Query 002216
Match_columns 952
No_of_seqs 254 out of 441
Neff 5.1
Searched_HMMs 46136
Date Thu Mar 28 19:09:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002216.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002216hhsearch_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 9E-223 2E-227 1897.4 69.2 841 90-947 146-1011(1088)
2 PHA00452 T3/T7-like RNA polyme 100.0 1E-187 2E-192 1668.4 79.9 725 176-949 3-744 (807)
3 COG5108 RPO41 Mitochondrial DN 100.0 1E-177 2E-182 1485.1 54.1 738 180-947 251-1026(1117)
4 PF00940 RNA_pol: DNA-dependen 100.0 1E-102 3E-107 883.5 18.6 325 620-949 1-328 (405)
5 PF14700 RPOL_N: DNA-directed 100.0 5E-48 1.1E-52 423.6 24.3 305 180-498 1-318 (318)
6 smart00482 POLAc DNA polymeras 89.3 0.47 1E-05 50.3 4.8 192 691-950 3-202 (206)
7 COG5108 RPO41 Mitochondrial DN 87.5 0.38 8.3E-06 58.3 2.8 76 778-857 859-934 (1117)
8 PRK14975 bifunctional 3'-5' ex 63.6 12 0.00026 45.6 6.1 176 708-950 326-509 (553)
9 cd08642 DNA_pol_A_pol_I_A Poly 54.9 46 0.00099 39.1 8.5 88 691-803 159-246 (378)
10 cd08637 DNA_pol_A_pol_I_C Poly 52.0 18 0.00039 42.1 4.7 192 691-950 140-339 (377)
11 TIGR00593 pola DNA polymerase 48.0 56 0.0012 42.4 8.5 179 708-950 659-846 (887)
12 PF14554 VEGF_C: VEGF heparin- 37.8 16 0.00034 31.0 0.9 19 130-148 5-23 (55)
13 cd08640 DNA_pol_A_plastid_like 37.3 36 0.00077 39.8 4.1 206 692-950 109-330 (371)
14 cd08638 DNA_pol_A_theta DNA po 35.3 34 0.00073 39.8 3.5 192 691-950 129-333 (373)
15 PF00476 DNA_pol_A: DNA polyme 32.9 27 0.00057 40.7 2.1 111 707-859 155-265 (383)
16 PF07739 TipAS: TipAS antibiot 31.1 79 0.0017 29.8 4.7 56 173-228 13-71 (118)
17 cd08643 DNA_pol_A_pol_I_B Poly 25.2 65 0.0014 38.4 3.6 144 691-873 176-326 (429)
18 PLN03188 kinesin-12 family pro 20.2 2.4E+03 0.051 29.3 18.4 45 220-264 1126-1170(1320)
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=9.2e-223 Score=1897.41 Aligned_cols=841 Identities=54% Similarity=0.891 Sum_probs=769.9
Q ss_pred hhccccccc-------chhhhhhhhhcccccccccccccccCCCCCcccccccCCcccceeecCCCchhHHHhh-----h
Q 002216 90 IENSVDFHI-------PTCEQEQNFHQRVENTETCADLVIPRSENSTNHQLMCLEPRRRIFVQDPPWFSSIFLK-----G 157 (952)
Q Consensus 90 ~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~ 157 (952)
+.+.++++. +.+++|.+..+-+-|++++.++ +.++++++.---+..-+...-++....|.++.+.. .
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 78888888733333334566677889998887633 3
Q ss_pred hhhhhh---HHHHhhhhHH-HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHcccCCCChh-HHHHHHHHHHHHHHHH
Q 002216 158 LYKRIK---LQEYREMKKR-KFNLLRRRQVKQETEAWERMVDEYK-ELEAKMIEKRLAPNLPH-IKGLFLGWFGPLSEAI 231 (952)
Q Consensus 158 ~~~~~~---~~~~~~~~~~-~~~~l~~RQ~~LE~~~~~~a~~r~r-~~~~~~~~~g~a~~~~~-~~~ll~~w~~~L~~~I 231 (952)
+...++ +++-++.+.. +|-.+.+||..+|.++|++|+++|+ +...+|++..+++++|| +++++++||++|.++|
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 5666677766 8888999999999999999999999 77779999999999999 9999999999999999
Q ss_pred HHHHHHHhhc--cCccchhhhhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 002216 232 EREQKMQRTK--KQKAAYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNY 309 (952)
Q Consensus 232 ~~e~~~~~~~--~~r~~y~p~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~a~~IG~aVe~E~~~~~~~~k~~k~ 309 (952)
++|+..++.. +.|..|+|||++||++++|+|||+++|+++++|++.+|+++++++.+||++||+|+|++.++++..++
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 88999999999999999999999999999999999999999999999999999999999998875443
Q ss_pred hhhhhhhhhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHhccccCCCCCCCC
Q 002216 310 KRKKIIADTEEVLSKEKELLRKRVNSLIKSKRVMEAQKLLKN-EETKPWGRDTQAKLGSRLVELLIETAYVQHPVNPADY 388 (952)
Q Consensus 310 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~W~~~~~~kvG~~Ll~~L~e~~~i~~~~~~~~~ 388 (952)
+... .....++....++.++.++++.++.+.+..... +...+|+.+++++||++|+++||++++|+++.+++.+
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 111124556667778888877776655555554 5677999999999999999999999999999998877
Q ss_pred CCCCccCceEEEEEeeecCCCCccceeEEEEecCHHHHHHHHhhhhcccCCCCceeeCCCCCcCCCCcccccCCccceec
Q 002216 389 SPPDVRPAFRHRFKTILKHPGQKTTKRYGVVECDPLVLEGLDRSAKHMLIPYVPMLVPPKKWKGYNKGGYLFLPSYVMRT 468 (952)
Q Consensus 389 ~~~~~~paF~h~~~~~~~~~g~~~~k~~gvi~~~~~~~~~l~~~~~~~~~~~LPMlvpPkpW~~~~~GGYL~~~s~~~R~ 468 (952)
+.++..|||.|.|++. +|+..+++||+|+|||.+..+|++.+.++.++++||||||+||+++++||||++++++||+
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 8889999999999965 4444478999999999999999998888899999999999999999999999999999999
Q ss_pred CCcHHHHHHH-HhccccChHHHHHHHHhhcCceeEEcHHHHHHHHHHHHcCCCCCCCCCCCCCCCCCCC-CCCCHHHHHH
Q 002216 469 HGSRKQQEAL-KSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRNDVLIPEKP-LSEDMTEVQK 546 (952)
Q Consensus 469 ~~~~~q~~~l-~~~~~~~l~~v~~aLN~Lqst~WrIN~~VL~vi~~~w~~g~~i~~l~~~~~~p~P~~p-~~~d~~~~~~ 546 (952)
+++++|..++ ++.+.++++.||+|||.||+||||||++||||+.++|++|+.+.+++++.+.|+|++| .++|+++++.
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 9999999965 4556789999999999999999999999999999999999999999999999999999 6789999999
Q ss_pred HHHHHHHHHHHHHHhhhhhhhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCccchhhhhhcccCccCCcc
Q 002216 547 WKWSVRKAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKS 626 (952)
Q Consensus 547 wk~~~~~~~~~~~~~~S~R~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL~FaegkpLG~~ 626 (952)
|+++.++..+.++++||+|||++|+|+||++|+|+ .||||||||||||+||+||||||.|+|+|||||+||+|+|||++
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 99999999999999999999999999999999998 59999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhhhhCCCCCCCCHHHHHHHHHHhHHHHHHhccCCCCCchhhhhCCChHHHHHHHHHHHHHHhcCCCCccee
Q 002216 627 GLRWLKIHLANLFSGGVEKLSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVIS 706 (952)
Q Consensus 627 Gl~WLKIhlAN~yG~G~DK~S~deRi~wv~~n~~~I~dsA~dPL~g~~wW~~AD~PwQfLA~C~El~~al~s~~P~~y~S 706 (952)
||+|||||+||+|| |+||+|+++|++|+++|+++|+|||++||+|++||++|||||||||+|||+++|++++||+.|+|
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 ccccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhccCcccc
Q 002216 707 HLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKL 786 (952)
Q Consensus 707 ~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~I~RKv 786 (952)
|+||||||||||||||||||||..||++|||+|+|+|||||++||..|.+.+++||++|+ ++|++|.+.|||||
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 68999999999999
Q ss_pred cccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcE
Q 002216 787 VKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIASENQPV 866 (952)
Q Consensus 787 VKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~~~~pV 866 (952)
|||||||+|||||++|||+||.++|++++.++|+.++|.+|+|+++++|+||+|||.+|++||+||++||++|++++.+|
T Consensus 849 VKQTVMT~VYGVTyvGAR~QI~krL~e~~~f~d~~~v~~as~Yltk~tf~aLrEmF~~araIq~WlgecAklIs~~~~~V 928 (1088)
T KOG1038|consen 849 VKQTVMTSVYGVTYVGARLQIKKRLKEIDDFPDEKEVFDASCYLTKKTFEALREMFTAARAIQDWLGECAKLISSENSPV 928 (1088)
T ss_pred hhhheeeeeeeeeEecHHHHHHHHhhhccCcchhHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCce
Confidence 99999999999999999999999999999999998899999999999999999999999999999999999999999999
Q ss_pred EEEcCCCCeEEeeeccCcceeEEeeeEEEEEe-cC-CCCCChhhhhcCCCCcchhhhhHHHHHHHHHHHhHcCCcEEEee
Q 002216 867 RWTTPLGLPVVQPYCKNERHLIRTSLQVLALQ-RE-GNLVKIRKQRTAFPPNFVHSLDGSHMMMTAVACRDAGLHFAGLS 944 (952)
Q Consensus 867 ~WtTPlGlpVvQpY~k~~~~~I~t~lq~v~l~-~~-~d~vd~rKQ~~Af~PNFIHSLDAsHmmlTa~~c~~~Gi~FaaVH 944 (952)
+||||+||||||||++.++++|+|.+|++++. .+ +++|+.|||++|||||||||||||||||||++|.++||+||+||
T Consensus 929 ~WtTPLGLPVVQPYr~~~~~qirt~lQt~~~~~~d~~~~vn~rkQktaFPPNFIHSLD~SHMmmTal~C~rqGl~FasVH 1008 (1088)
T KOG1038|consen 929 EWTTPLGLPVVQPYRQEKKKQIRTGLQTLFLSPRDLTNKVNARKQKTAFPPNFIHSLDGSHMMMTALACERQGLTFASVH 1008 (1088)
T ss_pred EEecCCCCcccchhhhhhhhcccccceEEeecchhhccccchhhhhccCCCchhhcccchHHHHHHHHHHhcCCceeeee
Confidence 99999999999999999999999999999998 34 78999999999999999999999999999999999999999999
Q ss_pred ccc
Q 002216 945 FQS 947 (952)
Q Consensus 945 Dn~ 947 (952)
|++
T Consensus 1009 Dsy 1011 (1088)
T KOG1038|consen 1009 DSY 1011 (1088)
T ss_pred cch
Confidence 997
No 2
>PHA00452 T3/T7-like RNA polymerase
Probab=100.00 E-value=1e-187 Score=1668.43 Aligned_cols=725 Identities=32% Similarity=0.509 Sum_probs=642.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCccchhhhhccCC
Q 002216 176 NLLRRRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQRTKKQKAAYAPHIELLP 255 (952)
Q Consensus 176 ~~l~~RQ~~LE~~~~~~a~~r~r~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~~~~~~r~~y~p~L~~l~ 255 (952)
..|.+||++||++++++|++||++++++++++|+++++|++++++.+||++|+++|+++++.++++|.++.|+|||+++|
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 hhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHHHh
Q 002216 256 ADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVNS 335 (952)
Q Consensus 256 ~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~a~~IG~aVe~E~~~~~~~~k~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 335 (952)
||+||+|||+++|++++++ ++.++++++++||++||+|++++++++++++..++.. ....+++.+.
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 4569999999999999999999999877655433211 0112222333
Q ss_pred HHHHHH-HHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHhc-cccCCCCCCCCCCCCccCceEEEEEeeecCCCCccc
Q 002216 336 LIKSKR-VMEAQKLLKNEETKPWGRDTQAKLGSRLVELLIETA-YVQHPVNPADYSPPDVRPAFRHRFKTILKHPGQKTT 413 (952)
Q Consensus 336 ~~~~~~-~~~~~~~~~~~~~~~W~~~~~~kvG~~Ll~~L~e~~-~i~~~~~~~~~~~~~~~paF~h~~~~~~~~~g~~~~ 413 (952)
..++.+ .+.++..+...++.+|+.+++++||++|+++|++++ .++++... ..++ +
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~W~~~~~~kvG~~Ll~~l~~~a~~~~~~~~~---------------------~~~~--~ 205 (807)
T PHA00452 149 VYHIAFMMVVEADMVLLGEWDPWPKEDYIHVGKWLLEALIESTGLVELVRHT---------------------GGNG--G 205 (807)
T ss_pred HHHHHHHHHHHHHhhhccCCCCCCHHHHHHHHHHHHHHHHHhhCceeeeecc---------------------cCCC--C
Confidence 332222 222333333334889999999999999999999996 55443111 0111 3
Q ss_pred eeEEEEecCHHHHHHHHhhhhc---ccCCCCceeeCCCCCcCCCCcccccCC---ccceecCCcHHHHHHHHhccccChH
Q 002216 414 KRYGVVECDPLVLEGLDRSAKH---MLIPYVPMLVPPKKWKGYNKGGYLFLP---SYVMRTHGSRKQQEALKSVTGNCMK 487 (952)
Q Consensus 414 k~~gvi~~~~~~~~~l~~~~~~---~~~~~LPMlvpPkpW~~~~~GGYL~~~---s~~~R~~~~~~q~~~l~~~~~~~l~ 487 (952)
+++|+|.+||++++.+++.... +.+.+|||||||+||+++.+||||+.+ +..+|+++...+..+ .+++|+
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 234499999999999999999999853 567888776555433 347899
Q ss_pred HHHHHHHhhcCceeEEcHHHHHHHHHHHHcCCCCCCCCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHHHhhhhh
Q 002216 488 KVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRNDVLIPEKPLS--EDMTEVQKWKWSVRKAKKINQERHSQR 565 (952)
Q Consensus 488 ~v~~aLN~Lqst~WrIN~~VL~vi~~~w~~g~~i~~l~~~~~~p~P~~p~~--~d~~~~~~wk~~~~~~~~~~~~~~S~R 565 (952)
.||++||+||+|||+||++||+||+++|++| .++++|+..+.|+|++|++ .+++++++|++++++++++++++||+|
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 456889999999999999999999999
Q ss_pred hhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCccchhhhhhcccCccCCcchhHHHHHHHhhhhCCCCCC
Q 002216 566 CDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANLFSGGVEK 645 (952)
Q Consensus 566 ~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL~FaegkpLG~~Gl~WLKIhlAN~yG~G~DK 645 (952)
|+++++|++|++|+|++.||||||+|||||+|| +|||||||+|+|||||+||+|+|||++|++|||||+||+| |+||
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 CCHHHHHHHHHHhHHHHHHhccCCCCCchhhhhCCChHHHHHHHHHHHHHHhcCCCCcceeccccccCCCcchhhHHHHh
Q 002216 646 LSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAAL 725 (952)
Q Consensus 646 ~S~deRi~wv~~n~~~I~dsA~dPL~g~~wW~~AD~PwQfLA~C~El~~al~s~~P~~y~S~lPVhqDGSCNGLQHyAAL 725 (952)
+||+||++||++|+++|+++|+|||+|. ||++||+||||||+|+||++|+++|+ +|+||||||||||||||||||||
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 99999999999999999999999886 99999999999999999999999
Q ss_pred hCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhccCcccccccceeeeecccchhhHHH
Q 002216 726 GRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGARE 805 (952)
Q Consensus 726 grD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~Gar~ 805 (952)
|||.+||++|||+|+|+|||||+.|++.|.+.+++|+.++.+ ......+++|..+|+||+|||||||+|||||++|+++
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 1233345678889999999999999999999999999
Q ss_pred HHHHHHHHcCCCCChhhH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCcEEEEcCCCCeEEeeecc
Q 002216 806 QIKRRLEEKGHITDDRQL--FAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIA-SENQPVRWTTPLGLPVVQPYCK 882 (952)
Q Consensus 806 QI~~~L~~~~~~~d~~~~--~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~-~~~~pV~WtTPlGlpVvQpY~k 882 (952)
||.++|+++|+..++... +.+++|+|++||+||+++|++|+.||+||++||++|+ +.+.||.||||+||||+|||++
T Consensus 594 qI~~~l~~~~~~~~~~~~~~~~~~~yla~~i~~ai~~~f~~a~~im~wL~~~a~~i~~~~~~pv~W~TP~GlpV~Q~Y~k 673 (807)
T PHA00452 594 YILEDLLQPGIDEGDGAMFTNQAASYMAKLIWDAISETVPAAVEAMNWLQQAAKLLAAKGAEALHWTTPTGFPVWQEYRK 673 (807)
T ss_pred HHHHHHHhcCCCcccchhhhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCCEEEECCCCCEEEeeecC
Confidence 999999998876544333 7899999999999999999999999999999999999 9999999999999999999999
Q ss_pred CcceeEEeeeE---EEEEecCCCCCChhhhhcCCCCcchhhhhHHHHHHHHHHHhHcCC-cEEEeeccccc
Q 002216 883 NERHLIRTSLQ---VLALQREGNLVKIRKQRTAFPPNFVHSLDGSHMMMTAVACRDAGL-HFAGLSFQSAL 949 (952)
Q Consensus 883 ~~~~~I~t~lq---~v~l~~~~d~vd~rKQ~~Af~PNFIHSLDAsHmmlTa~~c~~~Gi-~FaaVHDn~~~ 949 (952)
.++++|+|.+| .+++..+++++|++||++|||||||||||||||||||++|.+.|+ +||+|||||.-
T Consensus 674 ~~~~~v~t~~~~~~~i~~~~~~~~~d~~Kq~~a~~PNFIHSLDAsHm~~t~~~~~~~g~~~fa~VHDsfwT 744 (807)
T PHA00452 674 PEEKRVRLRLMGVARVQLYVNTDTIDARKHASGIAPNFVHSLDASHLRLTVVACAEKGIESFAVIHDSFGT 744 (807)
T ss_pred CCcEEEEEeeccceeEEeccCCCCCCHHHHhcccCCchhhhhhHHHHHHHHHHHHhcCCCcEEEeccCccc
Confidence 99999999987 577777888999999999999999999999999999999999986 79999999963
No 3
>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]
Probab=100.00 E-value=1.1e-177 Score=1485.15 Aligned_cols=738 Identities=37% Similarity=0.601 Sum_probs=654.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHH-Hh---------hccCccchhh
Q 002216 180 RRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKM-QR---------TKKQKAAYAP 249 (952)
Q Consensus 180 ~RQ~~LE~~~~~~a~~r~r~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~-~~---------~~~~r~~y~p 249 (952)
+||..||..++..|.|+|+..+++..++|-..--.-+.+.++.||..|..+.++|+.. .+ +.+.|..|+|
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 7899999999999999999999999998865444457889999999999999998874 22 2457899999
Q ss_pred hhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHH
Q 002216 250 HIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELL 329 (952)
Q Consensus 250 ~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~a~~IG~aVe~E~~~~~~~~k~~k~~~~~~~~~~~~~~~~~~~~~ 329 (952)
||++++++++|+|||+++++++.+++.+.||+++.+...+|++||+|++.++|...+++.+....+ +.-+.+
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 999999999999999999999999889999999999999999999999999987765443321110 011222
Q ss_pred HHHHHhHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHhccccCCCCCCCCC--CCCccCceEEEEEeeecC
Q 002216 330 RKRVNSLIKSKRVMEAQKLLKNEETKPWGRDTQAKLGSRLVELLIETAYVQHPVNPADYS--PPDVRPAFRHRFKTILKH 407 (952)
Q Consensus 330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~~~~kvG~~Ll~~L~e~~~i~~~~~~~~~~--~~~~~paF~h~~~~~~~~ 407 (952)
++.+.. .+..+-.+..++.+|.+||++++++||++++.+|+.+++|++...+...+ .....|||.|+|+|.
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 HNAVHN----KRSMTRHAKHKGAEWQDWPQDIKAKVGSVALCLLLSVAKIEVKLIDIATEQTLKGEFEAFRHSYQYH--- 475 (1117)
T ss_pred HHHHHH----HHhhhhhhhhcCcchhcChHHHHHHhhHHHHHHHHHhhhheeEeeechhhchhhhhHHHHHHhhhhc---
Confidence 222221 11111123445578899999999999999999999999999876654332 235679999999986
Q ss_pred CCCccceeEEEEecCHHHHHHHHhhhh--cccCCCCceeeCCCCCcCCCCcccccCCccceecCCcHHHHHHHHhc-ccc
Q 002216 408 PGQKTTKRYGVVECDPLVLEGLDRSAK--HMLIPYVPMLVPPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEALKSV-TGN 484 (952)
Q Consensus 408 ~g~~~~k~~gvi~~~~~~~~~l~~~~~--~~~~~~LPMlvpPkpW~~~~~GGYL~~~s~~~R~~~~~~q~~~l~~~-~~~ 484 (952)
+| +++|||.+|..+...+.+... .+.+.+|||||||+||+++..|||++....++|.+++.+|-+|+..+ ..+
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 55 579999999998877766543 23334899999999999999999999999999999999999998766 468
Q ss_pred ChHHHHHHHHhhcCceeEEcHHHHHHHHHHHHcCCCCCCCCCCCC-CCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHhh
Q 002216 485 CMKKVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRND-VLIPEKP-LSEDMTEVQKWKWSVRKAKKINQERH 562 (952)
Q Consensus 485 ~l~~v~~aLN~Lqst~WrIN~~VL~vi~~~w~~g~~i~~l~~~~~-~p~P~~p-~~~d~~~~~~wk~~~~~~~~~~~~~~ 562 (952)
||++||++||.||+|||+||.+|++|+.++|++|+.+..||.+.+ ..+|+.| .+.+|+++..|+.+.+.+...+...+
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 3455544 56789999999999999999999999
Q ss_pred hhhhhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCccchhhhhhcccCccCCcchhHHHHHHHhhhhCCC
Q 002216 563 SQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANLFSGG 642 (952)
Q Consensus 563 S~R~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL~FaegkpLG~~Gl~WLKIhlAN~yG~G 642 (952)
|+||+++|+|+||++|.|+ +|||||+||||||+||+|+||||||+|.|||||.||.|+|||++|++|||||+||+| |
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 CCCCCHHHHHHHHHHhHHHHHHhccCCCCCchhhhhCCChHHHHHHHHHHHHHHhcCCCCcceeccccccCCCcchhhHH
Q 002216 643 VEKLSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHLPIHQDGSCNGLQHY 722 (952)
Q Consensus 643 ~DK~S~deRi~wv~~n~~~I~dsA~dPL~g~~wW~~AD~PwQfLA~C~El~~al~s~~P~~y~S~lPVhqDGSCNGLQHy 722 (952)
+||+||.+|++||++|+.+|+|||+|||+|++||..||+|||.||+||||.+++++|||++|+||+||||||||||||||
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 HHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhccCcccccccceeeeecccchhh
Q 002216 723 AALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVG 802 (952)
Q Consensus 723 AALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~G 802 (952)
||||+|++||++|||+|+|+|+|||..||..|...++.+|+++ ++.|+.|++++||+|||+||||+|||||++|
T Consensus 789 aAlggD~eGa~qVNLvPSDkP~DvYa~VA~vv~~~L~~~Aeag------De~ak~lKDK~Tr~vVk~tvmtnvygvtyvG 862 (1117)
T COG5108 789 AALGGDEEGAAQVNLVPSDKPNDVYATVASVVIAKLRDIAEAG------DETAKELKDKETRTVVKETVMTNVYGVTYVG 862 (1117)
T ss_pred HHhcCccccceeeeccCCCCchhHHHHHHHHHHHHHHHHHHhh------hhHHHHHhhhhhhhhhhhccccceeeeEEee
Confidence 9999999999999999999999999999999999999999887 3679999999999999999999999999999
Q ss_pred HHHHHHHHHHHcCCCCChh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc------------------CC
Q 002216 803 AREQIKRRLEEKGHITDDR-QLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIAS------------------EN 863 (952)
Q Consensus 803 ar~QI~~~L~~~~~~~d~~-~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~------------------~~ 863 (952)
++.||.++|... ..+.+ +....+.|+++.+|.++++.|.+|+.|++||.+|++.|.. +-
T Consensus 863 at~qitk~l~~i--~g~~k~~~~d~~kyltk~vF~a~r~lF~~Ah~iqdwl~~c~~~i~~s~~~d~d~~~~k~gik~de~ 940 (1117)
T COG5108 863 ATRQITKRLTLI--YGASKFDTVDPWKYLTKEVFPAERTLFAAAHFIQDWLWDCVGEIVVSAAGDMDWLQKKAGIKADES 940 (1117)
T ss_pred hHHHHHHhcccc--cCchhccccCHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHHhHHHHhcccchhHHHHHhccCcccc
Confidence 999999998642 22221 2334578999999999999999999999999999998864 24
Q ss_pred CcEEEEcCCCCeEEeeeccCcceeEEeeeEEEEEecC--CCCCChhhhhcCCCCcchhhhhHHHHHHHHHHHhHcCCcEE
Q 002216 864 QPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE--GNLVKIRKQRTAFPPNFVHSLDGSHMMMTAVACRDAGLHFA 941 (952)
Q Consensus 864 ~pV~WtTPlGlpVvQpY~k~~~~~I~t~lq~v~l~~~--~d~vd~rKQ~~Af~PNFIHSLDAsHmmlTa~~c~~~Gi~Fa 941 (952)
.||+||||+||||+||||..+.++|.|.+|+|.|..+ +.+||+|||.+||||||||||||+||.|||.+|.++||.||
T Consensus 941 ~pViWtTplgLpivQpYr~~~~kq~etnlQtVfi~~~~a~~~v~~rkQ~sg~pPNfiHSlDA~HM~lt~~~C~~qgi~Fa 1020 (1117)
T COG5108 941 LPVIWTTPLGLPIVQPYRTSEQKQLETNLQTVFIQLDVASKKVDKRKQGSGIPPNFIHSLDAAHMQLTVSRCHDQGIRFA 1020 (1117)
T ss_pred cceeeccCCCCcccccchhhHHHHHHhhhheEEEeccccccccChhhccCCCCcchhhhccHHHHHHhHHHhhhcCCcee
Confidence 7999999999999999999999999999999988864 57999999999999999999999999999999999999999
Q ss_pred Eeeccc
Q 002216 942 GLSFQS 947 (952)
Q Consensus 942 aVHDn~ 947 (952)
+|||-.
T Consensus 1021 ~vHDSY 1026 (1117)
T COG5108 1021 LVHDSY 1026 (1117)
T ss_pred eeecch
Confidence 999964
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=1.3e-102 Score=883.49 Aligned_cols=325 Identities=52% Similarity=0.887 Sum_probs=284.2
Q ss_pred CccCCcchhHHHHHHHhhhhCCCCCCCCHHHHHHHHHHhHHHHHHhccCCCCCchhhhhCCChHHHHHHHHHHHHHHhcC
Q 002216 620 GRPLGKSGLRWLKIHLANLFSGGVEKLSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALKSS 699 (952)
Q Consensus 620 gkpLG~~Gl~WLKIhlAN~yG~G~DK~S~deRi~wv~~n~~~I~dsA~dPL~g~~wW~~AD~PwQfLA~C~El~~al~s~ 699 (952)
|||||++|++|||||+||+| |+||+||+||++||++|+++|+++|+||+++.+||.+||+||||||+|+||++++++|
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 CCCcceeccccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhh
Q 002216 700 SPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILI 779 (952)
Q Consensus 700 ~P~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~ 779 (952)
+|++|+||+|||||||||||||||||+||.+||++|||+|+++|+|||+.|++.|.+.+.+++... +....+++++.
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 999999999999999999999999999999999999999999999999999999999999883100 11268899999
Q ss_pred ccCcccccccceeeeecccchhhHHHHHHHHHHHcCCCC-ChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002216 780 DQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHIT-DDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKV 858 (952)
Q Consensus 780 ~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~-d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~ 858 (952)
.+|+||+|||+|||+|||||.+|+++||+++|++.+... +....+.++.|||+.|+++|+++|++|+.+|+||++||++
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 3457889999999999999999999999999999999999
Q ss_pred HHcCCCcEEEEcCCCCeEEeeeccCcceeEEeeeEEEEEecC--CCCCChhhhhcCCCCcchhhhhHHHHHHHHHHHhHc
Q 002216 859 IASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE--GNLVKIRKQRTAFPPNFVHSLDGSHMMMTAVACRDA 936 (952)
Q Consensus 859 i~~~~~pV~WtTPlGlpVvQpY~k~~~~~I~t~lq~v~l~~~--~d~vd~rKQ~~Af~PNFIHSLDAsHmmlTa~~c~~~ 936 (952)
+++++.||.|+||+||||+|+|++.+.++|+|.++....... .+.+|++||++||||||||||||||||||+.+|.+.
T Consensus 236 ~~~~~~pv~W~tP~Gl~V~Q~Y~~~~~~~i~~~~~~~~~~~~~~~~~~d~~Kq~~a~~PNFIHSlDAshl~~t~~~~~~~ 315 (405)
T PF00940_consen 236 IAKLNKPVSWTTPLGLPVVQPYRKSKKKRIKTYLQGVSRRRVIREDPVDKRKQKNAFAPNFIHSLDASHLMLTANACNKE 315 (405)
T ss_dssp HHCTCB-EEEEETTSEEEEE--EEESEEEEESSSTTTEEE--EEEEES-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHccCCcEEEECCCCCEEEecccccCceeeEeecceeEEeccCCCCCCCHHHHhcccCCchHhhHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999998764332221 234599999999999999999999999999999999
Q ss_pred CCcEEEeeccccc
Q 002216 937 GLHFAGLSFQSAL 949 (952)
Q Consensus 937 Gi~FaaVHDn~~~ 949 (952)
|++|++|||||..
T Consensus 316 ~~~f~~VHDsf~t 328 (405)
T PF00940_consen 316 GIPFATVHDSFWT 328 (405)
T ss_dssp T--EEECTTEEEE
T ss_pred CCeEEEEehhhhc
Confidence 9999999999963
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=5e-48 Score=423.63 Aligned_cols=305 Identities=33% Similarity=0.568 Sum_probs=219.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHHh----hccCccchhhhhccCC
Q 002216 180 RRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQR----TKKQKAAYAPHIELLP 255 (952)
Q Consensus 180 ~RQ~~LE~~~~~~a~~r~r~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~~----~~~~r~~y~p~L~~l~ 255 (952)
|||++||+++++.|++||++..+++.++|.+++++++++++++|+++|+++|+++++.+. ..++++.|+|||+.||
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 3577999999999999
Q ss_pred hhHHHHHHHHHHHHHHhcC-CCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHHH
Q 002216 256 ADKVAVIVMHKMMGLVMAG-HEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVN 334 (952)
Q Consensus 256 ~e~lA~Iti~~~l~~~~~~-~~~~~~~~~~~a~~IG~aVe~E~~~~~~~~k~~k~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 (952)
||++|+|||+++|++++++ +..+|++++.++.+||++||+|++++++.+...+.+.+............. .++.+.
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 9999999999999999943 456678999999999999999999998876644322211100000000000 001111
Q ss_pred hHHHHHHHHHHHHhhcCCCCCC--CCHHHHHHHHHHHHHHHHHhccccCCCCCCCCCCCCccCceEEEEEeeecCCCCcc
Q 002216 335 SLIKSKRVMEAQKLLKNEETKP--WGRDTQAKLGSRLVELLIETAYVQHPVNPADYSPPDVRPAFRHRFKTILKHPGQKT 412 (952)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~--W~~~~~~kvG~~Ll~~L~e~~~i~~~~~~~~~~~~~~~paF~h~~~~~~~~~g~~~ 412 (952)
..++........... +..+.. |+..++++||++|+++|+++++|++...++.+ ...+|||+|+|++. +|
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 99999999999999999999999987754322 56799999999875 33
Q ss_pred ceeEEEEecCHHHHHHHHhhhhc-----ccCCCCceeeCCCCCcCCCCcccccCCccceecCCcHHHHHHHH-hccccCh
Q 002216 413 TKRYGVVECDPLVLEGLDRSAKH-----MLIPYVPMLVPPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEALK-SVTGNCM 486 (952)
Q Consensus 413 ~k~~gvi~~~~~~~~~l~~~~~~-----~~~~~LPMlvpPkpW~~~~~GGYL~~~s~~~R~~~~~~q~~~l~-~~~~~~l 486 (952)
+++|+|++||.+.+.++..... .++.+|||||||+||+++++||||..++.+||++++ .|..+++ +...++|
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 5789999999999999877542 125599999999999999999999999999999887 5555554 4467899
Q ss_pred HHHHHHHHhhcC
Q 002216 487 KKVFEALDTLGS 498 (952)
Q Consensus 487 ~~v~~aLN~Lqs 498 (952)
+.||+|||+||+
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
>smart00482 POLAc DNA polymerase A domain.
Probab=89.35 E-value=0.47 Score=50.33 Aligned_cols=192 Identities=19% Similarity=0.190 Sum_probs=116.3
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 002216 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (952)
Q Consensus 691 El~~al~s~~P~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 770 (952)
++++++.. |++| +-|..|-|.==|=.+|.|.+|......-| ...|+|+.+|..+...-.+
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 34555542 2444 47889999999999999999988777765 3569999998765321110
Q ss_pred hHHHHHHhhccCcccccccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002216 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 850 (952)
Q Consensus 771 ~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~ 850 (952)
. .....|+..|+.+--..||.+..|..+++ | ++.+ -|+.+.+++.+.||+ +..
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 11246999999999999999977776553 3 2221 245566666777777 677
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEeeeccCcceeEEeeeEEEEEecCCCCCChhhhhcCCCCcchhhhhHHHHHHHH
Q 002216 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVKIRKQRTAFPPNFVHSLDGSHMMMTA 930 (952)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQpY~k~~~~~I~t~lq~v~l~~~~d~vd~rKQ~~Af~PNFIHSLDAsHmmlTa 930 (952)
|.+++.....+.+. .+|+.|-...-|-.. +.....+.+..-.+.|++=+=-|+=++..|
T Consensus 116 ~~~~~~~~a~~~g~---v~t~~Gr~r~~~~~~------------------~~~~~~~~~~~r~a~N~~iQgsaAdi~k~a 174 (206)
T smart00482 116 YIKRTLEEARRKGY---VTTLFGRRRYIPDID------------------SRNPVLRAAAERAAVNAPIQGSAADILKLA 174 (206)
T ss_pred HHHHHHHHHHhCCE---EEecCCCeeeCCCCC------------------CCCHHHHhHHHHHHHhHhhhhHHHHHHHHH
Confidence 88877666555542 256666432211100 111222222223367876665566444433
Q ss_pred -HHHhH----cCC---cEEEeecccccc
Q 002216 931 -VACRD----AGL---HFAGLSFQSALE 950 (952)
Q Consensus 931 -~~c~~----~Gi---~FaaVHDn~~~~ 950 (952)
+.+.+ .|+ -.+.|||..-+|
T Consensus 175 m~~~~~~~~~~~~~~~~vl~vHDElv~e 202 (206)
T smart00482 175 MIKMDEALKEKGLRARLLLQVHDELVFE 202 (206)
T ss_pred HHHHHHHHHhcCCCceEEEeeceeEEee
Confidence 23333 343 267799998776
No 7
>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]
Probab=87.50 E-value=0.38 Score=58.26 Aligned_cols=76 Identities=28% Similarity=0.403 Sum_probs=59.1
Q ss_pred hhccCcccccccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002216 778 LIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAK 857 (952)
Q Consensus 778 l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~ 857 (952)
..-+++|++.|| ||.+||...+-..+.- ++|- +.+++-..++|.+|.++...+|++.+++...+..-|+|++..++
T Consensus 859 tyvGat~qitk~--l~~i~g~~k~~~~d~~-kylt-k~vF~a~r~lF~~Ah~iqdwl~~c~~~i~~s~~~d~d~~~~k~g 934 (1117)
T COG5108 859 TYVGATRQITKR--LTLIYGASKFDTVDPW-KYLT-KEVFPAERTLFAAAHFIQDWLWDCVGEIVVSAAGDMDWLQKKAG 934 (1117)
T ss_pred EEeehHHHHHHh--cccccCchhccccCHH-HHHH-HhHhHHHHHHHHHHHHHHHHHHHHHhHHHHhcccchhHHHHHhc
Confidence 345899999999 9999999775333322 2221 22455555789999999999999999999999999999997765
No 8
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=63.59 E-value=12 Score=45.61 Aligned_cols=176 Identities=19% Similarity=0.127 Sum_probs=109.9
Q ss_pred cccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhccCccccc
Q 002216 708 LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 787 (952)
Q Consensus 708 lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~I~RKvV 787 (952)
.-|..|-|.==|=.+|.|.+|....++.| .-.|+|+.+|..+-.. + .+ . .-.|+..
T Consensus 326 ~lv~aDysqiElRvlA~ls~D~~l~~~~~-----~g~Dih~~~A~~~~~~---~----~~-----~-------~~~R~~a 381 (553)
T PRK14975 326 KLVVADASQIELRVLAAYSGDERMIEAFR-----TGGDLHRLTASVGFGK---P----EE-----E-------KEERALA 381 (553)
T ss_pred EEEEechhhhHHHHHHHHcCCHHHHHHHh-----cCCCHHHHHHHHHhCC---C----cc-----c-------hhHHHHH
Confidence 47889999999999999999999888776 3579999998877211 1 10 0 3459999
Q ss_pred ccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcEE
Q 002216 788 KQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIASENQPVR 867 (952)
Q Consensus 788 KqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~~~~pV~ 867 (952)
|..+--.+||.+..|..+++. .. + -|+.+.+...+.||+ +..|++++.+...+.| .|
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 999999999999998887763 11 1 134555666667776 6777777777655442 12
Q ss_pred EEcCCCCeEEeeeccCcceeEEeeeEEEEEecC-CCCCChhhhhcCCCCcchhhhhHHHHHHHH-HHHhH-----cCC-c
Q 002216 868 WTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE-GNLVKIRKQRTAFPPNFVHSLDGSHMMMTA-VACRD-----AGL-H 939 (952)
Q Consensus 868 WtTPlGlpVvQpY~k~~~~~I~t~lq~v~l~~~-~d~vd~rKQ~~Af~PNFIHSLDAsHmmlTa-~~c~~-----~Gi-~ 939 (952)
+|.+|=... +... +.....+.+..-++.|++=+==|+=++..| +.+.+ .+. -
T Consensus 439 -~T~~GR~~~-------------------~~~~~~~~~~~~~~~~r~a~N~~iQGsaAdi~k~am~~~~~~l~~~~~~~l 498 (553)
T PRK14975 439 -RTLLGRTSP-------------------PPGFAWRARRRARSRGRFTRNFPVQGTAADWAKLALALLRRRLAEGLDAEL 498 (553)
T ss_pred -ECCCCCeec-------------------CCCccccChhHHhHhhhhhcCccchhHHHHHHHHHHHHHHHHHhhcCCcEE
Confidence 244443211 1110 111122222223467996555555544443 23322 223 4
Q ss_pred EEEeecccccc
Q 002216 940 FAGLSFQSALE 950 (952)
Q Consensus 940 FaaVHDn~~~~ 950 (952)
...|||..-+|
T Consensus 499 vl~vHDEl~~e 509 (553)
T PRK14975 499 VFFVHDEVVVE 509 (553)
T ss_pred EEEecceeEEE
Confidence 67799998776
No 9
>cd08642 DNA_pol_A_pol_I_A 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 ,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. P
Probab=54.92 E-value=46 Score=39.06 Aligned_cols=88 Identities=14% Similarity=0.017 Sum_probs=63.1
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 002216 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (952)
Q Consensus 691 El~~al~s~~P~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 770 (952)
+++.++-. |.++ .-|.-|-|.==|-.+|.|.+|...-++-| ...|||...|..+-..=.++.
T Consensus 159 ~iR~aFva--~~G~---~lvsaDySQIElRVLAhlS~D~~li~af~-----~g~Dih~~tAs~if~vp~e~~-------- 220 (378)
T cd08642 159 LIRTAFIP--SEGH---RFIVSDFSAIEARVIAWLAGEQWRLDVFA-----THGKIYEASASQMFGVPVEKI-------- 220 (378)
T ss_pred HhHHheec--CCCC---EEEEecHHHHHHHHHHHHhCCHHHHHHHh-----cCCChHHHHHHHHhCCChhhc--------
Confidence 44565543 2344 35889999999999999999999877765 568999999887742210000
Q ss_pred hHHHHHHhhccCcccccccceeeeecccchhhH
Q 002216 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGA 803 (952)
Q Consensus 771 ~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~Ga 803 (952)
-...--|...|...--.+||.+.+|.
T Consensus 221 -------~v~~~~R~~AK~vnfGiiYG~g~~~L 246 (378)
T cd08642 221 -------GKNSHLRQKGKVAELALGYGGSVGAL 246 (378)
T ss_pred -------ccCHHHHHHhhhhhccceeccchHHH
Confidence 01123588999999999999998886
No 10
>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=52.03 E-value=18 Score=42.07 Aligned_cols=192 Identities=15% Similarity=0.185 Sum_probs=112.4
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 002216 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (952)
Q Consensus 691 El~~al~s~~P~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 770 (952)
+++.++..+ .+| .-|..|-|-==|=.+|.|.+|.......| ...|+|+.+|..+... +.+
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 344 47889999888889999999999887776 3579999988765321 000
Q ss_pred hHHHHHHhhccCcccccccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002216 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 850 (952)
Q Consensus 771 ~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~ 850 (952)
.. ..-.|+..|..+--..||.+..|..+++ |+ +.+ -|+.+.+...+.||+ +..
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---------EAKEYIDRYFARYPG---VKE 252 (377)
T ss_pred --hC-----CHHHHhhhhHhhcchhcCcchhHHHHHc-------CC-CHH---------HHHHHHHHHHHHCcc---HHH
Confidence 00 1124999999999999999888766544 32 222 235566666677777 556
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEeeeccCcceeEEeeeEEEEEecCCCCCChhhhhcCCCCcchhhhhHHHHHHHH
Q 002216 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVKIRKQRTAFPPNFVHSLDGSHMMMTA 930 (952)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQpY~k~~~~~I~t~lq~v~l~~~~d~vd~rKQ~~Af~PNFIHSLDAsHmmlTa 930 (952)
|.+++...+...+- .+|+.|-...-|--. +.....+-+..-.+.|++=+=-|+=+|..|
T Consensus 253 ~~~~~~~~a~~~g~---v~t~~GRrr~~~~~~------------------~~~~~~r~~~~r~a~N~~iQGsaAdi~k~a 311 (377)
T cd08637 253 YMEETVEEAREKGY---VETLFGRRRYIPEIN------------------SKNRNVRAFAERIAINTPIQGTAADIIKLA 311 (377)
T ss_pred HHHHHHHHHHHcCc---EEccCCCEEeCCccc------------------CCcHHHhhHHHHhHhcccchhHHHHHHHHH
Confidence 66666655544331 245555422111000 111111111112357777665555444333
Q ss_pred H-H----HhHcCC---cEEEeecccccc
Q 002216 931 V-A----CRDAGL---HFAGLSFQSALE 950 (952)
Q Consensus 931 ~-~----c~~~Gi---~FaaVHDn~~~~ 950 (952)
. . +.+.|+ -...|||..-+|
T Consensus 312 m~~~~~~l~~~~~~~~lvl~vHDEl~~e 339 (377)
T cd08637 312 MIRVHKALKEEGLKARMLLQVHDELVFE 339 (377)
T ss_pred HHHHHHHHHhcCCCeEEEeeEeeeeeEe
Confidence 2 2 233443 467799998766
No 11
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=47.99 E-value=56 Score=42.39 Aligned_cols=179 Identities=17% Similarity=0.169 Sum_probs=108.7
Q ss_pred cccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhccCccccc
Q 002216 708 LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 787 (952)
Q Consensus 708 lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~I~RKvV 787 (952)
.-|..|-|-==|-.+|.|.+|....++.| .-.|||+..|..+-..-.+ . ...-.|...
T Consensus 659 ~lv~aDySQIELRilAhls~D~~Li~af~-----~g~DiH~~tA~~~fg~~~e------------~-----vt~~~R~~A 716 (887)
T TIGR00593 659 LLISADYSQIELRVLAHLSQDENLIEAFQ-----NGEDIHTETASRLFGVEIE------------D-----VTPNMRRIA 716 (887)
T ss_pred eEEEechhHhHHHHHHHHcCCHHHHHHHh-----cCCChHHHHHHHHhCCChh------------h-----CCHHHHhhh
Confidence 36778888888889999999998777664 3469999988876321100 0 012249999
Q ss_pred ccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcEE
Q 002216 788 KQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIASENQPVR 867 (952)
Q Consensus 788 KqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~~~~pV~ 867 (952)
|...--.+||.+.+|..+++ |+ +.+ -|+.+.+..-+.||+ +..|+.++.....+.|- |
T Consensus 717 K~infGiiYG~g~~~La~~l-------~i-s~~---------eA~~~i~~yf~~yp~---v~~~~~~~~~~a~~~Gy-v- 774 (887)
T TIGR00593 717 KTINFGVVYGMSAFGLAQEL-------GI-SRK---------EAKEFIERYFARYPG---VKDYIENTVEEARKKGY-V- 774 (887)
T ss_pred hHhhcCcccccchhHHHHHc-------CC-CHH---------HHHHHHHHHHHHCcc---HHHHHHHHHHHHHHcCc-E-
Confidence 99999999999999887654 32 221 234455555566775 67788877776655542 2
Q ss_pred EEcCCCCeEEeeeccCcceeEEeeeEEEEEecC-CCCCChhhhhcCCCCcchhhhhHHHHHHHH-----HHHhHcCC---
Q 002216 868 WTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE-GNLVKIRKQRTAFPPNFVHSLDGSHMMMTA-----VACRDAGL--- 938 (952)
Q Consensus 868 WtTPlGlpVvQpY~k~~~~~I~t~lq~v~l~~~-~d~vd~rKQ~~Af~PNFIHSLDAsHmmlTa-----~~c~~~Gi--- 938 (952)
+|..|-. ..+..- +.....|.+.--.+-|.+=+==|+=+|..| .++.+.|+
T Consensus 775 -~Tl~GRr-------------------r~lp~i~s~n~~~r~~aeR~A~N~~iQGsAADi~K~Ami~v~~~l~~~~~~~~ 834 (887)
T TIGR00593 775 -ETLFGRR-------------------RYIPDINSRNRNVREAAERMAINAPIQGSAADIMKIAMIKLDKRLKERKLKAR 834 (887)
T ss_pred -EecCCCE-------------------eeCCCccccchhhHhHHHhhhhhhhhhhHHHHHHHHHHHHHHHHHHhcCCCeE
Confidence 4555521 011110 111112222223567887766666555443 23445674
Q ss_pred cEEEeecccccc
Q 002216 939 HFAGLSFQSALE 950 (952)
Q Consensus 939 ~FaaVHDn~~~~ 950 (952)
-...|||...+|
T Consensus 835 lvlqVHDElv~E 846 (887)
T TIGR00593 835 LLLQVHDELIFE 846 (887)
T ss_pred EEeeEceEeeee
Confidence 366799998776
No 12
>PF14554 VEGF_C: VEGF heparin-binding domain; PDB: 2VGH_A 4DEQ_A 1VGH_A 1KMX_A.
Probab=37.83 E-value=16 Score=31.03 Aligned_cols=19 Identities=58% Similarity=0.917 Sum_probs=11.8
Q ss_pred ccccccCCcccceeecCCC
Q 002216 130 NHQLMCLEPRRRIFVQDPP 148 (952)
Q Consensus 130 ~~~~~~~~~~~~~~~~~~~ 148 (952)
+|=..+.|.++++|||||-
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 13
>cd08640 DNA_pol_A_plastid_like DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during 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
Probab=37.35 E-value=36 Score=39.77 Aligned_cols=206 Identities=20% Similarity=0.109 Sum_probs=115.4
Q ss_pred HHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCC-------
Q 002216 692 LSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNK------- 764 (952)
Q Consensus 692 l~~al~s~~P~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~------- 764 (952)
+++++-. |+++ .-|..|-|-==|-.+|.|.+|....++.| .-.|||+..|..+-....++..+
T Consensus 109 iR~~Fva--~~G~---~lv~aDySQiElRvlA~lS~D~~Li~af~-----~g~DiH~~tA~~if~~~~e~v~~~~~~~~~ 178 (371)
T cd08640 109 IRKAFIA--SPGN---TLIVADYSQLELRLLAHMTRCKSMIEAFN-----AGGDFHSRTASGMYPHVAEAVANGEVLLEW 178 (371)
T ss_pred hhheEec--CCCC---EEEEechhhhhHHHHHHHcCCHHHHHHHH-----cCCCHHHHHHHHHhCCCHHHhccccccccc
Confidence 4555542 2344 35889999999999999999999887776 34699999887654322111110
Q ss_pred -CCCCChhHHHHHHhhccCcccccccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHH
Q 002216 765 -DPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFE 843 (952)
Q Consensus 765 -~~~~~~~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~ 843 (952)
+...++...... ...-.|+..|...--.+||.+..|...++ |+ +.+ -|+.+.+...+.||
T Consensus 179 ~~~~~~~~~~~~~--~~~~~R~~AK~infGi~YG~g~~~La~~l-------gi-s~~---------eA~~~i~~f~~~fP 239 (371)
T cd08640 179 KSEGKPPAPLLKD--KFKSERRKAKVLNFSIAYGKTAHGLAKDW-------KV-KLK---------EAERTVDAWYSDRP 239 (371)
T ss_pred ccccccccccccc--ccHHHHHHHHHHHHHHHhccchhHHHHHc-------CC-CHH---------HHHHHHHHHHHHCc
Confidence 000000000000 01345999999999999999999887544 32 221 13556666677777
Q ss_pred HHHHHHHHHHHHHHHHHcCCCcEEEEcCCCCeEEeeeccCcceeEEeeeEEEEEecCCCCCChhhhhcCCCCcchhhhhH
Q 002216 844 AARSIMGWLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVKIRKQRTAFPPNFVHSLDG 923 (952)
Q Consensus 844 ~A~~im~WL~~~A~~i~~~~~pV~WtTPlGlpVvQpY~k~~~~~I~t~lq~v~l~~~~d~vd~rKQ~~Af~PNFIHSLDA 923 (952)
+ +..|.+++.....+.| .| +|++|-...=|--.. .+ -..+.+.--.+-|++=+==|
T Consensus 240 ~---v~~~~~~~~~~a~~~G-yv--~T~~GRrr~lp~i~s-----------------~~-~~~~~~~eR~avN~~IQGsA 295 (371)
T cd08640 240 E---VEQWQKKTKKEARERG-YT--RTLLGRYRYLPDIKS-----------------RN-RKKRGHAERAAINTPIQGSA 295 (371)
T ss_pred c---HHHHHHHHHHHHHHcC-cE--EccCCCEEECCCccc-----------------cc-HhhhhhhHHHHHhhhhhHHH
Confidence 7 5677777766554443 22 256554321110000 00 00011111125577766666
Q ss_pred HHHHHHHH-HHh------HcCC-cEEEeecccccc
Q 002216 924 SHMMMTAV-ACR------DAGL-HFAGLSFQSALE 950 (952)
Q Consensus 924 sHmmlTa~-~c~------~~Gi-~FaaVHDn~~~~ 950 (952)
+=+|..|. .+. +.|. -...|||...+|
T Consensus 296 ADI~K~Ami~i~~~l~~~~~~~~lvlqVHDElv~e 330 (371)
T cd08640 296 ADIAMKAMLRIYRNLRLKRLGWKLLLQIHDEVILE 330 (371)
T ss_pred HHHHHHHHHHHHHHHhhccCCceEEEEEcceeEEE
Confidence 66655442 222 2344 357799998776
No 14
>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=35.30 E-value=34 Score=39.84 Aligned_cols=192 Identities=18% Similarity=0.157 Sum_probs=114.4
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 002216 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (952)
Q Consensus 691 El~~al~s~~P~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 770 (952)
++++++..+ .+| +-|..|-|-==|=.+|.|.+|.....+.| .-.|||+.+|..+-..- .
T Consensus 129 ~iR~~f~a~--~G~---~lv~~DysqiElRvlA~ls~D~~l~~~~~-----~g~Dih~~~A~~~~g~~---~-------- 187 (373)
T cd08638 129 SLRHAFIPP--PGR---VLLSADYSQLELRILAHLSGDPALIELLN-----SGGDVFKMIAAQWLGKP---V-------- 187 (373)
T ss_pred hhhheeeCC--CCC---EEEEechhhhHHHHHHHHhCCHHHHHHHh-----cCCCHHHHHHHHHhCCC---h--------
Confidence 456665432 344 47899999999999999999998887765 25799999887653210 0
Q ss_pred hHHHHHHhhccCcccccccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002216 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 850 (952)
Q Consensus 771 ~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~ 850 (952)
.. ...-.|+..|..+--..||.+..|...++ |+ +.+ -|+.+.+...+.||+ +..
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---------EAKQFIESFKNAYPG---VRR 241 (373)
T ss_pred -hh-----CCHHHHHHHhHHHHhhHhCCcHHHHHHHh-------CC-CHH---------HHHHHHHHHHHHCcc---HHH
Confidence 00 11246999999999999999999887654 32 221 245566666777877 456
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEeeeccCcceeEEeeeEEEEEecCCCCCChhhhhcCCCCcchhhhhHHHHHHHH
Q 002216 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVKIRKQRTAFPPNFVHSLDGSHMMMTA 930 (952)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQpY~k~~~~~I~t~lq~v~l~~~~d~vd~rKQ~~Af~PNFIHSLDAsHmmlTa 930 (952)
|.+++.....+.| .| +|+.|-...-|--.. .....+-..--.+.|++=+==|+=+|..|
T Consensus 242 ~~~~~~~~a~~~g-~v--~T~~GRrr~~p~~~~------------------~~~~~~~~~~r~a~N~~iQGsaAdi~K~a 300 (373)
T cd08638 242 FIRETIERARRNG-FV--ETLTGRRRYLPEINS------------------GNSSERAQAERQAVNTVIQGSAADIMKIA 300 (373)
T ss_pred HHHHHHHHHHHcC-cE--EccCCCEEeCCCCCC------------------CCHHHHHHHHHHHhchhhhhHHHHHHHHH
Confidence 6666555544332 22 255554332221111 00111111223566877666666555443
Q ss_pred H-HHhH-----------cCC-cEEEeecccccc
Q 002216 931 V-ACRD-----------AGL-HFAGLSFQSALE 950 (952)
Q Consensus 931 ~-~c~~-----------~Gi-~FaaVHDn~~~~ 950 (952)
. .+.+ .+. -...|||..-+|
T Consensus 301 mi~i~~~l~~~~~~~~~~~~~lvl~VHDEl~~e 333 (373)
T cd08638 301 MINIHEKLHSLLPNLPAGRARLVLQIHDELLFE 333 (373)
T ss_pred HHHHHHHHHhhcccccCCCeEEEEEEccEEEEE
Confidence 2 2222 122 467799998766
No 15
>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=32.86 E-value=27 Score=40.67 Aligned_cols=111 Identities=22% Similarity=0.272 Sum_probs=77.2
Q ss_pred ccccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhccCcccc
Q 002216 707 HLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKL 786 (952)
Q Consensus 707 ~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~I~RKv 786 (952)
++-|..|.|-==|=.+|.|.+|.....+.+ ...|+|..+|..+...-.++ .....|+.
T Consensus 155 ~~lv~aD~sqiElRvlA~ls~D~~l~~~~~-----~g~D~h~~~a~~~~~~~~~~-----------------v~~~~R~~ 212 (383)
T PF00476_consen 155 YVLVSADYSQIELRVLAHLSGDENLIEAFR-----NGEDIHTETASDIFGKPYEE-----------------VTKEERQK 212 (383)
T ss_dssp EEEEEEEESSHHHHHHHHHHTHHHHHHHHH-----TTCCHHHHHHHHHTTCHGGG-----------------TTHHHHHH
T ss_pred ceeeeeehhhhhHHHHHHhcccHHHHHhhc-----ccccHHHHHHHHhcCCCccc-----------------cchhhHHH
Confidence 347888998888889999999998766654 45799998877653221110 23467999
Q ss_pred cccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002216 787 VKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVI 859 (952)
Q Consensus 787 VKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i 859 (952)
.|..+--..||.+..|..+++. ++.+ -|+.+.++..+.||+ +..|..++....
T Consensus 213 aK~~~~g~~YG~g~~~la~~l~--------~s~~---------eA~~~~~~f~~~~p~---v~~~~~~~~~~a 265 (383)
T PF00476_consen 213 AKTVNFGLIYGMGAKGLAEQLG--------ISEE---------EAKELIDAFFEAFPG---VKKWMERVKKRA 265 (383)
T ss_dssp HHHHHHHHHTT-THHHHHHHHT--------SCHH---------HHHHHHHHHHHHSHH---HHHHHHHHHHHH
T ss_pred HhHHHHhhhhccCHHHHHHHcc--------CCHH---------HHHHHHHHHHHhCch---HHHHHHHHHHHH
Confidence 9999999999999988887763 3322 245566777777887 555655555443
No 16
>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=31.05 E-value=79 Score=29.83 Aligned_cols=56 Identities=21% Similarity=0.483 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HcccCCCChhHHHHHHHHHHHHH
Q 002216 173 RKFNLLRRRQVKQETEAWERMVDEYKELEAKMI---EKRLAPNLPHIKGLFLGWFGPLS 228 (952)
Q Consensus 173 ~~~~~l~~RQ~~LE~~~~~~a~~r~r~~~~~~~---~~g~a~~~~~~~~ll~~w~~~L~ 228 (952)
..|.+..+|...|..+.++....+|.+.++++. +.|+.++.+-++.++.+|+..+.
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 566666666666777777777777777766555 57888999999999999999665
No 17
>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=25.23 E-value=65 Score=38.42 Aligned_cols=144 Identities=13% Similarity=-0.009 Sum_probs=83.4
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 002216 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (952)
Q Consensus 691 El~~al~s~~P~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 770 (952)
+++.++-. |.++ +-|.-|.|.==|-.+|.|.+|..++..+.... -.|+++..|..+
T Consensus 176 ~iR~~Fva--~~G~---~lv~aDySQiELRiLAhls~d~~~~~l~~~~~---~~DiH~~ta~~~---------------- 231 (429)
T cd08643 176 ECRELFGV--PPGW---SLVGADASGLELRCLAHYLARYDGGAYTRKVL---GGDIHWANAQAM---------------- 231 (429)
T ss_pred hhhheEec--CCCC---EEEEecHHHHHHHHHHHHhcccchHHHHhhhc---ccchhHHHHHHh----------------
Confidence 45555542 2333 46888998888889999999876666555332 358887665431
Q ss_pred hHHHHHHhhccCcccccccceeeeecccchhhHHHHHHHHHHHcC-C---CC---ChhhHHHHHHHHHHHHHHHHHHHHH
Q 002216 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKG-H---IT---DDRQLFAAACYAAKVTLTALGEIFE 843 (952)
Q Consensus 771 ~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~-~---~~---d~~~~~~~a~Ylak~v~~ai~e~f~ 843 (952)
+...|+..|...--.+||.+..|.++++.-..++-. . ++ +......++..-++.+.+..-+.||
T Consensus 232 ---------g~~~R~~AK~i~fGiiYG~g~~~La~~lg~~~~eA~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~f~~~~P 302 (429)
T cd08643 232 ---------GLLSRDGAKTFIYAFLYGAGDEKLGQIVGDDLRTAKNLNAEWPQTKKGTIKKIADKAKGRVVRANFLKGLP 302 (429)
T ss_pred ---------ChHHHhhhHHHHHHHHHCCChhHHHHHhCCCHHHHHhhhhcccccccchhhhhhhhhhHHHHHHHHHHhCc
Confidence 114699999999999999999999887643222110 0 00 0001111223344555556566667
Q ss_pred HHHHHHHHHHHHHHHHHcCCCcEEEEcCCC
Q 002216 844 AARSIMGWLGDCAKVIASENQPVRWTTPLG 873 (952)
Q Consensus 844 ~A~~im~WL~~~A~~i~~~~~pV~WtTPlG 873 (952)
+. ..|++++-....+.+ . .+|..|
T Consensus 303 ~v---~~~~~~~~~~a~~~G-y--v~tl~G 326 (429)
T cd08643 303 AL---GKLIKKVKEAAKKRG-H--LVGLDG 326 (429)
T ss_pred cH---HHHHHHHHHHHHhCC-c--eeCCCC
Confidence 64 455555555433332 1 245555
No 18
>PLN03188 kinesin-12 family protein; Provisional
Probab=20.18 E-value=2.4e+03 Score=29.31 Aligned_cols=45 Identities=22% Similarity=0.234 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccCccchhhhhccCChhHHHHHHH
Q 002216 220 FLGWFGPLSEAIEREQKMQRTKKQKAAYAPHIELLPADKVAVIVM 264 (952)
Q Consensus 220 l~~w~~~L~~~I~~e~~~~~~~~~r~~y~p~L~~l~~e~lA~Iti 264 (952)
|..-+..+.+.|+.-.++..+.|.+..-..|+..|-+|--|.=+=
T Consensus 1126 ll~~hr~i~egi~dvkkaaakag~kg~~~~f~~alaae~s~l~~e 1170 (1320)
T PLN03188 1126 LLARHRRIQEGIDDVKKAAARAGVRGAESKFINALAAEISALKVE 1170 (1320)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHHH
Confidence 344455566667765555555666666678888886665544333
Done!