.9 265 588-857 1-266 (405)
5 PF14700 RPOL_N: DNA-directed 100.0 2.9E-48 6.3E-53 422.6 25.0 304 143-466 1-318 (318)
6 COG5108 RPO41 Mitochondrial DN 89.4 0.19 4.1E-06 60.0 1.9 76 747-826 860-935 (1117)
7 smart00482 POLAc DNA polymeras 59.1 6.1 0.00013 41.5 2.2 137 659-845 3-139 (206)
8 PF07739 TipAS: TipAS antibiot 30.8 53 0.0011 30.6 3.4 56 136-191 13-71 (118)
9 PF08849 DUF1819: Putative inn 29.5 93 0.002 32.2 5.3 29 322-350 133-161 (189)
10 cd08638 DNA_pol_A_theta DNA po 28.4 41 0.00089 38.6 2.7 139 659-847 129-267 (373)
11 PRK14975 bifunctional 3'-5' ex 26.0 33 0.00072 41.4 1.4 118 676-841 326-443 (553)
12 PF00476 DNA_pol_A: DNA polyme 23.4 39 0.00085 38.8 1.3 109 675-822 155-263 (383)
13 cd08637 DNA_pol_A_pol_I_C Poly 22.9 69 0.0015 36.9 3.1 136 659-844 140-275 (377)
14 cd08643 DNA_pol_A_pol_I_B Poly 22.3 70 0.0015 37.7 3.1 86 659-777 176-261 (429)
15 cd03316 MR_like Mandelate race 21.0 66 0.0014 36.2 2.5 101 593-705 152-269 (357)
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=3.8e-206 Score=1744.11 Aligned_cols=827 Identities=56% Similarity=0.937 Sum_probs=737.5
Q ss_pred Chhhhhhhh------hcccccc-CCC----C----Cccccccccc---ccc-cccccccCCCCCCccccccccccccccc
Q 003002 1 MWRNLARQS------STRNFKF-SPS----K----VSQTTNFLKK---ITS-LETQTLLDSSCPLLGFRRTSFLSSQKSN 61 (858)
Q Consensus 1 ~~~~~~~~~------~~~~~~~-~~~----~----~~~~~~~~~~---~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (858)
||+|+..++ .++.... +.+ + ++.-.++|+- ... |.... ..++++..|+++..+++-.|
T Consensus 89 ~~~~~l~~s~~~~t~~~~~~~~l~~~s~t~~l~~~~~~i~~~~S~~~~~lt~~~~~~-~~~p~~~~~~~~~~~l~~~n-- 165 (1088)
T KOG1038|consen 89 MWRNLLLKSFQNETMALRRHAALNPSSTTLGLLDPVEAISGIFSSLAKVLTTLRHKL-LVSPEHVRGIRQLLGLNNIN-- 165 (1088)
T ss_pred HhhhhHHHHhhhhhHHHHhhccCCchhhcccccchhhcchhhhhhhhhhhHHHhccc-ccCchhhhhhHHhhccchhh--
Confidence 799999998 5555443 222 1 1111134442 222 22222 35677788888888777666
Q ss_pred cCCCCCccCCCCcCccccccccChhhhhcc---ccccCchHHHHHHHHHHHhhcccc-----cccccccccccccccCCC
Q 003002 62 LGQSNFTQSIYPFGVLTSRSYASAAEAIAS---ESELSGSEEVQELIDQFNEKGVSI-----LDSSSMLDKQPKKKGTGM 133 (858)
Q Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~ 133 (858)
+|.+...+.+| ..+||+-+++..-+ +.+++.-+++.+++++|.++.... ......++...+.+..++
T Consensus 166 ----sF~~~~~~l~G-~~~g~s~a~e~~~~~~~~~~s~~~~~~~~~~~~m~ke~~~~~~~~~~~~~~~~~~~lk~v~k~~ 240 (1088)
T KOG1038|consen 166 ----SFPHSSEVLSG-LIKGSSLAGESENPTDQEGDSSNKQEINELVTKMEKEGNSLNQISSKFLEESRDLPLKAVRKGF 240 (1088)
T ss_pred ----cccchhhhhhc-ccccchHHHHHhCcccccccccchhhHHHHHhHhhhhhhhhhHHHHHHHHHHhcccHHHHHHhc
Confidence 45566555556 66788444455444 344555778999999999988431 112222334445677788
Q ss_pred Chh-HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHhcccCCCChh-HHHHHHHHHHHHHHHHHHHHHHhhhc--cCcc
Q 003002 134 GTA-KYYMLKRRQIKIETEAWEQAAKEYQ-DLLADMCEQKLAPNLPY-VKSLFLGWFEPLRDAIAKDQATAQDK--WKHM 208 (858)
Q Consensus 134 ~~~-~~~~l~eRQ~~lE~~~~~~a~~~~~-~~~~~~~~~g~a~~~~~-~~~ll~~w~~~L~~~I~~e~~~~~~~--~~r~ 208 (858)
+.. +|-.+.+||..+|+++|++|+++|+ ++..+||+..+++++|| +++++++||++|+++|++|++.++.. +.|.
T Consensus 241 ~~~~d~~~l~~Rq~~~e~~~~e~a~e~~k~el~~~~c~~~l~~~lp~~lk~lf~~W~~~l~~ai~ee~n~~r~~~~~~r~ 320 (1088)
T KOG1038|consen 241 GDFKDFFNLDRRQVKLETEAWERAAEEWKIELESDMCEGSLAPNLPYNLKSLFLGWFKPLRDAIKEEINLLRALVRKGRL 320 (1088)
T ss_pred cchHhHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Confidence 877 8999999999999999999999999 88899999999999999 99999999999999999999999876 8899
Q ss_pred ccccccccCCchhHHHHHHHHHHHHHhcCC--CCchHHHHHHHHHHHHHHHHHHhHHHHhhhhhccCCCCCCCCCCCCCC
Q 003002 209 TYAPYFNNLPADMMAVITMHKLVGLLMTNA--GEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTN 286 (858)
Q Consensus 209 ~y~p~L~~l~~e~lA~Iti~~~l~~~~~~~--~~~~~~~~~~~IG~aVe~E~~~~~~~~~~~k~~~~~~~~~~~~~~l~~ 286 (858)
.|+|||++||++++|+|||+++|+++++|+ +++++++++.+||++||+|+|++.+.++..|++.. +
T Consensus 321 ~Y~p~L~lL~a~k~aviti~el~~ll~tg~~~~~~~v~~aa~~~G~aveqe~ri~~~lq~~~k~~~~----~-------- 388 (1088)
T KOG1038|consen 321 NYAPFLKLLDADKMAVITIHELMGLLMTGGETGGVRVVQAAKSLGRAVEQEFRIEQFLQRKTKNKAG----D-------- 388 (1088)
T ss_pred ccchHHHhcChhhHHHHHHHHHHhhhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc----h--------
Confidence 999999999999999999999999999987 89999999999999999999999998875432221 0
Q ss_pred ChHHhHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCCCCCccCc
Q 003002 287 DPEKLIKEQEKLKKRVTSLIKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPA 366 (858)
Q Consensus 287 ~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~~~~kvG~~Li~~l~~~~~i~~~~~~~~~~~~~~~pa 366 (858)
.....++....++.++.++++.++.+....+..+....+|+..++++||++|+++||++++|+++.++..++.++..||
T Consensus 389 -~~~~~ke~~~~~~~v~~l~~~~k~~~~~~~~~~~~~~~pWp~~v~~kvGs~L~~lL~~~aki~~~~~~~~~~~~~~~pa 467 (1088)
T KOG1038|consen 389 -SYCELKELGKSRKEVRQLVQNLKLSQRLSGPESHLSEKPWPSAVQAKVGSRLIELLMQVAKIQVPADQPDTKLPDERPA 467 (1088)
T ss_pred -HHHHHHHhhcccHHHHHHHHHHHHHHHhcccccccccCCccHHHHHHHHHHHHHHHHHHhcCCCcccCcCcCccccchh
Confidence 1222355667788899999888888887777766778899999999999999999999999999999998889999999
Q ss_pred eeEEeeecccccCCCeEEEEEEeCHHHHHHHHhccccccCCCCCeeeCCcCcccCCCccccccCcceeecCchhhHHHH-
Q 003002 367 FVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRET- 445 (858)
Q Consensus 367 F~h~~~~~~~~~~~~k~~gvi~~~~~~~~~l~~~~~~~~~~~lPMlvpP~pW~~~~~GGYl~~~~~~~R~~~~~~q~~~- 445 (858)
|.|.|+ +++..+.+++||+|+|||.+...|++.+.++.++++||||||+||+++++||||++|+++||++++++|..+
T Consensus 468 f~h~f~-~~n~~~~~~~~g~ie~~pll~r~leks~~~~~~~~vPMLvpPkpWt~~~~Ggyl~~~s~lmRt~g~~~Q~~~l 546 (1088)
T KOG1038|consen 468 FVHTFQ-VTNGQKGGRKYGVIECHPLLSRGLEKSALHFVPPLVPMLVPPKPWTGYDSGGYLFLPSYLMRTHGAKEQVDYL 546 (1088)
T ss_pred hhhhee-eecccccceeeeeeecCHHHHHHhhhhhccccccccccccCCCCCCCCCCCceEecchhhhhcCCcHHHHHHH
Confidence 999999 444444588999999999999999999989999999999999999999999999999999999999999885
Q ss_pred HHcCCCCChhhHHHHHHhhcCcccEechHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHH
Q 003002 446 IKMTPRSQLEPVFQALDTLGSTKWRVNKRILGVIDRMWASGGCLAGLVDQEDVPLPEKP-NTDDETEIKKWKWKVKTAKK 524 (858)
Q Consensus 446 l~~~~~~~l~~v~~aLN~Lq~t~w~IN~~vL~vi~~~w~~g~~i~~l~~~~~~p~P~~p-~~~d~~~~~~wk~~~~~~~~ 524 (858)
+++.+.+++++||+|||.||+||||||++||||+.++|++||.+.++|++.+.|+|++| ..+|+.+++.|+++.+...+
T Consensus 547 lkas~~~~l~~v~daL~~LG~t~WrVN~rvldvV~riw~~Gg~~~~~v~r~~~~lP~~P~~s~dp~~~~~wk~e~k~~~k 626 (1088)
T KOG1038|consen 547 LKASPPGQLDPVFDALDTLGNTKWRVNRRVLDVVIRIWQNGGCFLLIVPREDVPLPPKPTLSEDPAELKAWKWEVKKAQK 626 (1088)
T ss_pred HhcCChhhhHHHHHHHHHhcCCCeeecchHHHHHHHHHhcCCCccCCCCCCCCCCCCCCCCCcChHHHHHhHHHHHHHHH
Confidence 55667889999999999999999999999999999999999999999999999999999 67899999999999999999
Q ss_pred HHhHhhhhhhhHHHHHHHHHhccCCCceeeccccCCCCccccCCCCCCCCCcchhhhhhccccCccCccchhHHHHHHHH
Q 003002 525 QNSEKHSQRCDIELKLSVARKMKDEEGFYYPHNLDFRGRAYPMHPYLNHLGSDLCRGVLEFEEGHPLGKAGLHWLKIHLA 604 (858)
Q Consensus 525 ~~~~~~s~R~~~~~~L~iA~~f~~~~~fYfP~nlDFRGR~Yp~~~~Ln~qGsDl~RsLL~FaegkpLG~~Gl~WLkIhlA 604 (858)
.++++||+|||++|+|+||++|+|+ .||||||||||||+||+||||||.|||+|||||+||+|||||++||+|||||+|
T Consensus 627 ~~~e~HS~RCD~~ykLsvAr~~~de-~Fy~PHNmDFRGRaYP~~PHlNHLgsDlcRglLeF~~GkPLG~sGL~WLKIHla 705 (1088)
T KOG1038|consen 627 VNRERHSLRCDAEYKLSVARKMKDE-EFYYPHNMDFRGRAYPLPPHLNHLGSDLCRGLLEFAEGKPLGPSGLRWLKIHLA 705 (1088)
T ss_pred hhhhhhhhhhhHHHHHHHHHHhccC-eeecCcccCcCCccCCCCchhcccchHHHHHHHHHhcCCcCCccchhHHHHHHH
Confidence 9999999999999999999999998 599999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCCCCHHHHHHHHHhhHHHHHHhccCCcCcchhhhcCCchHHHHHHHHHHHHhhcCCCCCCccccccccccCCC
Q 003002 605 NLYAGGVDKLSYEGRVAFTENHLDDIFDSADRPLEGRRWWLGAEDPFQCLATCINLSEALRSPSPESTISHIPVHMDGSC 684 (858)
Q Consensus 605 N~~G~G~DK~s~~eRi~wv~~n~~~I~~sA~~Pl~~~~wW~~Ad~P~QfLA~C~El~~a~~s~~P~~y~S~lPVhqDGSC 684 (858)
|+|| |+||+|+++|++|+++|+++|+|||++||+|++||++|||||||||+||||++|++++||+.|+||+||||||||
T Consensus 706 NL~~-g~~kl~~~~RlAF~E~hl~DI~DSAd~PLtG~rWW~~AedPfQ~LA~C~elaea~RspdPeayiSH~PIHQDGSC 784 (1088)
T KOG1038|consen 706 NLYA-GVDKLSLRDRLAFTEEHLDDIFDSADRPLTGRRWWLKAEDPFQCLAACMELAEALRSPDPEAYISHIPIHQDGSC 784 (1088)
T ss_pred HHhc-ccccccHHHHHHHHHHHHHHHhhcccCCCcccchhhcCCChHHHHHHHHHHHHHHcCCCHHHHHhcCCcccCCCc
Confidence 9998 999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhHHHHhhCCcccccccccCCCCCCcchhHHHHHHHHHHHHhhhcCCCCCCcchHHHHHhhccCccccccceeeeeec
Q 003002 685 NGLQHYAALGRDKLGAAAVNLVGGDKPADVYSGIAARVLEIMRADADKDPATYPYASCARLLINQVDRKLVKQTVMTSVY 764 (858)
Q Consensus 685 NGLQHyAAL~rD~~Ga~~VNL~p~d~P~DvYs~Va~~V~~~l~~da~~~~~~~~~~~~a~~l~~~i~RKvVKqtVMT~vY 764 (858)
||||||||||||..||++|||+|||+|||||++||..|.+.+++||++|+ .+|++|.+.||||||||||||+||
T Consensus 785 NGLQHYAALGrD~~GA~~VNLvpsdkPqDVYs~VA~~V~~~~k~DAe~g~------e~Ak~L~~~V~RKvVKQTVMT~VY 858 (1088)
T KOG1038|consen 785 NGLQHYAALGRDSEGAAAVNLVPSDKPQDVYSAVAARVEKIMKQDAEKGP------EVAKILKDQVTRKVVKQTVMTSVY 858 (1088)
T ss_pred chHHHHHHhcCccccchhccccCCCCchhHHHHHHHHHHHHHHHhhhcCh------HHHHHHHHHHhHHHhhhheeeeee
Confidence 99999999999999999999999999999999999999999999999986 699999999999999999999999
Q ss_pred ccchhhHHHHHHHHHhhccCCCCchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEEEEcCCCCeE
Q 003002 765 GVTYIGARDQIKKRLKERCAIEDDSKLFGAACYAAKTTLTALGEMFEAARSIMSWLGECAKVIASENQAVRWTTPLGLPV 844 (858)
Q Consensus 765 GvT~~Ga~~qI~~~L~~~g~~~d~~~~~~~a~yla~~i~~ai~e~f~~A~~im~WL~~~a~~i~~~~~pV~WtTPlGlpV 844 (858)
|||++|||+||.++|++++.++|+.++|.+|||++++||+||+|||.+|++||+||++||++|+++++||+||||+||||
T Consensus 859 GVTyvGAR~QI~krL~e~~~f~d~~~v~~as~Yltk~tf~aLrEmF~~araIq~WlgecAklIs~~~~~V~WtTPLGLPV 938 (1088)
T KOG1038|consen 859 GVTYVGARLQIKKRLKEIDDFPDEKEVFDASCYLTKKTFEALREMFTAARAIQDWLGECAKLISSENSPVEWTTPLGLPV 938 (1088)
T ss_pred eeeEecHHHHHHHHhhhccCcchhHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEecCCCCcc
Confidence 99999999999999999999999988999999999999999999999999999999999999999999999999999999
Q ss_pred eeeccCCCceeee
Q 003002 845 VQPYHQLGRHLVM 857 (858)
Q Consensus 845 vQ~Y~k~~~~~v~ 857 (858)
|||||+.++++|-
T Consensus 939 VQPYr~~~~~qir 951 (1088)
T KOG1038|consen 939 VQPYRQEKKKQIR 951 (1088)
T ss_pred cchhhhhhhhccc
Confidence 9999999999873
No 2
>PHA00452 T3/T7-like RNA polymerase
Probab=100.00 E-value=6.8e-169 Score=1494.14 Aligned_cols=665 Identities=31% Similarity=0.499 Sum_probs=589.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHHHHHHHHhhhccCccccccccccCC
Q 003002 139 YMLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQDKWKHMTYAPYFNNLP 218 (858)
Q Consensus 139 ~~l~eRQ~~lE~~~~~~a~~~~~~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~~~~~~r~~y~p~L~~l~ 218 (858)
..|.+||++||++++++|++||++++++++++|+++++|++++++.+||++|+++|+++++.+++++.++.|+|||+++|
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 46889999999999999999999999999999999999999999999999999999999999877888999999999999
Q ss_pred chhHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHhHHHHhhhhhccCCCCCCCCCCCCCCChHHhHHHHHHH
Q 003002 219 ADMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPEKLIKEQEKL 298 (858)
Q Consensus 219 ~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~~IG~aVe~E~~~~~~~~~~~k~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 298 (858)
||++|+|||+++|+++++ +++.++++++++||+|||+|++++.++++.++.+++. .....
T Consensus 83 ~d~lA~Iti~~~l~~l~~-~~~~~~~~~~~~iG~aie~E~r~~~~~~~~~~~~~~~-------------------~~~~~ 142 (807)
T PHA00452 83 PEVLAVITLKVTLDMLLS-KETPTAQAVATAIGRAIEDEIRFGRIEDLNPKYFKKV-------------------VEYLK 142 (807)
T ss_pred HHHHHHHHHHHHHHHHhc-CCCchHHHHHHHHHHHHHHHHHHHHHHHhChHHHHHH-------------------HHHHH
Confidence 999999999999999998 4567999999999999999999999987765433210 01122
Q ss_pred HHHHHHHHHHHH-HHHHHhhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHc-cccCCCCCCCCCCCCccCceeEEeeeccc
Q 003002 299 KKRVTSLIKKQK-LQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETA-YIQPPVDQLGDSPPDIRPAFVHTLKSFTK 376 (858)
Q Consensus 299 r~~~~~~~~~~~-~~~~~~~~~~~~~~~~W~~~~~~kvG~~Li~~l~~~~-~i~~~~~~~~~~~~~~~paF~h~~~~~~~ 376 (858)
+++.+...++.+ .+.+++.+..+ ++.+|+.+++++||++|+++|++++ .++++.. .
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~W~~~~~~kvG~~Ll~~l~~~a~~~~~~~~-------------------~-- 200 (807)
T PHA00452 143 RSRTGSVYHIAFMMVVEADMVLLG-EWDPWPKEDYIHVGKWLLEALIESTGLVELVRH-------------------T-- 200 (807)
T ss_pred hcccchHHHHHHHHHHHHHhhhcc-CCCCCCHHHHHHHHHHHHHHHHHhhCceeeeec-------------------c--
Confidence 233333333322 33444444432 4889999999999999999999996 5543211 1
Q ss_pred ccCCCeEEEEEEeCHHHHHHHHhccccc--cCC-CCCeeeCCcCcccCCCccccccC---cceeecCchhhHHHHHHcCC
Q 003002 377 EALKGRRYGVIECDPLVRKGLEKTGRHM--IIP-YMPMLVPPLNWRGYNRGGHFFLP---SYVMRTHGARQQRETIKMTP 450 (858)
Q Consensus 377 ~~~~~k~~gvi~~~~~~~~~l~~~~~~~--~~~-~lPMlvpP~pW~~~~~GGYl~~~---~~~~R~~~~~~q~~~l~~~~ 450 (858)
..++++++|+|++||.+.+.+++...++ ..| +|||||||+||+++.+||||+.+ +..+|+++...+..+ .
T Consensus 201 ~~~~~~~~g~i~~~~~~~~~l~~~~~~~~~~~p~~lPMlvpP~pW~~~~~GGyl~~~~~~~~~~~~~~~~~~~~~----~ 276 (807)
T PHA00452 201 GGNGGKDHEYLELSEEAVELLQDIAAAAAGISPMYQPMVVPPKPWTSIVGGGYHTEGRRPLAPLVRKTKKALRRY----R 276 (807)
T ss_pred cCCCCceeeEEEeCHHHHHHHHhhhhhhhhcCcccCceeccCcccCCCCCCCceeccccccceeEecCHHHHHHH----H
Confidence 1234678899999999999998875432 244 99999999999999999999853 567888777655544 3
Q ss_pred CCChhhHHHHHHhhcCcccEechHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHhH
Q 003002 451 RSQLEPVFQALDTLGSTKWRVNKRILGVIDRMWASGGCLAGLVDQEDVPLPEKPNT--DDETEIKKWKWKVKTAKKQNSE 528 (858)
Q Consensus 451 ~~~l~~v~~aLN~Lq~t~w~IN~~vL~vi~~~w~~g~~i~~l~~~~~~p~P~~p~~--~d~~~~~~wk~~~~~~~~~~~~ 528 (858)
.++|+.||++||+||+|||+||++||+||+++|++| .++++|+..+.|+|++|++ ++++++++|+++++++++++++
T Consensus 277 ~~~l~~v~~aLN~Lg~t~w~IN~~vl~v~~~~~~~~-~~~~~~~~~~~~~P~~P~~~~~~~~~~~~wk~~~~~~~~~~~~ 355 (807)
T PHA00452 277 QKQMPEVYKAVNALQNTAWRINKDVLAVVNEVVNWG-PVGDVLGIPRRPLPPKPEFLDENEEAFKAWKRAAAAWYTKEKE 355 (807)
T ss_pred hhhhHHHHHHHHHHhcCCceecHHHHHHHHHHHhcC-CcccCCCCCCCCCCCCCCCcccCHHHHHHHHHHHHHHHHHHHH
Confidence 379999999999999999999999999999999999 8888888888889988865 4568899999999999999999
Q ss_pred hhhhhhhHHHHHHHHHhccCCCceeeccccCCCCccccCCCCCCCCCcchhhhhhccccCccCccchhHHHHHHHHHhhc
Q 003002 529 KHSQRCDIELKLSVARKMKDEEGFYYPHNLDFRGRAYPMHPYLNHLGSDLCRGVLEFEEGHPLGKAGLHWLKIHLANLYA 608 (858)
Q Consensus 529 ~~s~R~~~~~~L~iA~~f~~~~~fYfP~nlDFRGR~Yp~~~~Ln~qGsDl~RsLL~FaegkpLG~~Gl~WLkIhlAN~~G 608 (858)
+||+||+++++|++|++|+|++.||||||+|||||+|| +|||||||+|+|||||+||+|+|||++|++|||||+||+|
T Consensus 356 ~~S~r~~~~~~l~iA~~f~~~~~fYfP~n~DfRGR~Yp-~~~ln~qg~Dl~RsLL~Fa~gkpLG~~Gl~WLkih~AN~~- 433 (807)
T PHA00452 356 RVSKRRRLEFMLRVANKFADYKAIYFPYNMDWRGRVYA-VSMLNPQGSDLQKALLRFAEGKPLGKRGLYWLKVHGANCY- 433 (807)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCceeccccccCCCCCCC-CCCCCCCCchHHHHHHHhcCCCCCChhHHHHHHHHHHHHh-
Confidence 99999999999999999999889999999999999999 9999999999999999999999999999999999999999
Q ss_pred CCCCCCCHHHHHHHHHhhHHHHHHhccCCcCcchhhhcCCchHHHHHHHHHHHHhhcCCCCCCccccccccccCCCchhh
Q 003002 609 GGVDKLSYEGRVAFTENHLDDIFDSADRPLEGRRWWLGAEDPFQCLATCINLSEALRSPSPESTISHIPVHMDGSCNGLQ 688 (858)
Q Consensus 609 ~G~DK~s~~eRi~wv~~n~~~I~~sA~~Pl~~~~wW~~Ad~P~QfLA~C~El~~a~~s~~P~~y~S~lPVhqDGSCNGLQ 688 (858)
|+||+||+||++||++|+++|++||+|||++. ||++||+||||||+|+||++|+++|+ +|+|||||||||||||||
T Consensus 434 -G~dK~s~~eR~~wv~~n~~~I~~~A~dPl~~~-ww~~Ad~P~qfLA~c~El~~a~~~~~--~~~s~lPI~qDgSCnGlQ 509 (807)
T PHA00452 434 -GVDKVTFDERAAWVDENHDNILAAAEDPLNNT-WWAEADSPLCFLAACFEYAAAVHSGT--SYVSGLPVAMDGTCSGLQ 509 (807)
T ss_pred -CCCcCCHHHHHHHHHHHHHHHHHHHhCcCCch-hhhcCCCHHHHHHHHHHHHHHHhCCC--ccccccccccCCcccHHH
Confidence 89999999999999999999999999999988 99999999999999999999999887 999999999999999999
Q ss_pred HHHHhhCCcccccccccCCCCCCcchhHHHHHHHHHHHHhhhcCCCCCCcchHHHHHhhccCccccccceeeeeecccch
Q 003002 689 HYAALGRDKLGAAAVNLVGGDKPADVYSGIAARVLEIMRADADKDPATYPYASCARLLINQVDRKLVKQTVMTSVYGVTY 768 (858)
Q Consensus 689 HyAAL~rD~~Ga~~VNL~p~d~P~DvYs~Va~~V~~~l~~da~~~~~~~~~~~~a~~l~~~i~RKvVKqtVMT~vYGvT~ 768 (858)
||||||||.+||++|||+|+|+|||||+.|++.|.+.+++|+.++.+ .+....+++|..+|+||+|||||||+|||||+
T Consensus 510 HyAAL~rD~~ga~~VNL~p~d~p~DvY~~Va~~v~~~i~~d~~~~~~-~~~~~~~~~l~~~i~RkvvKqtVMT~vYGvT~ 588 (807)
T PHA00452 510 HFSAMLRDEVGGRAVNLLPSDKPQDIYGIVAEVVNEKLERDAINGTD-NTRALARLWLAYGITRSLTKRPVMTLPYGSTR 588 (807)
T ss_pred HHHHHhCCHHhHHHhCCCCCCCCccHHHHHHHHHHHHHHHHHhCCCc-chHHHHHHHHhCCCChhhcccccccceeCCch
Confidence 99999999999999999999999999999999999999999876432 12233446788899999999999999999999
Q ss_pred hhHHHHHHHHHhhccCCCCchhh--hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCeEEEEcCCCCeEe
Q 003002 769 IGARDQIKKRLKERCAIEDDSKL--FGAACYAAKTTLTALGEMFEAARSIMSWLGECAKVIA-SENQAVRWTTPLGLPVV 845 (858)
Q Consensus 769 ~Ga~~qI~~~L~~~g~~~d~~~~--~~~a~yla~~i~~ai~e~f~~A~~im~WL~~~a~~i~-~~~~pV~WtTPlGlpVv 845 (858)
+|+++||.++|+++|+..++... +.+++|+|++||+||+++|++|+.||+||++||++|+ +.+.||.||||+||||+
T Consensus 589 ~g~~~qI~~~l~~~~~~~~~~~~~~~~~~~yla~~i~~ai~~~f~~a~~im~wL~~~a~~i~~~~~~pv~W~TP~GlpV~ 668 (807)
T PHA00452 589 FSCRDYILEDLLQPGIDEGDGAMFTNQAASYMAKLIWDAISETVPAAVEAMNWLQQAAKLLAAKGAEALHWTTPTGFPVW 668 (807)
T ss_pred hhhHHHHHHHHHhcCCCcccchhhhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCCEEEECCCCCEEE
Confidence 99999999999998876544333 7889999999999999999999999999999999999 99999999999999999
Q ss_pred eeccCCCceeee
Q 003002 846 QPYHQLGRHLVM 857 (858)
Q Consensus 846 Q~Y~k~~~~~v~ 857 (858)
|||++.++++|.
T Consensus 669 Q~Y~k~~~~~v~ 680 (807)
T PHA00452 669 QEYRKPEEKRVR 680 (807)
T ss_pred eeecCCCcEEEE
Confidence 999999999885
No 3
>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]
Probab=100.00 E-value=6.1e-158 Score=1313.61 Aligned_cols=677 Identities=35% Similarity=0.596 Sum_probs=593.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHHHHHHHH-hh---------hccCcccccc
Q 003002 143 RRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQAT-AQ---------DKWKHMTYAP 212 (858)
Q Consensus 143 eRQ~~lE~~~~~~a~~~~~~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~-~~---------~~~~r~~y~p 212 (858)
+||..||..++..|.+.|+..+++..++|-..--.-+.+.++.||..+..+.++|+.. .. +.+.|..|+|
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 6799999999999999999999999988854333346788999999999999988874 22 1356899999
Q ss_pred ccccCCchhHHHHHHHHHHHHHhcCC--CCchHHHHHHHHHHHHHHHHHHhHHHHhhhhhccCCCCCCCCCCCCCCChHH
Q 003002 213 YFNNLPADMMAVITMHKLVGLLMTNA--GEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPEK 290 (858)
Q Consensus 213 ~L~~l~~e~lA~Iti~~~l~~~~~~~--~~~~~~~~~~~IG~aVe~E~~~~~~~~~~~k~~~~~~~~~~~~~~l~~~~~~ 290 (858)
||++++++++|+|||+++++++++++ .|+|++.+...+|++||+|++.++|....++.++...++. +
T Consensus 331 yLkl~d~~k~a~lTi~el~~l~s~~~~~~gmr~t~l~i~lg~~vE~Ef~seq~~~~e~~ay~d~~kk~---------p-- 399 (1117)
T COG5108 331 YLKLADLDKVAHLTIRELFDLVSMRRYDRGMRLTPLSIRLGAMVEDEFFSEQFKGHEKDAYEDARKKI---------P-- 399 (1117)
T ss_pred ceeccCcccchhhhHHHHHHhhccccccccceeehhHHHHHHHHHHHHHHHHHhhhhhHHHHHHhhcC---------h--
Confidence 99999999999999999999998876 7899999999999999999999988877654443211110 0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHccccCCCCCCCC--CCCCccCcee
Q 003002 291 LIKEQEKLKKRVTSLIKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGD--SPPDIRPAFV 368 (858)
Q Consensus 291 ~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~~~~kvG~~Li~~l~~~~~i~~~~~~~~~--~~~~~~paF~ 368 (858)
+..++.+.+ .+. ..+.....+.+|.+|+++++++||++++.+|+++++|.+...+... ......|||.
T Consensus 400 -----~~f~~aV~n----~rs-~tr~~~~~~~~~~~Wpq~i~akvGsv~l~lll~vaki~v~~id~~t~~~l~ge~~af~ 469 (1117)
T COG5108 400 -----EQFHNAVHN----KRS-MTRHAKHKGAEWQDWPQDIKAKVGSVALCLLLSVAKIEVKLIDIATEQTLKGEFEAFR 469 (1117)
T ss_pred -----HHHHHHHHH----HHh-hhhhhhhcCcchhcChHHHHHHhhHHHHHHHHHhhhheeEeeechhhchhhhhHHHHH
Confidence 111122221 110 0111112246788999999999999999999999999988766433 3457899999
Q ss_pred EEeeecccccCCCeEEEEEEeCHHHHHHHHhccc--cccCCCCCeeeCCcCcccCCCccccccCcceeecCchhhHHHHH
Q 003002 369 HTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGR--HMIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETI 446 (858)
Q Consensus 369 h~~~~~~~~~~~~k~~gvi~~~~~~~~~l~~~~~--~~~~~~lPMlvpP~pW~~~~~GGYl~~~~~~~R~~~~~~q~~~l 446 (858)
|+|++. +|+++|||.+|..+...+.+..+ ++.+.+|||||||+||+++..|||++....+.|..++.+|-+|+
T Consensus 470 h~yqyh-----Ng~kigvv~~h~tl~~ll~~~~~~a~l~PqlLPmLV~PkPWtsw~~GGY~y~r~~llRlk~t~eqv~yl 544 (1117)
T COG5108 470 HSYQYH-----NGTKIGVVATHETLDWLLTENSRLAPLSPQLLPMLVPPKPWTSWFRGGYWYGRVRLLRLKKTGEQVRYL 544 (1117)
T ss_pred Hhhhhc-----CCceeEEEeeHHHHHHHhhcccccCCCChhhhccccCCCCCcCcccCceeeccceeeeecCcHHHHHHH
Confidence 999975 68999999999998777766543 23334999999999999999999999999999999999998888
Q ss_pred HcCC-CCChhhHHHHHHhhcCcccEechHHHHHHHHHHhcCCCCCCCCCCCCC-CCCCC-CCCCCHHHHHHHHHHHHHHH
Q 003002 447 KMTP-RSQLEPVFQALDTLGSTKWRVNKRILGVIDRMWASGGCLAGLVDQEDV-PLPEK-PNTDDETEIKKWKWKVKTAK 523 (858)
Q Consensus 447 ~~~~-~~~l~~v~~aLN~Lq~t~w~IN~~vL~vi~~~w~~g~~i~~l~~~~~~-p~P~~-p~~~d~~~~~~wk~~~~~~~ 523 (858)
..++ .+||++||++||.||+|||+||.+|++|+.++|++|+.+..||.+++. -+|+. +.+.+|+++..|+-+.+.+.
T Consensus 545 ~~asengd~d~vy~~in~lg~t~W~iN~rvf~V~~~~Wn~ge~fl~IP~a~d~~~~Pp~p~~~~~P~~~~~Wk~~rktia 624 (1117)
T COG5108 545 LMASENGDMDKVYHSINALGNTAWSINHRVFEVMASLWNNGETFLCIPQADDMWLAPPMPREDMSPEEFSRWKSERKTIA 624 (1117)
T ss_pred HHhhhcCChHHHHHHHHHhccCchhhhHHHHHHHHHHHhCCCceeccCchhccccCCCCCcccCCHHHHHHHHHHHHHHH
Confidence 7664 689999999999999999999999999999999999999999987652 34443 45788999999999999999
Q ss_pred HHHhHhhhhhhhHHHHHHHHHhccCCCceeeccccCCCCccccCCCCCCCCCcchhhhhhccccCccCccchhHHHHHHH
Q 003002 524 KQNSEKHSQRCDIELKLSVARKMKDEEGFYYPHNLDFRGRAYPMHPYLNHLGSDLCRGVLEFEEGHPLGKAGLHWLKIHL 603 (858)
Q Consensus 524 ~~~~~~~s~R~~~~~~L~iA~~f~~~~~fYfP~nlDFRGR~Yp~~~~Ln~qGsDl~RsLL~FaegkpLG~~Gl~WLkIhl 603 (858)
..+...+|+||+++|+|+||++|.|+ .|||||++|||||+||+|+||||||+|.|||||.||.|+|||++|++|||||+
T Consensus 625 ~~~~~a~S~RcdfnykLeiAraFl~E-kfYFPH~lDFRGRaYpls~hlnh~gnD~srGLL~F~~gkplgp~Gl~WLkiHl 703 (1117)
T COG5108 625 EANARAVSKRCDFNYKLEIARAFLDE-KFYFPHQLDFRGRAYPLSLHLNHQGNDASRGLLQFANGKPLGPEGLDWLKIHL 703 (1117)
T ss_pred HhhhhhhhhhcchHHHHHHHHHhccC-ccccccccccCcccccCccccccccchhhhhHHHhhcCCcCCcchhhHHHHHh
Confidence 99999999999999999999999996 89999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCCCCHHHHHHHHHhhHHHHHHhccCCcCcchhhhcCCchHHHHHHHHHHHHhhcCCCCCCccccccccccCC
Q 003002 604 ANLYAGGVDKLSYEGRVAFTENHLDDIFDSADRPLEGRRWWLGAEDPFQCLATCINLSEALRSPSPESTISHIPVHMDGS 683 (858)
Q Consensus 604 AN~~G~G~DK~s~~eRi~wv~~n~~~I~~sA~~Pl~~~~wW~~Ad~P~QfLA~C~El~~a~~s~~P~~y~S~lPVhqDGS 683 (858)
||+| |+||+||.+|++||++|+.+|+|||+|||+|++||..||+|||.||+||||.+++++|||+.|+||+|||||||
T Consensus 704 anLf--GvdK~~~~~Rvafv~~n~qei~dSAenPldgnrwW~tAdkPwQALA~CFE~~e~v~~gd~e~fiSH~PvqqDGT 781 (1117)
T COG5108 704 ANLF--GVDKCSMNERVAFVMANQQEILDSAENPLDGNRWWLTADKPWQALAFCFEWQEYVAEGDHEAFISHLPVQQDGT 781 (1117)
T ss_pred hccc--CcccCcHHHHHHHHHhhHHHHHhhccCCCCCCcchhcCCChHHHHHHHHHHHHHHhcCChHHhhhcCcccccCc
Confidence 9999 89999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhhHHHHhhCCcccccccccCCCCCCcchhHHHHHHHHHHHHhhhcCCCCCCcchHHHHHhhccCccccccceeeeee
Q 003002 684 CNGLQHYAALGRDKLGAAAVNLVGGDKPADVYSGIAARVLEIMRADADKDPATYPYASCARLLINQVDRKLVKQTVMTSV 763 (858)
Q Consensus 684 CNGLQHyAAL~rD~~Ga~~VNL~p~d~P~DvYs~Va~~V~~~l~~da~~~~~~~~~~~~a~~l~~~i~RKvVKqtVMT~v 763 (858)
|||||||||||+|++||.+|||+|+|+|+|||..||..|...++.+|+++. ..|+.|++++||+|||+||||+|
T Consensus 782 CNGLQhyaAlggD~eGa~qVNLvPSDkP~DvYa~VA~vv~~~L~~~AeagD------e~ak~lKDK~Tr~vVk~tvmtnv 855 (1117)
T COG5108 782 CNGLQHYAALGGDEEGAAQVNLVPSDKPNDVYATVASVVIAKLRDIAEAGD------ETAKELKDKETRTVVKETVMTNV 855 (1117)
T ss_pred cchHHHHHHhcCccccceeeeccCCCCchhHHHHHHHHHHHHHHHHHHhhh------hHHHHHhhhhhhhhhhhccccce
Confidence 999999999999999999999999999999999999999999999998873 78999999999999999999999
Q ss_pred cccchhhHHHHHHHHHhhccCCCCch-hhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-------------
Q 003002 764 YGVTYIGARDQIKKRLKERCAIEDDS-KLFGAACYAAKTTLTALGEMFEAARSIMSWLGECAKVIAS------------- 829 (858)
Q Consensus 764 YGvT~~Ga~~qI~~~L~~~g~~~d~~-~~~~~a~yla~~i~~ai~e~f~~A~~im~WL~~~a~~i~~------------- 829 (858)
||||++|++.||.++|.-. ..+.+ +....+.|+++.+|.++++.|.+|+.|++||.+|++.|..
T Consensus 856 ygvtyvGat~qitk~l~~i--~g~~k~~~~d~~kyltk~vF~a~r~lF~~Ah~iqdwl~~c~~~i~~s~~~d~d~~~~k~ 933 (1117)
T COG5108 856 YGVTYVGATRQITKRLTLI--YGASKFDTVDPWKYLTKEVFPAERTLFAAAHFIQDWLWDCVGEIVVSAAGDMDWLQKKA 933 (1117)
T ss_pred eeeEEeehHHHHHHhcccc--cCchhccccCHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHHhHHHHhcccchhHHHHHh
Confidence 9999999999999998643 11221 3445679999999999999999999999999999998854
Q ss_pred -----CCCeEEEEcCCCCeEeeeccCCCceee
Q 003002 830 -----ENQAVRWTTPLGLPVVQPYHQLGRHLV 856 (858)
Q Consensus 830 -----~~~pV~WtTPlGlpVvQ~Y~k~~~~~v 856 (858)
+..||+||||+||||+||||..++++|
T Consensus 934 gik~de~~pViWtTplgLpivQpYr~~~~kq~ 965 (1117)
T COG5108 934 GIKADESLPVIWTTPLGLPIVQPYRTSEQKQL 965 (1117)
T ss_pred ccCcccccceeeccCCCCcccccchhhHHHHH
Confidence 248999999999999999999988775
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=3.6e-83 Score=719.30 Aligned_cols=265 Identities=54% Similarity=0.917 Sum_probs=236.0
Q ss_pred CccCccchhHHHHHHHHHhhcCCCCCCCHHHHHHHHHhhHHHHHHhccCCcCcchhhhcCCchHHHHHHHHHHHHhhcCC
Q 003002 588 GHPLGKAGLHWLKIHLANLYAGGVDKLSYEGRVAFTENHLDDIFDSADRPLEGRRWWLGAEDPFQCLATCINLSEALRSP 667 (858)
Q Consensus 588 gkpLG~~Gl~WLkIhlAN~~G~G~DK~s~~eRi~wv~~n~~~I~~sA~~Pl~~~~wW~~Ad~P~QfLA~C~El~~a~~s~ 667 (858)
|||||++|++|||||+||+| |+||+||+||++||++|+++|+++|+||+++..||.+||+||||||+|+||++|++++
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 CCCCccccccccccCCCchhhHHHHhhCCcccccccccCCCCCCcchhHHHHHHHHHHHHhhhcCCCCCCcchHHHHHhh
Q 003002 668 SPESTISHIPVHMDGSCNGLQHYAALGRDKLGAAAVNLVGGDKPADVYSGIAARVLEIMRADADKDPATYPYASCARLLI 747 (858)
Q Consensus 668 ~P~~y~S~lPVhqDGSCNGLQHyAAL~rD~~Ga~~VNL~p~d~P~DvYs~Va~~V~~~l~~da~~~~~~~~~~~~a~~l~ 747 (858)
||++|+||+|||||||||||||||||+||.+||++|||+|+++|+|||+.|++.|.+.+.+++... .....+++++.
T Consensus 79 ~~~~~~s~lPV~~DgSCsGlQH~sal~rD~~ga~~vNLip~~~p~DiY~~V~~~v~~~l~~~~~~~---~~~~~~~~~l~ 155 (405)
T PF00940_consen 79 NPEEFVSHLPVHQDGSCSGLQHYSALLRDEVGAKAVNLIPSDKPQDIYSEVAEEVKKRLEEDADDA---EEDNSLAKWLK 155 (405)
T ss_dssp SGCCSEE-SEEEEEBSTHHHHHHHHHTT-HHHHHHTTSSSSSS---HHHHHHHHHHHHHHHHHHEH---HCCHHHHHHCC
T ss_pred CchheeecceeeecCcccHHHHHHHHccCHhhChhcCCCCCCCCCchHHHHHHHHHHHHHHhhccc---ccchHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999999999999884210 11258899999
Q ss_pred ccCccccccceeeeeecccchhhHHHHHHHHHhhccCCC-CchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 003002 748 NQVDRKLVKQTVMTSVYGVTYIGARDQIKKRLKERCAIE-DDSKLFGAACYAAKTTLTALGEMFEAARSIMSWLGECAKV 826 (858)
Q Consensus 748 ~~i~RKvVKqtVMT~vYGvT~~Ga~~qI~~~L~~~g~~~-d~~~~~~~a~yla~~i~~ai~e~f~~A~~im~WL~~~a~~ 826 (858)
.+|+||+|||+|||+|||||++|+++||+++|++.+... +....+.++.|||++|+++|+++|++|+.+|+||++||++
T Consensus 156 ~~i~Rk~vK~~vMT~~YG~T~~g~~~qi~~~l~~~~~~~~~~~~~~~~~~~la~~i~~~i~~~~~~a~~~m~wL~~~a~~ 235 (405)
T PF00940_consen 156 GGITRKLVKRPVMTIVYGVTFYGARDQIKEQLKEKGDEEEDKIESYKAAMYLAKIIFEAIKEVFPGARNIMDWLQEIAKI 235 (405)
T ss_dssp CT--HHHHHHHHHHHHHT-TCCHHHHHHHHHCHCHCCCTTTTTTHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHH
T ss_pred CCCChhhcccceEEeeeCcchhhHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999886544 3446788999999999999999999999999999999999
Q ss_pred HhcCCCeEEEEcCCCCeEeeeccCCCceeee
Q 003002 827 IASENQAVRWTTPLGLPVVQPYHQLGRHLVM 857 (858)
Q Consensus 827 i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~v~ 857 (858)
+++.+.||.|+||+||||+|+|++.+++.|.
T Consensus 236 ~~~~~~pv~W~tP~Gl~V~Q~Y~~~~~~~i~ 266 (405)
T PF00940_consen 236 IAKLNKPVSWTTPLGLPVVQPYRKSKKKRIK 266 (405)
T ss_dssp HHCTCB-EEEEETTSEEEEE--EEESEEEEE
T ss_pred HHccCCcEEEECCCCCEEEecccccCceeeE
Confidence 9999999999999999999999999998875
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=2.9e-48 Score=422.60 Aligned_cols=304 Identities=32% Similarity=0.535 Sum_probs=220.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCChhHHHHHHHHHHHHHHHHHHHHHHhh----hccCccccccccccCC
Q 003002 143 RRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQ----DKWKHMTYAPYFNNLP 218 (858)
Q Consensus 143 eRQ~~lE~~~~~~a~~~~~~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~~----~~~~r~~y~p~L~~l~ 218 (858)
+||++||+++++.|+++|++..+++.++|.+++++++++++.+|+++|+++|+++++.+. ..+.++.|+|||+.||
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 3567999999999999
Q ss_pred chhHHHHHHHHHHHHHhcCC---CCchHHHHHHHHHHHHHHHHHHhHHHHhhhhhccCCCCCCCCCCCCCCChHHhHHHH
Q 003002 219 ADMMAVITMHKLVGLLMTNA---GEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPEKLIKEQ 295 (858)
Q Consensus 219 ~e~lA~Iti~~~l~~~~~~~---~~~~~~~~~~~IG~aVe~E~~~~~~~~~~~k~~~~~~~~~~~~~~l~~~~~~~~~~~ 295 (858)
||++|+|||+++|+++++++ +++++++++.+||++||+|++++.+.+..++.+....+.... .....
T Consensus 81 ~e~lA~Iti~~~l~~~~~~~~~~~g~~~~~~~~~IG~aVe~E~~~~~~~~~~~~~~~~~~~~~~~--~~~~~-------- 150 (318)
T PF14700_consen 81 PEKLAVITIREVLNLLSSSEGYSKGMKLTRLAIAIGRAVEQEYRFQQLEKAEPKYYKKLKKNFKK--KRSKS-------- 150 (318)
T ss_dssp HHHHHHHHHHHHHHHHTTSSSE----EHHHHHHHHHHHHHHHHHHHHHHHCHCCCCCCHHHHCHC--CSTSC--------
T ss_pred HHHHHHHHHHHHHHHhccCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh--cccch--------
Confidence 99999999999999999543 567999999999999999999998877644322110000000 00000
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhCCCCCC--CCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCCCCCccCceeEEeee
Q 003002 296 EKLKKRVTSLIKKQKLQQVRGIVKGHVDSK--PWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKS 373 (858)
Q Consensus 296 ~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~--~W~~~~~~kvG~~Li~~l~~~~~i~~~~~~~~~~~~~~~paF~h~~~~ 373 (858)
..++.+...++..+.......+ ...+. +|+..++++||++|+++|+++++|+++..+... ...+|||+|.+++
T Consensus 151 -~~~r~~~~~~~~~~~~~~~~~~--~~~~~~~~W~~~~~~~vG~~Ll~~l~~~~~i~~~~~~~~~--~~~~paf~~~~~~ 225 (318)
T PF14700_consen 151 -QQKRHVWQLLKNRKDSSGKPSL--EEEWSDSPWPSDIRAKVGSFLLELLMETAKIPVERKDPET--SEEQPAFYHSYRY 225 (318)
T ss_dssp -HHCHHHHHHHHHHHSHSS-STT--T-TCCC--SCHHHHHHHHHHHHHHHHHCTCEEEEEESTT-------BSEEEEE--
T ss_pred -hhHHHHHHHHHHHHHhcccccc--ccccccCCCCHHHHHHHHHHHHHHHHhheeeccccCCccc--cccccchhhhhcc
Confidence 0001222222222111111111 12343 499999999999999999999999887743322 6789999999986
Q ss_pred cccccCCCeEEEEEEeCHHHHHHHHhcccc-----ccCCCCCeeeCCcCcccCCCccccccCcceeecCchhhHHHHHHc
Q 003002 374 FTKEALKGRRYGVIECDPLVRKGLEKTGRH-----MIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETIKM 448 (858)
Q Consensus 374 ~~~~~~~~k~~gvi~~~~~~~~~l~~~~~~-----~~~~~lPMlvpP~pW~~~~~GGYl~~~~~~~R~~~~~~q~~~l~~ 448 (858)
. +++++|+|++||.+.+.+...... ..+.+|||||||+||+++++||||..++++||+++..++....++
T Consensus 226 ~-----~~~~~g~i~~~~~~~~~l~~~~~~~~~~~~~~~~lPMlvpP~PW~~~~~GGYl~~~~~l~R~~~~~~~~~~~~~ 300 (318)
T PF14700_consen 226 R-----KGKKVGVIKPHPELVKLLSDEPEKSLLQATFPRYLPMLVPPKPWTSPNDGGYLLSPTPLMRTKDSEQQQYLKKA 300 (318)
T ss_dssp ------TTT-EEEEEE-HHHHHHHHHHCH---CCCCCCCCS-BSS--EEECCTCCEESSSSSEBSEE-STTHHCHHHHHT
T ss_pred c-----cCceEEEEeeCHHHHHHHHhhhhhhhhhhcccccCcCCCCCCCCcCCCcceeeeeCchhhcccchhhHHHHHHH
Confidence 4 477889999999999999876541 124599999999999999999999999999999887333444555
Q ss_pred CCCCChhhHHHHHHhhcC
Q 003002 449 TPRSQLEPVFQALDTLGS 466 (858)
Q Consensus 449 ~~~~~l~~v~~aLN~Lq~ 466 (858)
...++|+.||+|||+||+
T Consensus 301 ~~~~~l~~v~~~Ln~Lg~ 318 (318)
T PF14700_consen 301 LRRGDLDPVFDALNALGS 318 (318)
T ss_dssp TTCCGGHHHHHHHHHHHT
T ss_pred ccccchHHHHHHHHHhcC
Confidence 678899999999999996
No 6
>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]
Probab=89.42 E-value=0.19 Score=60.05 Aligned_cols=76 Identities=25% Similarity=0.399 Sum_probs=58.3
Q ss_pred hccCccccccceeeeeecccchhhHHHHHHHHHhhccCCCCchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 003002 747 INQVDRKLVKQTVMTSVYGVTYIGARDQIKKRLKERCAIEDDSKLFGAACYAAKTTLTALGEMFEAARSIMSWLGECAKV 826 (858)
Q Consensus 747 ~~~i~RKvVKqtVMT~vYGvT~~Ga~~qI~~~L~~~g~~~d~~~~~~~a~yla~~i~~ai~e~f~~A~~im~WL~~~a~~ 826 (858)
.-+++|++.|| ||.+||...+-..+.- ++|-. .+++-..++|.+|.++...+|+|.+++..++..-|+|++..+++
T Consensus 860 yvGat~qitk~--l~~i~g~~k~~~~d~~-kyltk-~vF~a~r~lF~~Ah~iqdwl~~c~~~i~~s~~~d~d~~~~k~gi 935 (1117)
T COG5108 860 YVGATRQITKR--LTLIYGASKFDTVDPW-KYLTK-EVFPAERTLFAAAHFIQDWLWDCVGEIVVSAAGDMDWLQKKAGI 935 (1117)
T ss_pred EeehHHHHHHh--cccccCchhccccCHH-HHHHH-hHhHHHHHHHHHHHHHHHHHHHHHhHHHHhcccchhHHHHHhcc
Confidence 45899999999 9999999765332221 22211 23444457899999999999999999999999999999987753
No 7
>smart00482 POLAc DNA polymerase A domain.
Probab=59.14 E-value=6.1 Score=41.48 Aligned_cols=137 Identities=23% Similarity=0.245 Sum_probs=89.2
Q ss_pred HHHHhhcCCCCCCccccccccccCCCchhhHHHHhhCCcccccccccCCCCCCcchhHHHHHHHHHHHHhhhcCCCCCCc
Q 003002 659 NLSEALRSPSPESTISHIPVHMDGSCNGLQHYAALGRDKLGAAAVNLVGGDKPADVYSGIAARVLEIMRADADKDPATYP 738 (858)
Q Consensus 659 El~~a~~s~~P~~y~S~lPVhqDGSCNGLQHyAAL~rD~~Ga~~VNL~p~d~P~DvYs~Va~~V~~~l~~da~~~~~~~~ 738 (858)
++++++.. |++| +-|..|-|.==|=.+|.|.+|......-| ...|+|+.+|..+...-.+
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 2344 57889999999999999999987766655 3569999988765322110
Q ss_pred chHHHHHhhccCccccccceeeeeecccchhhHHHHHHHHHhhccCCCCchhhhhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 003002 739 YASCARLLINQVDRKLVKQTVMTSVYGVTYIGARDQIKKRLKERCAIEDDSKLFGAACYAAKTTLTALGEMFEAARSIMS 818 (858)
Q Consensus 739 ~~~~a~~l~~~i~RKvVKqtVMT~vYGvT~~Ga~~qI~~~L~~~g~~~d~~~~~~~a~yla~~i~~ai~e~f~~A~~im~ 818 (858)
. .....|+..|+.+--..||.+..|..+++ | ++.+ -|+.+.++..+.||+ +..
T Consensus 63 --~-----v~~~~R~~aK~~~~g~~YG~g~~~la~~l-------g-~s~~---------ea~~~~~~f~~~~p~---v~~ 115 (206)
T smart00482 63 --E-----VTKELRRAAKAINFGIIYGMGAKGLAEQL-------G-ISEA---------EAKELIKAYFARFPG---VKR 115 (206)
T ss_pred --h-----CCHHHHHHHhHHHHHhhhccchhHHHHHc-------C-CCHH---------HHHHHHHHHHHHCcc---HHH
Confidence 0 01346999999999999999977766553 2 1211 245566666666665 456
Q ss_pred HHHHHHHHHhcCCCeEEEEcCCCCeEe
Q 003002 819 WLGECAKVIASENQAVRWTTPLGLPVV 845 (858)
Q Consensus 819 WL~~~a~~i~~~~~pV~WtTPlGlpVv 845 (858)
|.+++.....+.+ .| +|+.|-...
T Consensus 116 ~~~~~~~~a~~~g-~v--~t~~Gr~r~ 139 (206)
T smart00482 116 YIKRTLEEARRKG-YV--TTLFGRRRY 139 (206)
T ss_pred HHHHHHHHHHhCC-EE--EecCCCeee
Confidence 7777666555544 23 688876443
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=30.83 E-value=53 Score=30.59 Aligned_cols=56 Identities=27% Similarity=0.560 Sum_probs=25.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHhcccCCCChhHHHHHHHHHHHHH
Q 003002 136 AKYYMLKRRQIKIETEAWEQAAKEYQDLLA---DMCEQKLAPNLPYVKSLFLGWFEPLR 191 (858)
Q Consensus 136 ~~~~~l~eRQ~~lE~~~~~~a~~~~~~~~~---~~~~~g~a~~~~~~~~ll~~w~~~L~ 191 (858)
..|....++...+..+.++....+|.+++. .+.+.|+.++.+-++.++.+|+..+.
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 455555555555666666666666666554 45667888999999999999999766
No 9
>PF08849 DUF1819: Putative inner membrane protein (DUF1819); InterPro: IPR014948 These proteins are functionally uncharacterised. Several are annotated as putative inner membrane proteins. ; PDB: 3BHW_A.
Probab=29.51 E-value=93 Score=32.19 Aligned_cols=29 Identities=17% Similarity=0.429 Sum_probs=22.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHcccc
Q 003002 322 VDSKPWGQDALVKVGCRLIQLLMETAYIQ 350 (858)
Q Consensus 322 ~~~~~W~~~~~~kvG~~Li~~l~~~~~i~ 350 (858)
.....|+..++-||++.+..+|.|++.+.
T Consensus 133 ~~i~~WSdsT~~Kl~~~~~~~L~eaGlL~ 161 (189)
T PF08849_consen 133 PEIASWSDSTIKKLRQVLFRILREAGLLE 161 (189)
T ss_dssp TTS----HHHHHHHHHHHHHHHHHTTSBS
T ss_pred CcccccCHHHHHHHHHHHHHHHHHcCCcc
Confidence 45678999999999999999999999884
No 10
>cd08638 DNA_pol_A_theta DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation. DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis (TLS) and in somatic hypermutation (SHM). DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Pol theta is an exception among family A polymerases and generates processive single base substitutions. Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondri
Probab=28.45 E-value=41 Score=38.65 Aligned_cols=139 Identities=23% Similarity=0.286 Sum_probs=89.2
Q ss_pred HHHHhhcCCCCCCccccccccccCCCchhhHHHHhhCCcccccccccCCCCCCcchhHHHHHHHHHHHHhhhcCCCCCCc
Q 003002 659 NLSEALRSPSPESTISHIPVHMDGSCNGLQHYAALGRDKLGAAAVNLVGGDKPADVYSGIAARVLEIMRADADKDPATYP 738 (858)
Q Consensus 659 El~~a~~s~~P~~y~S~lPVhqDGSCNGLQHyAAL~rD~~Ga~~VNL~p~d~P~DvYs~Va~~V~~~l~~da~~~~~~~~ 738 (858)
.+++++..+ .+ ++-|..|-|-==|=.+|.|.+|.....+.| .-.|||+.+|..+... +.
T Consensus 129 ~iR~~f~a~--~G---~~lv~~DysqiElRvlA~ls~D~~l~~~~~-----~g~Dih~~~A~~~~g~--------~~--- 187 (373)
T cd08638 129 SLRHAFIPP--PG---RVLLSADYSQLELRILAHLSGDPALIELLN-----SGGDVFKMIAAQWLGK--------PV--- 187 (373)
T ss_pred hhhheeeCC--CC---CEEEEechhhhHHHHHHHHhCCHHHHHHHh-----cCCCHHHHHHHHHhCC--------Ch---
Confidence 455665432 23 457899999999999999999998777665 2569999988766321 10
Q ss_pred chHHHHHhhccCccccccceeeeeecccchhhHHHHHHHHHhhccCCCCchhhhhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 003002 739 YASCARLLINQVDRKLVKQTVMTSVYGVTYIGARDQIKKRLKERCAIEDDSKLFGAACYAAKTTLTALGEMFEAARSIMS 818 (858)
Q Consensus 739 ~~~~a~~l~~~i~RKvVKqtVMT~vYGvT~~Ga~~qI~~~L~~~g~~~d~~~~~~~a~yla~~i~~ai~e~f~~A~~im~ 818 (858)
.. ...-.|+..|..+--..||.+..|...++ |+ +.+ -|+.+.+...+.||+.. .
T Consensus 188 -~~-----v~~~~R~~aK~~~fg~~YG~g~~~La~~l-------~~-s~~---------eA~~~i~~f~~~~p~v~---~ 241 (373)
T cd08638 188 -EE-----VTDEERQQAKQLVYGILYGMGAKSLAEQL-------GV-SEE---------EAKQFIESFKNAYPGVR---R 241 (373)
T ss_pred -hh-----CCHHHHHHHhHHHHhhHhCCcHHHHHHHh-------CC-CHH---------HHHHHHHHHHHHCccHH---H
Confidence 00 01246999999999999999999887654 32 211 14556666667777655 5
Q ss_pred HHHHHHHHHhcCCCeEEEEcCCCCeEeee
Q 003002 819 WLGECAKVIASENQAVRWTTPLGLPVVQP 847 (858)
Q Consensus 819 WL~~~a~~i~~~~~pV~WtTPlGlpVvQ~ 847 (858)
|.+++-....+.+ .| +|+.|-...-|
T Consensus 242 ~~~~~~~~a~~~g-~v--~T~~GRrr~~p 267 (373)
T cd08638 242 FIRETIERARRNG-FV--ETLTGRRRYLP 267 (373)
T ss_pred HHHHHHHHHHHcC-cE--EccCCCEEeCC
Confidence 5554444433332 23 46777654433
No 11
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=26.00 E-value=33 Score=41.40 Aligned_cols=118 Identities=24% Similarity=0.253 Sum_probs=82.1
Q ss_pred ccccccCCCchhhHHHHhhCCcccccccccCCCCCCcchhHHHHHHHHHHHHhhhcCCCCCCcchHHHHHhhccCccccc
Q 003002 676 IPVHMDGSCNGLQHYAALGRDKLGAAAVNLVGGDKPADVYSGIAARVLEIMRADADKDPATYPYASCARLLINQVDRKLV 755 (858)
Q Consensus 676 lPVhqDGSCNGLQHyAAL~rD~~Ga~~VNL~p~d~P~DvYs~Va~~V~~~l~~da~~~~~~~~~~~~a~~l~~~i~RKvV 755 (858)
.-|..|-|.==|=.+|.|.+|.....+.| .-.|||+.+|..+-.. +.+ . .-.|+..
T Consensus 326 ~lv~aDysqiElRvlA~ls~D~~l~~~~~-----~g~Dih~~~A~~~~~~-------~~~-----~-------~~~R~~a 381 (553)
T PRK14975 326 KLVVADASQIELRVLAAYSGDERMIEAFR-----TGGDLHRLTASVGFGK-------PEE-----E-------KEERALA 381 (553)
T ss_pred EEEEechhhhHHHHHHHHcCCHHHHHHHh-----cCCCHHHHHHHHHhCC-------Ccc-----c-------hhHHHHH
Confidence 57889999999999999999999877776 3579999988877211 110 0 3469999
Q ss_pred cceeeeeecccchhhHHHHHHHHHhhccCCCCchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEE
Q 003002 756 KQTVMTSVYGVTYIGARDQIKKRLKERCAIEDDSKLFGAACYAAKTTLTALGEMFEAARSIMSWLGECAKVIASENQAVR 835 (858)
Q Consensus 756 KqtVMT~vYGvT~~Ga~~qI~~~L~~~g~~~d~~~~~~~a~yla~~i~~ai~e~f~~A~~im~WL~~~a~~i~~~~~pV~ 835 (858)
|..+--.+||.+..|..+++. .. . -|+.+.+...+.||+ +..|++++.+...+.| .|
T Consensus 382 K~~~~g~~YG~g~~~l~~~~~-~~-------------~----ea~~~~~~~~~~~p~---v~~~~~~~~~~a~~~g-~v- 438 (553)
T PRK14975 382 KAANFGAIYGATSKGLQEYAK-NY-------------G----EAARLLERLRRAYPR---AVGWVERAAREGERGG-VV- 438 (553)
T ss_pred HHHHHHhhhCCcHHHHHHHcC-CH-------------H----HHHHHHHHHHHHCcc---HHHHHHHHHHHHHHCC-eE-
Confidence 999999999999998887753 11 0 134455555566665 5566666666554443 23
Q ss_pred EEcCCC
Q 003002 836 WTTPLG 841 (858)
Q Consensus 836 WtTPlG 841 (858)
+|++|
T Consensus 439 -~T~~G 443 (553)
T PRK14975 439 -RTLLG 443 (553)
T ss_pred -ECCCC
Confidence 36666
No 12
>PF00476 DNA_pol_A: DNA polymerase family A; InterPro: IPR001098 Synonym(s): DNA nucleotidyltransferase (DNA-directed) DNA-directed DNA polymerases(2.7.7.7 from EC) are the key enzymes catalysing the accurate replication of DNA. They require either a small RNA molecule or a protein as a primer for the de novo synthesis of a DNA chain. A number of polymerases belong to this family [, , ].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=23.41 E-value=39 Score=38.80 Aligned_cols=109 Identities=21% Similarity=0.246 Sum_probs=74.8
Q ss_pred cccccccCCCchhhHHHHhhCCcccccccccCCCCCCcchhHHHHHHHHHHHHhhhcCCCCCCcchHHHHHhhccCcccc
Q 003002 675 HIPVHMDGSCNGLQHYAALGRDKLGAAAVNLVGGDKPADVYSGIAARVLEIMRADADKDPATYPYASCARLLINQVDRKL 754 (858)
Q Consensus 675 ~lPVhqDGSCNGLQHyAAL~rD~~Ga~~VNL~p~d~P~DvYs~Va~~V~~~l~~da~~~~~~~~~~~~a~~l~~~i~RKv 754 (858)
++-|..|-|-==|=.+|.|.+|.....+.+ ...|+|..+|..+...-.. . .....|+.
T Consensus 155 ~~lv~aD~sqiElRvlA~ls~D~~l~~~~~-----~g~D~h~~~a~~~~~~~~~------------~-----v~~~~R~~ 212 (383)
T PF00476_consen 155 YVLVSADYSQIELRVLAHLSGDENLIEAFR-----NGEDIHTETASDIFGKPYE------------E-----VTKEERQK 212 (383)
T ss_dssp EEEEEEEESSHHHHHHHHHHTHHHHHHHHH-----TTCCHHHHHHHHHTTCHGG------------G-----TTHHHHHH
T ss_pred ceeeeeehhhhhHHHHHHhcccHHHHHhhc-----ccccHHHHHHHHhcCCCcc------------c-----cchhhHHH
Confidence 467888999888889999999997655554 4579999887765322100 0 23468999
Q ss_pred ccceeeeeecccchhhHHHHHHHHHhhccCCCCchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 003002 755 VKQTVMTSVYGVTYIGARDQIKKRLKERCAIEDDSKLFGAACYAAKTTLTALGEMFEAARSIMSWLGE 822 (858)
Q Consensus 755 VKqtVMT~vYGvT~~Ga~~qI~~~L~~~g~~~d~~~~~~~a~yla~~i~~ai~e~f~~A~~im~WL~~ 822 (858)
.|..+--..||.+..|..+++. ++.+ -|+.+.++..+.||+....++.+..
T Consensus 213 aK~~~~g~~YG~g~~~la~~l~--------~s~~---------eA~~~~~~f~~~~p~v~~~~~~~~~ 263 (383)
T PF00476_consen 213 AKTVNFGLIYGMGAKGLAEQLG--------ISEE---------EAKELIDAFFEAFPGVKKWMERVKK 263 (383)
T ss_dssp HHHHHHHHHTT-THHHHHHHHT--------SCHH---------HHHHHHHHHHHHSHHHHHHHHHHHH
T ss_pred HhHHHHhhhhccCHHHHHHHcc--------CCHH---------HHHHHHHHHHHhCchHHHHHHHHHH
Confidence 9999999999999888877764 2211 2456667777777775554444444
No 13
>cd08637 DNA_pol_A_pol_I_C Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuc
Probab=22.89 E-value=69 Score=36.90 Aligned_cols=136 Identities=18% Similarity=0.230 Sum_probs=86.2
Q ss_pred HHHHhhcCCCCCCccccccccccCCCchhhHHHHhhCCcccccccccCCCCCCcchhHHHHHHHHHHHHhhhcCCCCCCc
Q 003002 659 NLSEALRSPSPESTISHIPVHMDGSCNGLQHYAALGRDKLGAAAVNLVGGDKPADVYSGIAARVLEIMRADADKDPATYP 738 (858)
Q Consensus 659 El~~a~~s~~P~~y~S~lPVhqDGSCNGLQHyAAL~rD~~Ga~~VNL~p~d~P~DvYs~Va~~V~~~l~~da~~~~~~~~ 738 (858)
+++.++..+ .+| .-|..|-|-==|=.+|.|.+|.....+.| ...|+|+.+|..+... +++
T Consensus 140 ~~R~~f~~~--~G~---~lv~aDysqiElRilA~ls~D~~l~~~~~-----~g~Dih~~~A~~~~g~-------~~~--- 199 (377)
T cd08637 140 EIRKAFVAE--EGW---VLLSADYSQIELRILAHLSGDEALIEAFK-----NGEDIHTRTAAEVFGV-------PPE--- 199 (377)
T ss_pred hHHHheeCC--CCC---EEEEechhHhHHHHHHHHhCCHHHHHHHh-----cCCCHHHHHHHHHhCC-------Chh---
Confidence 466666532 233 57889999888889999999998877766 3579999988766321 000
Q ss_pred chHHHHHhhccCccccccceeeeeecccchhhHHHHHHHHHhhccCCCCchhhhhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 003002 739 YASCARLLINQVDRKLVKQTVMTSVYGVTYIGARDQIKKRLKERCAIEDDSKLFGAACYAAKTTLTALGEMFEAARSIMS 818 (858)
Q Consensus 739 ~~~~a~~l~~~i~RKvVKqtVMT~vYGvT~~Ga~~qI~~~L~~~g~~~d~~~~~~~a~yla~~i~~ai~e~f~~A~~im~ 818 (858)
.. ..-.|+..|..+--..||.+..|...++ |+ +.+ -|+.+.+...+.||+.. .
T Consensus 200 --~v-----~~~~R~~aK~~~~g~~YG~g~~~la~~l-------g~-s~~---------eA~~~~~~f~~~~p~v~---~ 252 (377)
T cd08637 200 --EV-----TPEMRRIAKAVNFGIIYGISAFGLSQQL-------GI-SRK---------EAKEYIDRYFARYPGVK---E 252 (377)
T ss_pred --hC-----CHHHHhhhhHhhcchhcCcchhHHHHHc-------CC-CHH---------HHHHHHHHHHHHCccHH---H
Confidence 00 1124999999999999999887766543 22 211 13556666666677655 4
Q ss_pred HHHHHHHHHhcCCCeEEEEcCCCCeE
Q 003002 819 WLGECAKVIASENQAVRWTTPLGLPV 844 (858)
Q Consensus 819 WL~~~a~~i~~~~~pV~WtTPlGlpV 844 (858)
|..++...+...+- .+|+.|-..
T Consensus 253 ~~~~~~~~a~~~g~---v~t~~GRrr 275 (377)
T cd08637 253 YMEETVEEAREKGY---VETLFGRRR 275 (377)
T ss_pred HHHHHHHHHHHcCc---EEccCCCEE
Confidence 55555544443332 256666533
No 14
>cd08643 DNA_pol_A_pol_I_B Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5
Probab=22.27 E-value=70 Score=37.67 Aligned_cols=86 Identities=19% Similarity=0.079 Sum_probs=61.1
Q ss_pred HHHHhhcCCCCCCccccccccccCCCchhhHHHHhhCCcccccccccCCCCCCcchhHHHHHHHHHHHHhhhcCCCCCCc
Q 003002 659 NLSEALRSPSPESTISHIPVHMDGSCNGLQHYAALGRDKLGAAAVNLVGGDKPADVYSGIAARVLEIMRADADKDPATYP 738 (858)
Q Consensus 659 El~~a~~s~~P~~y~S~lPVhqDGSCNGLQHyAAL~rD~~Ga~~VNL~p~d~P~DvYs~Va~~V~~~l~~da~~~~~~~~ 738 (858)
+++.++-.+ .+ ++=|.-|.|.==|-.+|.|.+|..++..+.... -.||++..|..+
T Consensus 176 ~iR~~Fva~--~G---~~lv~aDySQiELRiLAhls~d~~~~~l~~~~~---~~DiH~~ta~~~---------------- 231 (429)
T cd08643 176 ECRELFGVP--PG---WSLVGADASGLELRCLAHYLARYDGGAYTRKVL---GGDIHWANAQAM---------------- 231 (429)
T ss_pred hhhheEecC--CC---CEEEEecHHHHHHHHHHHHhcccchHHHHhhhc---ccchhHHHHHHh----------------
Confidence 455555422 23 346888998888889999999876666655333 358887655432
Q ss_pred chHHHHHhhccCccccccceeeeeecccchhhHHHHHHH
Q 003002 739 YASCARLLINQVDRKLVKQTVMTSVYGVTYIGARDQIKK 777 (858)
Q Consensus 739 ~~~~a~~l~~~i~RKvVKqtVMT~vYGvT~~Ga~~qI~~ 777 (858)
+...|+..|...--.+||.+..|..+++.-
T Consensus 232 ---------g~~~R~~AK~i~fGiiYG~g~~~La~~lg~ 261 (429)
T cd08643 232 ---------GLLSRDGAKTFIYAFLYGAGDEKLGQIVGD 261 (429)
T ss_pred ---------ChHHHhhhHHHHHHHHHCCChhHHHHHhCC
Confidence 114699999999999999999999988743
No 15
>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=21.00 E-value=66 Score=36.15 Aligned_cols=101 Identities=11% Similarity=0.172 Sum_probs=62.6
Q ss_pred cchhHHHHHHHHHhhcCCCCCCCHHHHHHHHHhhHHHHHHhcc-C-CcC--cchhhhcCCchHHHHHHHHHHHHh----h
Q 003002 593 KAGLHWLKIHLANLYAGGVDKLSYEGRVAFTENHLDDIFDSAD-R-PLE--GRRWWLGAEDPFQCLATCINLSEA----L 664 (858)
Q Consensus 593 ~~Gl~WLkIhlAN~~G~G~DK~s~~eRi~wv~~n~~~I~~sA~-~-Pl~--~~~wW~~Ad~P~QfLA~C~El~~a----~ 664 (858)
+.|++-+|||++.-+ ..+ +|.++..+.+..|.+... + +|. .+..| ++-+++.+|-.+.++ +
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 358888888875433 122 888888888888887652 2 332 22333 455666666666442 3
Q ss_pred cCCCCCCc---------cccccccccCCCchhhHHHHhhCCccccccccc
Q 003002 665 RSPSPEST---------ISHIPVHMDGSCNGLQHYAALGRDKLGAAAVNL 705 (858)
Q Consensus 665 ~s~~P~~y---------~S~lPVhqDGSCNGLQHyAAL~rD~~Ga~~VNL 705 (858)
+.+-|... .+.+||..|.+|.++..+..+.++. .+..||+
T Consensus 221 EqP~~~~~~~~~~~l~~~~~ipi~~dE~~~~~~~~~~~i~~~-~~d~v~~ 269 (357)
T cd03316 221 EEPVPPDDLEGLARLRQATSVPIAAGENLYTRWEFRDLLEAG-AVDIIQP 269 (357)
T ss_pred cCCCCccCHHHHHHHHHhCCCCEEeccccccHHHHHHHHHhC-CCCEEec
Confidence 33332211 2568999999999988888877654 4556665
Done!