Query 001795
Match_columns 1012
No_of_seqs 254 out of 446
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 09:30:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001795.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001795hhsearch_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 3E-245 6E-250 2095.0 76.3 857 140-1012 202-1088(1088)
2 PHA00452 T3/T7-like RNA polyme 100.0 8E-209 2E-213 1861.5 86.3 787 176-1012 3-807 (807)
3 COG5108 RPO41 Mitochondrial DN 100.0 9E-199 2E-203 1663.4 60.1 803 180-1012 251-1117(1117)
4 PF00940 RNA_pol: DNA-dependen 100.0 5E-123 1E-127 1057.4 19.5 385 620-1012 1-405 (405)
5 PF14700 RPOL_N: DNA-directed 100.0 1.4E-47 3E-52 423.1 24.1 305 180-498 1-318 (318)
6 smart00482 POLAc DNA polymeras 90.9 0.3 6.5E-06 52.2 4.8 192 691-950 3-202 (206)
7 COG5108 RPO41 Mitochondrial DN 88.1 0.34 7.3E-06 59.0 2.9 75 779-857 860-934 (1117)
8 cd08637 DNA_pol_A_pol_I_C Poly 84.8 4.4 9.6E-05 47.4 9.7 209 691-967 140-358 (377)
9 cd08638 DNA_pol_A_theta DNA po 83.5 4.1 9E-05 47.5 8.8 211 691-969 129-354 (373)
10 PRK14975 bifunctional 3'-5' ex 81.9 3 6.6E-05 51.0 7.2 192 708-966 326-527 (553)
11 cd08642 DNA_pol_A_pol_I_A Poly 75.0 15 0.00033 43.2 9.8 185 691-954 159-344 (378)
12 cd08640 DNA_pol_A_plastid_like 74.6 8.1 0.00018 45.3 7.4 211 709-967 121-349 (371)
13 TIGR00593 pola DNA polymerase 73.5 12 0.00025 48.7 9.1 196 708-967 659-865 (887)
14 cd08643 DNA_pol_A_pol_I_B Poly 72.4 11 0.00024 45.0 8.0 198 708-969 188-406 (429)
15 PRK05755 DNA polymerase I; Pro 68.3 15 0.00033 47.6 8.6 209 691-967 640-858 (880)
16 cd08639 DNA_pol_A_Aquificae_li 68.0 24 0.00053 40.6 9.2 188 708-965 104-300 (324)
17 PF00476 DNA_pol_A: DNA polyme 39.0 21 0.00045 41.9 2.5 196 707-967 155-362 (383)
18 PF07739 TipAS: TipAS antibiot 33.0 69 0.0015 30.5 4.7 56 173-228 13-71 (118)
19 PLN03188 kinesin-12 family pro 23.3 2.1E+03 0.046 29.9 18.2 44 220-263 1126-1169(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=2.6e-245 Score=2095.02 Aligned_cols=857 Identities=58% Similarity=0.973 Sum_probs=797.9
Q ss_pred cceeecCCCchhHHHhh-----hhhhhhh---HHHHhhhhHH-HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHccc
Q 001795 140 RRIFVQDPPWFSSIFLK-----GLYKRIK---LQEYREMKKR-KFNLLRRRQVKQETEAWERMVDEYK-ELEAKMIEKRL 209 (1012)
Q Consensus 140 ~~~~~~~~~~~~~~~~~-----~~~~~~~---~~~~~~~~~~-~~~~l~~RQ~~lE~~~~~~a~~r~~-~~~~~~~~~g~ 209 (1012)
..-......|.++.+.. .....++ +...++.+.. +|-.+.+||..+|.++|++|+++|+ +...+|++..+
T Consensus 202 ~~~~~~~~m~ke~~~~~~~~~~~~~~~~~~~lk~v~k~~~~~~d~~~l~~Rq~~~e~~~~e~a~e~~k~el~~~~c~~~l 281 (1088)
T KOG1038|consen 202 EINELVTKMEKEGNSLNQISSKFLEESRDLPLKAVRKGFGDFKDFFNLDRRQVKLETEAWERAAEEWKIELESDMCEGSL 281 (1088)
T ss_pred hHHHHHhHhhhhhhhhhHHHHHHHHHHhcccHHHHHHhccchHhHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhc
Confidence 44456677887777633 3333233 5677777766 8999999999999999999999999 77778999999
Q ss_pred CCCChh-HHHHHHHHHHHHHHHHHHHHHHHhhc--cCccchhhhhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHH
Q 001795 210 APNLPH-IKGLFLGWFGPLSEAIEREQKMQRTK--KQKAAYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAA 286 (1012)
Q Consensus 210 a~~~~~-~~~ll~~w~~~L~~~I~~e~~~~~~~--~~r~~y~p~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~~ 286 (1012)
++++|| +++++++||++|.++|++|++.++.. +.|..|+|||++||++++|+|||+++|+++++|++.+++++++++
T Consensus 282 ~~~lp~~lk~lf~~W~~~l~~ai~ee~n~~r~~~~~~r~~Y~p~L~lL~a~k~aviti~el~~ll~tg~~~~~~~v~~aa 361 (1088)
T KOG1038|consen 282 APNLPYNLKSLFLGWFKPLRDAIKEEINLLRALVRKGRLNYAPFLKLLDADKMAVITIHELMGLLMTGGETGGVRVVQAA 361 (1088)
T ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccchHHHhcChhhHHHHHHHHHHhhhccCCCccchhHHHHH
Confidence 999999 99999999999999999999998875 889999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC-CCCCCCCHHHHHHH
Q 001795 287 VHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVNSLIKSKRVMEAQKLLKN-EETKPWGRDTQAKL 365 (1012)
Q Consensus 287 ~~IG~aVe~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~W~~~~~~kv 365 (1012)
.+||++||+|+|++.++++..+++.-. ....-++....++.++.++++.++.+.+..... ....+|+..++++|
T Consensus 362 ~~~G~aveqe~ri~~~lq~~~k~~~~~-----~~~~~ke~~~~~~~v~~l~~~~k~~~~~~~~~~~~~~~pWp~~v~~kv 436 (1088)
T KOG1038|consen 362 KSLGRAVEQEFRIEQFLQRKTKNKAGD-----SYCELKELGKSRKEVRQLVQNLKLSQRLSGPESHLSEKPWPSAVQAKV 436 (1088)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcccch-----HHHHHHHhhcccHHHHHHHHHHHHHHHhcccccccccCCccHHHHHHH
Confidence 999999999999999988654432211 111124555667778888877776666655555 56789999999999
Q ss_pred HHHHHHHHHHHccccCCCCCCCCCCCCccCceeEeeeeeecCCCCCcceeEEEEecCHHHHHHHHhhhhcccCCCCceee
Q 001795 366 GSRLVELLIETAYVQHPVNPADYSPPDVRPAFRHRFKTILKHPGQKTTKRYGVVECDPLVLEGLDRSAKHMLIPYVPMLV 445 (1012)
Q Consensus 366 G~~Li~~L~e~~~i~~~~~~~~~~~~~~~paF~h~~~~~~~~~g~~~~k~~gvi~~~~~~~~~l~~~~~~~~~~~lPMlv 445 (1012)
|++|+++||++++|+++.+++.++.++.+|||.|+|++. +|+..+++||+|+|||.+..+|++.+.++.++++||||
T Consensus 437 Gs~L~~lL~~~aki~~~~~~~~~~~~~~~paf~h~f~~~---n~~~~~~~~g~ie~~pll~r~leks~~~~~~~~vPMLv 513 (1088)
T KOG1038|consen 437 GSRLIELLMQVAKIQVPADQPDTKLPDERPAFVHTFQVT---NGQKGGRKYGVIECHPLLSRGLEKSALHFVPPLVPMLV 513 (1088)
T ss_pred HHHHHHHHHHHhcCCCcccCcCcCccccchhhhhheeee---cccccceeeeeeecCHHHHHHhhhhhcccccccccccc
Confidence 999999999999999999998888889999999999965 44434789999999999999999988888999999999
Q ss_pred CCCCCcCCCCceecccCccceecCCcHHHHHHH-HhccccChHHHHHHHHhhcCceeEEcHHHHHHHHHHHHcCCCCCCC
Q 001795 446 PPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEAL-KSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGL 524 (1012)
Q Consensus 446 pP~pW~~~~~GGYl~~~~~~~R~~~s~~q~~~l-~~~~~~~l~~v~~aLN~Lqst~wrIN~~VL~vi~~~w~~g~~i~~l 524 (1012)
||+||+++++||||++++++||++++++|..|+ ++.+.++++.||+|||.||+||||||++||||+.++|++|+.+.++
T Consensus 514 pPkpWt~~~~Ggyl~~~s~lmRt~g~~~Q~~~llkas~~~~l~~v~daL~~LG~t~WrVN~rvldvV~riw~~Gg~~~~~ 593 (1088)
T KOG1038|consen 514 PPKPWTGYDSGGYLFLPSYLMRTHGAKEQVDYLLKASPPGQLDPVFDALDTLGNTKWRVNRRVLDVVIRIWQNGGCFLLI 593 (1088)
T ss_pred CCCCCCCCCCCceEecchhhhhcCCcHHHHHHHHhcCChhhhHHHHHHHHHhcCCCeeecchHHHHHHHHHhcCCCccCC
Confidence 999999999999999999999999999999865 4556889999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCC
Q 001795 525 VDRNDVLIPEKP-LSEDMTEVQKWKWSVRKAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHL 603 (1012)
Q Consensus 525 ~~~~~~plP~~p-~~~d~~~~~~wk~~~~~~~~~~~~~~S~R~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~L 603 (1012)
+++.+.++|++| ..+|+++++.|+++.+++.+.++++||+|||++|+|+||++|+|+ .||||||||||||+||+||||
T Consensus 594 v~r~~~~lP~~P~~s~dp~~~~~wk~e~k~~~k~~~e~HS~RCD~~ykLsvAr~~~de-~Fy~PHNmDFRGRaYP~~PHl 672 (1088)
T KOG1038|consen 594 VPREDVPLPPKPTLSEDPAELKAWKWEVKKAQKVNRERHSLRCDAEYKLSVARKMKDE-EFYYPHNMDFRGRAYPLPPHL 672 (1088)
T ss_pred CCCCCCCCCCCCCCCcChHHHHHhHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhccC-eeecCcccCcCCccCCCCchh
Confidence 999999999999 678999999999999999999999999999999999999999998 699999999999999999999
Q ss_pred CCCCccchhhhhccccCccCCcchhHHHHHHHhhhhCCCCCCCCHHHHHHHHHHHHHHHHHhccCCCCCchhhhcCCChH
Q 001795 604 NHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANLFSGGVEKLSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPF 683 (1012)
Q Consensus 604 n~qGsDl~RsLL~FaegkpLG~~Gl~WLkIhlAN~~G~G~DK~S~deRi~wv~~n~~~I~~sA~dPl~g~~wW~~Ad~Pw 683 (1012)
||.|||+|||||+||+|+|||++||+|||||+||+|| |+||+|+++|++|+++|+++|+|||++||+|++||++|||||
T Consensus 673 NHLgsDlcRglLeF~~GkPLG~sGL~WLKIHlaNL~~-g~~kl~~~~RlAF~E~hl~DI~DSAd~PLtG~rWW~~AedPf 751 (1088)
T KOG1038|consen 673 NHLGSDLCRGLLEFAEGKPLGPSGLRWLKIHLANLYA-GVDKLSLRDRLAFTEEHLDDIFDSADRPLTGRRWWLKAEDPF 751 (1088)
T ss_pred cccchHHHHHHHHHhcCCcCCccchhHHHHHHHHHhc-ccccccHHHHHHHHHHHHHHHhhcccCCCcccchhhcCCChH
Confidence 9999999999999999999999999999999999997 999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcC
Q 001795 684 QCLAACINLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSN 763 (1012)
Q Consensus 684 QfLA~C~El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~ 763 (1012)
||||+|||+++|++++||+.|+||+||||||||||||||||||||..||++|||+|+|+|||||++||..|.+++++||+
T Consensus 752 Q~LA~C~elaea~RspdPeayiSH~PIHQDGSCNGLQHYAALGrD~~GA~~VNLvpsdkPqDVYs~VA~~V~~~~k~DAe 831 (1088)
T KOG1038|consen 752 QCLAACMELAEALRSPDPEAYISHIPIHQDGSCNGLQHYAALGRDSEGAAAVNLVPSDKPQDVYSAVAARVEKIMKQDAE 831 (1088)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHhcCCcccCCCcchHHHHHHhcCccccchhccccCCCCchhHHHHHHHHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCChhHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHH
Q 001795 764 KDPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFE 843 (1012)
Q Consensus 764 ~~~~~~~~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~ylak~v~~ai~e~f~ 843 (1012)
+|+ .+|++|.+.||||||||||||+|||||++|||+||.++|++++.++|++++|.+|+|+++++|+||+|||.
T Consensus 832 ~g~------e~Ak~L~~~V~RKvVKQTVMT~VYGVTyvGAR~QI~krL~e~~~f~d~~~v~~as~Yltk~tf~aLrEmF~ 905 (1088)
T KOG1038|consen 832 KGP------EVAKILKDQVTRKVVKQTVMTSVYGVTYVGARLQIKKRLKEIDDFPDEKEVFDASCYLTKKTFEALREMFT 905 (1088)
T ss_pred cCh------HHHHHHHHHHhHHHhhhheeeeeeeeeEecHHHHHHHHhhhccCcchhHhhhhHHHHHHHHHHHHHHHHHH
Confidence 985 68999999999999999999999999999999999999999999999988999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEe-cC-CCccchhhhhccCCCccchhh
Q 001795 844 AARSIMGWLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQ-RE-GNLVEIRKQRTAFPPNFVHSL 921 (1012)
Q Consensus 844 ~A~~im~WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~-~~-~d~vd~rKQ~~af~PNFIHSL 921 (1012)
+|+.||+||++||++|++++.+|+||||+||||||||++.++++|+|.+|++++. .+ +++||.|||++||||||||||
T Consensus 906 ~araIq~WlgecAklIs~~~~~V~WtTPLGLPVVQPYr~~~~~qirt~lQt~~~~~~d~~~~vn~rkQktaFPPNFIHSL 985 (1088)
T KOG1038|consen 906 AARAIQDWLGECAKLISSENSPVEWTTPLGLPVVQPYRQEKKKQIRTGLQTLFLSPRDLTNKVNARKQKTAFPPNFIHSL 985 (1088)
T ss_pred HHHHHHHHHHHHHHHHhcCCCceEEecCCCCcccchhhhhhhhcccccceEEeecchhhccccchhhhhccCCCchhhcc
Confidence 9999999999999999999999999999999999999999999999999999998 34 789999999999999999999
Q ss_pred hhHHHHHHHHHHhhcCCcEEEeeccccCCCCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHh------------CCCCC
Q 001795 922 DGSHMMMTAVACRDAGLHFAGVHDSFWTHACDVDEMNQILRKKFVELYNMPMLENLLESFQTS------------YPTLS 989 (1012)
Q Consensus 922 DAsHmmlta~~~~~~Gi~FasVHDSFwThA~dvd~M~~ilRe~FV~Lys~~il~~l~e~f~~~------------~~~~~ 989 (1012)
|||||||||++|.++||+||+|||||||||||||+||++|||+||+|||+|||++|+|+|++| |+.+.
T Consensus 986 D~SHMmmTal~C~rqGl~FasVHDsyWTHAcDVd~MN~ilREqFV~Lhs~pIle~L~e~f~~ry~~~~~~~~~~s~l~l~ 1065 (1088)
T KOG1038|consen 986 DGSHMMMTALACERQGLTFASVHDSYWTHACDVDVMNRILREQFVELHSQPILERLLESFEKRYKFKDSDFKNDSQLPLI 1065 (1088)
T ss_pred cchHHHHHHHHHHhcCCceeeeecchhccccchHHHHHHHHHHHHHHcccHHHHHHHHHHHHHhccccchhhhhccCCcc
Confidence 999999999999999999999999999999999999999999999999999999999999994 56678
Q ss_pred CCCCCCCCCCChhhhccCCCCCC
Q 001795 990 FPPLPERGNFDLEEVLESPYFFN 1012 (1012)
Q Consensus 990 ~p~~P~~G~LDL~~Vl~S~YFF~ 1012 (1012)
||++|++|+|||+.||+|+||||
T Consensus 1066 fpplP~rGdfDLk~Vl~S~YFFs 1088 (1088)
T KOG1038|consen 1066 FPPLPKRGDFDLKKVLDSTYFFS 1088 (1088)
T ss_pred CCCCCCCCCccHHHHhccccccC
Confidence 99999999999999999999997
No 2
>PHA00452 T3/T7-like RNA polymerase
Probab=100.00 E-value=8.3e-209 Score=1861.52 Aligned_cols=787 Identities=33% Similarity=0.548 Sum_probs=704.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCccchhhhhccCC
Q 001795 176 NLLRRRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQRTKKQKAAYAPHIELLP 255 (1012)
Q Consensus 176 ~~l~~RQ~~lE~~~~~~a~~r~~~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~~~~~~r~~y~p~L~~l~ 255 (1012)
..|.+||++||++++++|++||++++++++++|+++++|++++++.+||++|+++|+++++.++++|.++.|+|||++++
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 36889999999999999999999999999999999999999999999999999999999999877888999999999999
Q ss_pred hhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHHHH
Q 001795 256 ADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVNS 335 (1012)
Q Consensus 256 ~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~~~~IG~aVe~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 335 (1012)
||+||+|||+++|++++++ ++.++++++++||++||+|++++.+++++++...+.. ....+++.+.
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 4569999999999999999999999877665432211 0112222333
Q ss_pred HHHHHH-HHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHc-cccCCCCCCCCCCCCccCceeEeeeeeecCCCCCcc
Q 001795 336 LIKSKR-VMEAQKLLKNEETKPWGRDTQAKLGSRLVELLIETA-YVQHPVNPADYSPPDVRPAFRHRFKTILKHPGQKTT 413 (1012)
Q Consensus 336 ~~~~~~-~~~~~~~~~~~~~~~W~~~~~~kvG~~Li~~L~e~~-~i~~~~~~~~~~~~~~~paF~h~~~~~~~~~g~~~~ 413 (1012)
..++.+ .+.++..+...++.+|+.+++++||++|+++|++++ .++++... ..++ +
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 222333333335889999999999999999999996 55542111 0111 3
Q ss_pred eeEEEEecCHHHHHHHHhhhhc---ccCCCCceeeCCCCCcCCCCceecccC---ccceecCCcHHHHHHHHhccccChH
Q 001795 414 KRYGVVECDPLVLEGLDRSAKH---MLIPYVPMLVPPKKWKGYNKGGYLFLP---SYVMRTHGSRKQQEALKSVTGNCMK 487 (1012)
Q Consensus 414 k~~gvi~~~~~~~~~l~~~~~~---~~~~~lPMlvpP~pW~~~~~GGYl~~~---~~~~R~~~s~~q~~~l~~~~~~~l~ 487 (1012)
+++|+|.+||++++.+++.... +.+.+|||||||+||+++.+||||+.+ +..||+++...+..+ .+++|+
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 5789999999999999886543 233499999999999999999999853 567888776555443 347999
Q ss_pred HHHHHHHhhcCceeEEcHHHHHHHHHHHHcCCCCCCCCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHHHhhhhh
Q 001795 488 KVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRNDVLIPEKPLS--EDMTEVQKWKWSVRKAKKINQERHSQR 565 (1012)
Q Consensus 488 ~v~~aLN~Lqst~wrIN~~VL~vi~~~w~~g~~i~~l~~~~~~plP~~p~~--~d~~~~~~wk~~~~~~~~~~~~~~S~R 565 (1012)
.||++||+||+|||+||++||+||+++|++| .++++++..+.|+|++|++ ++++++++|++++++++++++++||+|
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 8888888878888988864 456899999999999999999999999
Q ss_pred hhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCccchhhhhccccCccCCcchhHHHHHHHhhhhCCCCCC
Q 001795 566 CDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANLFSGGVEK 645 (1012)
Q Consensus 566 ~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL~FaegkpLG~~Gl~WLkIhlAN~~G~G~DK 645 (1012)
|+++++|++|++|+|++.||||||+|||||+|| +|||||||+|+|||||+||+|+|||++|++|||||+||+| |+||
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 CCHHHHHHHHHHHHHHHHHhccCCCCCchhhhcCCChHHHHHHHHHHHHHHhcCCCCcceeccccccCCCcchhhHHHHh
Q 001795 646 LSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAAL 725 (1012)
Q Consensus 646 ~S~deRi~wv~~n~~~I~~sA~dPl~g~~wW~~Ad~PwQfLA~C~El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHyAAL 725 (1012)
+||+||++||++|+++|++||+|||+|. ||++||+||||||+|+||++|+++|+ +|+||||||||||||||||||||
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 hCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccccccceeeecccchhhHHH
Q 001795 726 GRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGARE 805 (1012)
Q Consensus 726 ~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~ 805 (1012)
|||.+||++|||+|+|+|||||+.||+.|.+.+++|+.++.+ ......+++|..+|+||+|||||||+|||||++|+++
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 001795 806 QIKRRLEEKGHITDDRQL--FAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIA-SENQPVRWTTPLGLPVVQPYCK 882 (1012)
Q Consensus 806 QI~~~L~~~~~~~d~~~~--~~~a~ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~-~~~~pV~WtTPlGlpVvQ~Y~k 882 (1012)
||.++|+++|+..++... +.+++|+|++||+||+++|++|+.||+||++||++|+ +.+.||.||||+||||+|||++
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 999999998876554333 7899999999999999999999999999999999999 9999999999999999999999
Q ss_pred CcceeEEeeeE---EEEEecCCCccchhhhhccCCCccchhhhhHHHHHHHHHHhhcCC-cEEEeeccccCCCCChhHHH
Q 001795 883 NERHLIRTSLQ---VLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAVACRDAGL-HFAGVHDSFWTHACDVDEMN 958 (1012)
Q Consensus 883 ~~~~~I~t~lq---~~~l~~~~d~vd~rKQ~~af~PNFIHSLDAsHmmlta~~~~~~Gi-~FasVHDSFwThA~dvd~M~ 958 (1012)
.++++|+|.+| .+++..+++++|++||++|||||||||||||||||||++|.+.|+ +|++|||||||||||||.|+
T Consensus 674 ~~~~~v~t~~~~~~~i~~~~~~~~~d~~Kq~~a~~PNFIHSLDAsHm~~t~~~~~~~g~~~fa~VHDsfwTha~dvd~m~ 753 (807)
T PHA00452 674 PEEKRVRLRLMGVARVQLYVNTDTIDARKHASGIAPNFVHSLDASHLRLTVVACAEKGIESFAVIHDSFGTHAADADNLH 753 (807)
T ss_pred CCcEEEEEeeccceeEEeccCCCCCCHHHHhcccCCchhhhhhHHHHHHHHHHHHhcCCCcEEEeccCcccChhhHHHHH
Confidence 99999999987 577777888999999999999999999999999999999999986 89999999999999999999
Q ss_pred HHHHHHHHHhcCc-chHHHHHHHHHHhCCCCCCCCCCCCCCCChhhhccCCCCCC
Q 001795 959 QILRKKFVELYNM-PMLENLLESFQTSYPTLSFPPLPERGNFDLEEVLESPYFFN 1012 (1012)
Q Consensus 959 ~ilRe~FV~Lys~-~il~~l~e~f~~~~~~~~~p~~P~~G~LDL~~Vl~S~YFF~ 1012 (1012)
++|||+||+|||+ |+|++|+++|..+| .+++|++|++|+|||++||+|+|||+
T Consensus 754 ~~lRe~FV~lys~~~~L~~l~~~~~~~~-~~~~p~~P~~G~lDL~~Vl~S~yfF~ 807 (807)
T PHA00452 754 RAIRETFVEMYEENDVLADFADQFGDQL-QLKMPELPEKGSLDLEEVLDSDFFFC 807 (807)
T ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHHh-hccCCCCCCCCCCCHHHHhCCCCCCC
Confidence 9999999999999 99999999999999 67999999999999999999999996
No 3
>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]
Probab=100.00 E-value=9.3e-199 Score=1663.44 Aligned_cols=803 Identities=38% Similarity=0.635 Sum_probs=717.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHH-Hh---------hccCccchhh
Q 001795 180 RRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKM-QR---------TKKQKAAYAP 249 (1012)
Q Consensus 180 ~RQ~~lE~~~~~~a~~r~~~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~-~~---------~~~~r~~y~p 249 (1012)
+||..||.+++..|.|+|+..+++..++|-..--.-+.+.++.||..|..+.++|+.. .. +.+.|..|+|
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 21 2457899999
Q ss_pred hhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHH
Q 001795 250 HIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELL 329 (1012)
Q Consensus 250 ~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~~~~IG~aVe~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 329 (1012)
||++++++++|+|||+++++++.+++.+.||+++.+...+|++||+|++.++|...+++.+....+ +.-+.+
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 999999999999999999999999889999999999999999999999999987765443221110 011222
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCC--CCCccCceeEeeeeeecC
Q 001795 330 RKRVNSLIKSKRVMEAQKLLKNEETKPWGRDTQAKLGSRLVELLIETAYVQHPVNPADYS--PPDVRPAFRHRFKTILKH 407 (1012)
Q Consensus 330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~~~~kvG~~Li~~L~e~~~i~~~~~~~~~~--~~~~~paF~h~~~~~~~~ 407 (1012)
++.+.+ .+..+-.+..++.+|.+|+++++++||++++.+|+.+++|++...+...+ .....|||.|+|+|.
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--cccCCCCceeeCCCCCcCCCCceecccCccceecCCcHHHHHHHHhcc-cc
Q 001795 408 PGQKTTKRYGVVECDPLVLEGLDRSAK--HMLIPYVPMLVPPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEALKSVT-GN 484 (1012)
Q Consensus 408 ~g~~~~k~~gvi~~~~~~~~~l~~~~~--~~~~~~lPMlvpP~pW~~~~~GGYl~~~~~~~R~~~s~~q~~~l~~~~-~~ 484 (1012)
+| +++|||.+|..+...+.+... .+.+.+|||||||+||+++.+|||++....++|..++.+|-+|+..++ .+
T Consensus 476 Ng----~kigvv~~h~tl~~ll~~~~~~a~l~PqlLPmLV~PkPWtsw~~GGY~y~r~~llRlk~t~eqv~yl~~aseng 551 (1117)
T COG5108 476 NG----TKIGVVATHETLDWLLTENSRLAPLSPQLLPMLVPPKPWTSWFRGGYWYGRVRLLRLKKTGEQVRYLLMASENG 551 (1117)
T ss_pred CC----ceeEEEeeHHHHHHHhhcccccCCCChhhhccccCCCCCcCcccCceeeccceeeeecCcHHHHHHHHHhhhcC
Confidence 54 589999999998887766543 233348999999999999999999999999999999999999987764 68
Q ss_pred ChHHHHHHHHhhcCceeEEcHHHHHHHHHHHHcCCCCCCCCCCCC-CCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHhh
Q 001795 485 CMKKVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRND-VLIPEKP-LSEDMTEVQKWKWSVRKAKKINQERH 562 (1012)
Q Consensus 485 ~l~~v~~aLN~Lqst~wrIN~~VL~vi~~~w~~g~~i~~l~~~~~-~plP~~p-~~~d~~~~~~wk~~~~~~~~~~~~~~ 562 (1012)
+|++||++||.||+|||+||.+|++|+.++|++|+.+..||.+.+ .-+|+.| .+.+|+++..|+.+.+.+...++..+
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 3445544 56789999999999999999999999
Q ss_pred hhhhhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCccchhhhhccccCccCCcchhHHHHHHHhhhhCCC
Q 001795 563 SQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANLFSGG 642 (1012)
Q Consensus 563 S~R~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL~FaegkpLG~~Gl~WLkIhlAN~~G~G 642 (1012)
|+||+++|+|+||++|.|+ +|||||+||||||+||+|+||||||+|.|||||.||.|+|||++|++|||||+||+| |
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 9999999999999999996 899999999999999999999999999999999999999999999999999999999 8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhccCCCCCchhhhcCCChHHHHHHHHHHHHHHhcCCCCcceeccccccCCCcchhhHH
Q 001795 643 VEKLSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHLPIHQDGSCNGLQHY 722 (1012)
Q Consensus 643 ~DK~S~deRi~wv~~n~~~I~~sA~dPl~g~~wW~~Ad~PwQfLA~C~El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHy 722 (1012)
+||+||.+|++||++|+.+|+|||+||++|++||..||+|||.||+||||.+++++|||++|+||+||||||||||||||
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 HHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccccccceeeecccchhh
Q 001795 723 AALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVG 802 (1012)
Q Consensus 723 AAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~G 802 (1012)
||||+|++||+||||+|+|+|+|||..||..|...++.+|+++ +..|+.|++++||+|||+||||+|||||++|
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 4679999999999999999999999999999
Q ss_pred HHHHHHHHHHHcCCCCChh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc------------------CC
Q 001795 803 AREQIKRRLEEKGHITDDR-QLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIAS------------------EN 863 (1012)
Q Consensus 803 ar~QI~~~L~~~~~~~d~~-~~~~~a~ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~------------------~~ 863 (1012)
++.||.++|.-. ..+.+ +....+.|+++.+|.++++.|..|+.|++||.+|++.|.. +-
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 22222 2334578999999999999999999999999999998864 24
Q ss_pred CcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecC--CCccchhhhhccCCCccchhhhhHHHHHHHHHHhhcCCcEE
Q 001795 864 QPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE--GNLVEIRKQRTAFPPNFVHSLDGSHMMMTAVACRDAGLHFA 941 (1012)
Q Consensus 864 ~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~--~d~vd~rKQ~~af~PNFIHSLDAsHmmlta~~~~~~Gi~Fa 941 (1012)
.||+||||+||||+||||..++++|.|.+|+|.|+.+ +.+||+|||.+||||||||||||+||.|||.+|.++||.|+
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 7999999999999999999999999999999988865 56899999999999999999999999999999999999999
Q ss_pred EeeccccCCCCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHhCCC--------------------------CCCCCCCC
Q 001795 942 GVHDSFWTHACDVDEMNQILRKKFVELYNMPMLENLLESFQTSYPT--------------------------LSFPPLPE 995 (1012)
Q Consensus 942 sVHDSFwThA~dvd~M~~ilRe~FV~Lys~~il~~l~e~f~~~~~~--------------------------~~~p~~P~ 995 (1012)
+|||||||||||+|.||.+|||+||+||+.+++.+|.++|.+||.+ +++||+|+
T Consensus 1021 ~vHDSYwTHA~d~d~Mn~~LRE~Fvklh~~~~vlrlk~EF~~ryk~~l~~~k~~ka~dedl~aklg~~t~ipl~lPplP~ 1100 (1117)
T COG5108 1021 LVHDSYWTHAGDADAMNQFLREEFVKLHGDHDVLRLKAEFGRRYKGFLVSKKAIKANDEDLTAKLGEGTYIPLELPPLPE 1100 (1117)
T ss_pred eeecchhccccCHHHHHHHHHHHHHHHhcchHHHHHHHHHhHHhhchhhhhhhhccchHHHHhhcCCCCcccccCCCCCC
Confidence 9999999999999999999999999999999999999999998842 35899999
Q ss_pred CCCCChhhhccCCCCCC
Q 001795 996 RGNFDLEEVLESPYFFN 1012 (1012)
Q Consensus 996 ~G~LDL~~Vl~S~YFF~ 1012 (1012)
+|+|||..||+|.|||+
T Consensus 1101 kG~lDls~vleS~yFFs 1117 (1117)
T COG5108 1101 KGSLDLSQVLESAYFFS 1117 (1117)
T ss_pred CCCccHHHHHhhhhccC
Confidence 99999999999999997
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=4.5e-123 Score=1057.37 Aligned_cols=385 Identities=55% Similarity=0.981 Sum_probs=339.4
Q ss_pred CccCCcchhHHHHHHHhhhhCCCCCCCCHHHHHHHHHHHHHHHHHhccCCCCCchhhhcCCChHHHHHHHHHHHHHHhcC
Q 001795 620 GRPLGKSGLRWLKIHLANLFSGGVEKLSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALKSS 699 (1012)
Q Consensus 620 gkpLG~~Gl~WLkIhlAN~~G~G~DK~S~deRi~wv~~n~~~I~~sA~dPl~g~~wW~~Ad~PwQfLA~C~El~~a~~~~ 699 (1012)
|||||++|++|||||+||+| |+||+||+||++||++|+++|+++|+||+++.+||.+||+||||||+|+||++|++++
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 CCCcceeccccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhc---CCCCCCChhHHHHH
Q 001795 700 SPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDS---NKDPSKHPQALLAK 776 (1012)
Q Consensus 700 ~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da---~~~~~~~~~~~~ak 776 (1012)
+|++|+||+||||||||||||||||||||.+||++|||+|+++|+|||+.|++.|.+.+.+++ .. ...+++
T Consensus 79 ~~~~~~s~lPV~~DgSCsGlQH~sal~rD~~ga~~vNLip~~~p~DiY~~V~~~v~~~l~~~~~~~~~------~~~~~~ 152 (405)
T PF00940_consen 79 NPEEFVSHLPVHQDGSCSGLQHYSALLRDEVGAKAVNLIPSDKPQDIYSEVAEEVKKRLEEDADDAEE------DNSLAK 152 (405)
T ss_dssp SGCCSEE-SEEEEEBSTHHHHHHHHHTT-HHHHHHTTSSSSSS---HHHHHHHHHHHHHHHHHHEHHC------CHHHHH
T ss_pred CchheeecceeeecCcccHHHHHHHHccCHhhChhcCCCCCCCCCchHHHHHHHHHHHHHHhhccccc------chHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999883 22 268899
Q ss_pred HhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCC-ChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001795 777 ILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHIT-DDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDC 855 (1012)
Q Consensus 777 ~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~-d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~WL~~~ 855 (1012)
++..+|+||+|||+|||+|||||.+|+++||+++|++.+... +....+.++.|||+.|+++|+++|++|+.+|+||++|
T Consensus 153 ~l~~~i~Rk~vK~~vMT~~YG~T~~g~~~qi~~~l~~~~~~~~~~~~~~~~~~~la~~i~~~i~~~~~~a~~~m~wL~~~ 232 (405)
T PF00940_consen 153 WLKGGITRKLVKRPVMTIVYGVTFYGARDQIKEQLKEKGDEEEDKIESYKAAMYLAKIIFEAIKEVFPGARNIMDWLQEI 232 (405)
T ss_dssp HCCCT--HHHHHHHHHHHHHT-TCCHHHHHHHHHCHCHCCCTTTTTTHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHH
T ss_pred HhcCCCChhhcccceEEeeeCcchhhHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 999999999999999999999999999999999999886544 3457889999999999999999999999999999999
Q ss_pred HHHHHcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecC--CCccchhhhhccCCCccchhhhhHHHHHHHHHH
Q 001795 856 AKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE--GNLVEIRKQRTAFPPNFVHSLDGSHMMMTAVAC 933 (1012)
Q Consensus 856 A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~--~d~vd~rKQ~~af~PNFIHSLDAsHmmlta~~~ 933 (1012)
|+++++++.||.|+||+||||+|+|++.++++|+|.++....... .+.+|++||++||||||||||||||||||+.+|
T Consensus 233 a~~~~~~~~pv~W~tP~Gl~V~Q~Y~~~~~~~i~~~~~~~~~~~~~~~~~~d~~Kq~~a~~PNFIHSlDAshl~~t~~~~ 312 (405)
T PF00940_consen 233 AKIIAKLNKPVSWTTPLGLPVVQPYRKSKKKRIKTYLQGVSRRRVIREDPVDKRKQKNAFAPNFIHSLDASHLMLTANAC 312 (405)
T ss_dssp HHHHHCTCB-EEEEETTSEEEEE--EEESEEEEESSSTTTEEE--EEEEES-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHccCCcEEEECCCCCEEEecccccCceeeEeecceeEEeccCCCCCCCHHHHhcccCCchHhhHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999998753332221 234599999999999999999999999999999
Q ss_pred hhcCCcEEEeeccccCCCCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHhCCC--------------CCCCCCCCCCCC
Q 001795 934 RDAGLHFAGVHDSFWTHACDVDEMNQILRKKFVELYNMPMLENLLESFQTSYPT--------------LSFPPLPERGNF 999 (1012)
Q Consensus 934 ~~~Gi~FasVHDSFwThA~dvd~M~~ilRe~FV~Lys~~il~~l~e~f~~~~~~--------------~~~p~~P~~G~L 999 (1012)
.+.|++|++||||||||||||+.|+++||++||+||++++|++|+++|..+++. +.+|++|++|+|
T Consensus 313 ~~~~~~f~~VHDsf~tha~~~~~L~~~lRe~Fv~lys~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~P~~G~l 392 (405)
T PF00940_consen 313 NKEGIPFATVHDSFWTHACDVDTLNEILREQFVELYSPDILEDFAEDFKARLPDSYQNIWEKKNEFVPIKFPPLPERGDL 392 (405)
T ss_dssp HHTT--EEECTTEEEEEHHHHHHHHHHHHHHHHHHHHCTHHHHHHHHHHCCCTGGTTSHHHHH--HHCCCCHS-----S-
T ss_pred HhcCCeEEEEehhhhcCHHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHhhhhhccccccchhhhhccCCCCCCCCCc
Confidence 999999999999999999999999999999999999999999999999999986 789999999999
Q ss_pred ChhhhccCCCCCC
Q 001795 1000 DLEEVLESPYFFN 1012 (1012)
Q Consensus 1000 DL~~Vl~S~YFF~ 1012 (1012)
||++|++|+||||
T Consensus 393 dl~~V~~S~YfFs 405 (405)
T PF00940_consen 393 DLNEVLKSEYFFS 405 (405)
T ss_dssp SGGGGGG-TTTBB
T ss_pred cHHHHhCCCCCCC
Confidence 9999999999997
No 5
>PF14700 RPOL_N: DNA-directed RNA polymerase N-terminal; PDB: 3SPA_A 1CEZ_A 1H38_B 1S77_D 1QLN_A 1S0V_D 3E2E_A 2PI4_A 3E3J_B 1S76_D ....
Probab=100.00 E-value=1.4e-47 Score=423.14 Aligned_cols=305 Identities=33% Similarity=0.569 Sum_probs=219.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHHh----hccCccchhhhhccCC
Q 001795 180 RRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQR----TKKQKAAYAPHIELLP 255 (1012)
Q Consensus 180 ~RQ~~lE~~~~~~a~~r~~~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~~----~~~~r~~y~p~L~~l~ 255 (1012)
|||++||+++++.|++||++..+++.++|.+++++++++++++|+++|+++|+++++.+. ..++++.|+|||+.||
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 4577899999999999
Q ss_pred hhHHHHHHHHHHHHHHhcC-CCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHHH
Q 001795 256 ADKVAVIVMHKMMGLVMAG-HEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVN 334 (1012)
Q Consensus 256 ~e~lA~Iti~~~l~~~~~~-~~~~~~~~~~~~~~IG~aVe~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 (1012)
||++|+|||+++|++++++ +..+|++++.++.+||++||+|++++++.+...+.+.+............. .++.+.
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 9999999999999999843 456678999999999999999999998876644322211100000000000 001111
Q ss_pred HHHHHHHHHHHHHhhcCCCCC--CCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCCCCCccCceeEeeeeeecCCCCCc
Q 001795 335 SLIKSKRVMEAQKLLKNEETK--PWGRDTQAKLGSRLVELLIETAYVQHPVNPADYSPPDVRPAFRHRFKTILKHPGQKT 412 (1012)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~--~W~~~~~~kvG~~Li~~L~e~~~i~~~~~~~~~~~~~~~paF~h~~~~~~~~~g~~~ 412 (1012)
..++........... +..+. +|+..++++||++|+++|+++++|++...++.+ ...+|||+|+|++. +
T Consensus 158 ~~~~~~~~~~~~~~~-~~~~~~~~W~~~~~~~vG~~Ll~~l~~~~~i~~~~~~~~~--~~~~paf~~~~~~~---~---- 227 (318)
T PF14700_consen 158 QLLKNRKDSSGKPSL-EEEWSDSPWPSDIRAKVGSFLLELLMETAKIPVERKDPET--SEEQPAFYHSYRYR---K---- 227 (318)
T ss_dssp HHHHHHHSHSS-STT-T-TCCC--SCHHHHHHHHHHHHHHHHHCTCEEEEEESTT-------BSEEEEE------T----
T ss_pred HHHHHHHHhcccccc-ccccccCCCCHHHHHHHHHHHHHHHHhheeeccccCCccc--cccccchhhhhccc---c----
Confidence 111111000000000 12344 499999999999999999999999987754322 56799999999875 3
Q ss_pred ceeEEEEecCHHHHHHHHhhhhc-----ccCCCCceeeCCCCCcCCCCceecccCccceecCCcHHHHHHHH-hccccCh
Q 001795 413 TKRYGVVECDPLVLEGLDRSAKH-----MLIPYVPMLVPPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEALK-SVTGNCM 486 (1012)
Q Consensus 413 ~k~~gvi~~~~~~~~~l~~~~~~-----~~~~~lPMlvpP~pW~~~~~GGYl~~~~~~~R~~~s~~q~~~l~-~~~~~~l 486 (1012)
++++|+|++||.+.+.++..... .++.+|||||||+||+++++||||+.++.+||++++ .|..+++ +...++|
T Consensus 228 ~~~~g~i~~~~~~~~~l~~~~~~~~~~~~~~~~lPMlvpP~PW~~~~~GGYl~~~~~l~R~~~~-~~~~~~~~~~~~~~l 306 (318)
T PF14700_consen 228 GKKVGVIKPHPELVKLLSDEPEKSLLQATFPRYLPMLVPPKPWTSPNDGGYLLSPTPLMRTKDS-EQQQYLKKALRRGDL 306 (318)
T ss_dssp TT-EEEEEE-HHHHHHHHHHCH---CCCCCCCCS-BSS--EEECCTCCEESSSSSEBSEE-STT-HHCHHHHHTTTCCGG
T ss_pred CceEEEEeeCHHHHHHHHhhhhhhhhhhcccccCcCCCCCCCCcCCCcceeeeeCchhhcccch-hhHHHHHHHccccch
Confidence 35789999999999999877542 125599999999999999999999999999999887 5545554 4467899
Q ss_pred HHHHHHHHhhcC
Q 001795 487 KKVFEALDTLGS 498 (1012)
Q Consensus 487 ~~v~~aLN~Lqs 498 (1012)
+.||+|||+||+
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=90.88 E-value=0.3 Score=52.21 Aligned_cols=192 Identities=20% Similarity=0.213 Sum_probs=115.5
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001795 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (1012)
Q Consensus 691 El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 770 (1012)
++++++.. |++| +-|..|-|.==|=.+|.|.+|......-| ...|+|+.+|..+...-.+
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 47889999999999999999998877765 3569999998765322110
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001795 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 850 (1012)
Q Consensus 771 ~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~ 850 (1012)
. .....|+..|+.+--..||.+..|..+++ | ++.+ -|+.+.++..+.||+ +..
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 11346999999999999999987776543 3 2221 245566677777877 667
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCccchhhhhHHHHHHH
Q 001795 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 930 (1012)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~af~PNFIHSLDAsHmmlta 930 (1012)
|.+++.....+.|. .+|+.|-...-|-.. +.....+.+..-.+.|++=+=-|+=++..|
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 88777666555542 256666433221100 111222222223367876665565544433
Q ss_pred H-HH----hhcCC--c-EEEeeccccCC
Q 001795 931 V-AC----RDAGL--H-FAGVHDSFWTH 950 (1012)
Q Consensus 931 ~-~~----~~~Gi--~-FasVHDSFwTh 950 (1012)
. .+ .+.|+ . .+.|||+....
T Consensus 175 m~~~~~~~~~~~~~~~~vl~vHDElv~e 202 (206)
T smart00482 175 MIKMDEALKEKGLRARLLLQVHDELVFE 202 (206)
T ss_pred HHHHHHHHHhcCCCceEEEeeceeEEee
Confidence 2 22 23333 3 55699998654
No 7
>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]
Probab=88.14 E-value=0.34 Score=59.02 Aligned_cols=75 Identities=28% Similarity=0.414 Sum_probs=59.0
Q ss_pred hcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001795 779 IDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAK 857 (1012)
Q Consensus 779 ~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~WL~~~A~ 857 (1012)
.-+++|++.|| ||.+||...+-..+.- ++|. +.+++-..++|.+|.++...++++.+++...+..-|+|++..++
T Consensus 860 yvGat~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 860 YVGATRQITKR--LTLIYGASKFDTVDPW-KYLT-KEVFPAERTLFAAAHFIQDWLWDCVGEIVVSAAGDMDWLQKKAG 934 (1117)
T ss_pred EeehHHHHHHh--cccccCchhccccCHH-HHHH-HhHhHHHHHHHHHHHHHHHHHHHHHhHHHHhcccchhHHHHHhc
Confidence 34899999999 9999999765333322 2222 12455556899999999999999999999999999999997765
No 8
>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=84.78 E-value=4.4 Score=47.38 Aligned_cols=209 Identities=15% Similarity=0.216 Sum_probs=122.5
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001795 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (1012)
Q Consensus 691 El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 770 (1012)
+++.++..+ .+| .-|..|-|-==|=.+|.|.+|....+..| ...|+|+.+|..+... ..
T Consensus 140 ~~R~~f~~~--~G~---~lv~aDysqiElRilA~ls~D~~l~~~~~-----~g~Dih~~~A~~~~g~-------~~---- 198 (377)
T cd08637 140 EIRKAFVAE--EGW---VLLSADYSQIELRILAHLSGDEALIEAFK-----NGEDIHTRTAAEVFGV-------PP---- 198 (377)
T ss_pred hHHHheeCC--CCC---EEEEechhHhHHHHHHHHhCCHHHHHHHh-----cCCCHHHHHHHHHhCC-------Ch----
Confidence 466666532 344 47889999888889999999999888876 3579999988765321 00
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001795 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 850 (1012)
Q Consensus 771 ~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~ 850 (1012)
... ..-.|+..|..+--..||.+..|..+++ |+ +.+ -|+.+.+...+.||+ +..
T Consensus 199 -~~v-----~~~~R~~aK~~~~g~~YG~g~~~la~~l-------g~-s~~---------eA~~~~~~f~~~~p~---v~~ 252 (377)
T cd08637 199 -EEV-----TPEMRRIAKAVNFGIIYGISAFGLSQQL-------GI-SRK---------EAKEYIDRYFARYPG---VKE 252 (377)
T ss_pred -hhC-----CHHHHhhhhHhhcchhcCcchhHHHHHc-------CC-CHH---------HHHHHHHHHHHHCcc---HHH
Confidence 000 1124999999999999999888766543 32 222 235566666777887 555
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCccchhhhhHHHHHHH
Q 001795 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 930 (1012)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~af~PNFIHSLDAsHmmlta 930 (1012)
|.+++...+...+- .+|+.|-...-|--. +.....+-+..-.+.|++=+=-|+=+|..+
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 66666555444331 245555422111000 011111111112467777666555544433
Q ss_pred H-H----HhhcCC---cEEEeeccccCC--CCChhHHHHHHHHHHHH
Q 001795 931 V-A----CRDAGL---HFAGVHDSFWTH--ACDVDEMNQILRKKFVE 967 (1012)
Q Consensus 931 ~-~----~~~~Gi---~FasVHDSFwTh--A~dvd~M~~ilRe~FV~ 967 (1012)
. . +...|+ -...|||+.... ..+++...+++++.+-+
T Consensus 312 m~~~~~~l~~~~~~~~lvl~vHDEl~~ev~~~~~~~~~~~l~~~M~~ 358 (377)
T cd08637 312 MIRVHKALKEEGLKARMLLQVHDELVFEVPEEELEEVAALVKEEMEN 358 (377)
T ss_pred HHHHHHHHHhcCCCeEEEeeEeeeeeEecCHHHHHHHHHHHHHHHhh
Confidence 2 2 233343 355699998755 35566667777776533
No 9
>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=83.54 E-value=4.1 Score=47.55 Aligned_cols=211 Identities=19% Similarity=0.196 Sum_probs=126.5
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001795 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (1012)
Q Consensus 691 El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 770 (1012)
.+++++..+ .+| +-|..|-|-==|=.+|.|.+|.....+.| .-.|||+.+|..+-..- .
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 455555432 344 47899999999999999999999888775 25699999887653210 0
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001795 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 850 (1012)
Q Consensus 771 ~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~ 850 (1012)
.. ...-.|+..|..+--..||.+..|...++ |+ +.+ -|+.+.+...+.||+. ..
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---------EAKQFIESFKNAYPGV---RR 241 (373)
T ss_pred -hh-----CCHHHHHHHhHHHHhhHhCCcHHHHHHHh-------CC-CHH---------HHHHHHHHHHHHCccH---HH
Confidence 00 11246999999999999999999888654 32 221 2455667777788874 55
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCccchhhhhHHHHHHH
Q 001795 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 930 (1012)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~af~PNFIHSLDAsHmmlta 930 (1012)
|.+++.....+.| .| +|+.|-...-|--.. .....+-..--.+.|++=+==|+=+|..|
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 6665555444332 22 355554332221111 01111112223566877666666555443
Q ss_pred H-HHh----h-------cCC-cEEEeeccccC--CCCChhHHHHHHHHHHHHhc
Q 001795 931 V-ACR----D-------AGL-HFAGVHDSFWT--HACDVDEMNQILRKKFVELY 969 (1012)
Q Consensus 931 ~-~~~----~-------~Gi-~FasVHDSFwT--hA~dvd~M~~ilRe~FV~Ly 969 (1012)
. .+. . .+. -...|||+... +..+++.+.+++++.+-.-.
T Consensus 301 mi~i~~~l~~~~~~~~~~~~~lvl~VHDEl~~ev~~~~~~~~~~~i~~~Me~~~ 354 (373)
T cd08638 301 MINIHEKLHSLLPNLPAGRARLVLQIHDELLFEVPESDVDEVARIIKRSMENAA 354 (373)
T ss_pred HHHHHHHHHhhcccccCCCeEEEEEEccEEEEEeCHHHHHHHHHHHHHHHhCcc
Confidence 2 222 2 123 35569999764 45667777788887774443
No 10
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=81.90 E-value=3 Score=51.05 Aligned_cols=192 Identities=19% Similarity=0.153 Sum_probs=119.6
Q ss_pred cccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccc
Q 001795 708 LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 787 (1012)
Q Consensus 708 lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~i~RKvV 787 (1012)
.-|..|-|.==|=.+|.|.+|....++.| .-.|+|+.+|..+-.. ..+ . .-.|+..
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 47889999999999999999999988876 3579999998877211 100 0 3459999
Q ss_pred cccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcEE
Q 001795 788 KQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIASENQPVR 867 (1012)
Q Consensus 788 KqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~~~~pV~ 867 (1012)
|..+.-.+||.+..|..+++. .. + -|+.+.+...+.||+ +..|++++.+...+.| .|
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 999999999999998887653 11 1 135556666677777 6677777776655442 22
Q ss_pred EEcCCCCeEEEeeccCcceeEEeeeEEEEEecC-CCccchhhhhccCCCccchhhhhHHHHHHHH-HHhh-----cCCc-
Q 001795 868 WTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE-GNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-ACRD-----AGLH- 939 (1012)
Q Consensus 868 WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~-~d~vd~rKQ~~af~PNFIHSLDAsHmmlta~-~~~~-----~Gi~- 939 (1012)
+|.+|=... +... +.....+.+..-++.|++=+==|+=++..|. .+.+ .+..
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 245443211 1110 1111222223334679965555555554432 2222 2333
Q ss_pred EEEeeccccCCC--CChhHHHHHHHHHHH
Q 001795 940 FAGVHDSFWTHA--CDVDEMNQILRKKFV 966 (1012)
Q Consensus 940 FasVHDSFwThA--~dvd~M~~ilRe~FV 966 (1012)
...|||....+. .+++.+.+++++.+-
T Consensus 499 vl~vHDEl~~e~~~~~~~~~~~~i~~~M~ 527 (553)
T PRK14975 499 VFFVHDEVVVECPEEEAEEVAAAIEEAME 527 (553)
T ss_pred EEEecceeEEEecHHHHHHHHHHHHHHHH
Confidence 556999988764 445566667766653
No 11
>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=75.03 E-value=15 Score=43.16 Aligned_cols=185 Identities=16% Similarity=0.052 Sum_probs=109.0
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001795 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (1012)
Q Consensus 691 El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 770 (1012)
+++.++..+ .++ .-|..|-|.==|-.+|.|.+|...-++-| ...|||+..|..+-..=.++.
T Consensus 159 ~iR~aFva~--~G~---~lvsaDySQIElRVLAhlS~D~~li~af~-----~g~Dih~~tAs~if~vp~e~~-------- 220 (378)
T cd08642 159 LIRTAFIPS--EGH---RFIVSDFSAIEARVIAWLAGEQWRLDVFA-----THGKIYEASASQMFGVPVEKI-------- 220 (378)
T ss_pred HhHHheecC--CCC---EEEEecHHHHHHHHHHHHhCCHHHHHHHh-----cCCChHHHHHHHHhCCChhhc--------
Confidence 345555432 343 35889999999999999999999877765 568999999887742210000
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001795 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 850 (1012)
Q Consensus 771 ~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~ 850 (1012)
-...--|...|...--++||.+.+|.+..-.+ +.|+ +.+ + |+.+.+...+.||+.+..|.
T Consensus 221 -------~v~~~~R~~AK~vnfGiiYG~g~~~L~~~aa~---~lgi-s~~-E--------A~~~i~~yf~~yP~v~~~~~ 280 (378)
T cd08642 221 -------GKNSHLRQKGKVAELALGYGGSVGALKAMGAL---EMGL-TED-E--------LPGIVDAWRNANPNIVKLWW 280 (378)
T ss_pred -------ccCHHHHHHhhhhhccceeccchHHHHHhhhh---hcCC-CHH-H--------HHHHHHHHHHHCccHHHHHH
Confidence 01123588999999999999999886321111 2243 221 1 23445556677787554333
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCccchhhhhHHHHHHH
Q 001795 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 930 (1012)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~af~PNFIHSLDAsHmmlta 930 (1012)
=.++.++...+.+. |... -+|. .=|-|..-=|--|-+.-
T Consensus 281 ~~~~~~~~a~~~g~-v~t~------------------------------------g~r~----~~n~IQGtAADi~k~Am 319 (378)
T cd08642 281 DVDKAAKKAVKERK-TVKL------------------------------------GGKL----VENIVQAIARDCLAEAM 319 (378)
T ss_pred HHHHHHHHHHHcCc-eEee------------------------------------hHhh----hhcccchhHHHHHHHHH
Confidence 33333544334432 2211 0111 11445544344444444
Q ss_pred HHHhhcCCc-EEEeeccccCCCCCh
Q 001795 931 VACRDAGLH-FAGVHDSFWTHACDV 954 (1012)
Q Consensus 931 ~~~~~~Gi~-FasVHDSFwThA~dv 954 (1012)
+.+.+.|.. +..|||..-.+..+.
T Consensus 320 i~l~~~g~~ivLqVHDElv~Evp~~ 344 (378)
T cd08642 320 LRLEKAGYDIVMHVHDEVVIEVPEG 344 (378)
T ss_pred HHHHhcCCeEEEEECceeEEeeccc
Confidence 456667774 456999999998874
No 12
>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=74.64 E-value=8.1 Score=45.28 Aligned_cols=211 Identities=20% Similarity=0.128 Sum_probs=120.0
Q ss_pred ccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCC--------CCCCChhHHHHHHhhc
Q 001795 709 PIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNK--------DPSKHPQALLAKILID 780 (1012)
Q Consensus 709 PV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~--------~~~~~~~~~~ak~l~~ 780 (1012)
-|..|-|-==|-.+|.|.+|....++.| .-.|+|+..|..+-....++..+ +.+.++....+. ..
T Consensus 121 lv~aDySQiElRvlA~lS~D~~Li~af~-----~g~DiH~~tA~~if~~~~e~v~~~~~~~~~~~~~~~~~~~~~~--~~ 193 (371)
T cd08640 121 LIVADYSQLELRLLAHMTRCKSMIEAFN-----AGGDFHSRTASGMYPHVAEAVANGEVLLEWKSEGKPPAPLLKD--KF 193 (371)
T ss_pred EEEechhhhhHHHHHHHcCCHHHHHHHH-----cCCCHHHHHHHHHhCCCHHHhcccccccccccccccccccccc--cc
Confidence 5889999999999999999999887776 34699999887654332211110 000000000000 01
Q ss_pred ccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001795 781 QVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIA 860 (1012)
Q Consensus 781 ~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~ 860 (1012)
.-.|+..|...--.+||.+..|...++ |+ +.+ -|+.+.+...+.||+ +..|.+++.....
T Consensus 194 ~~~R~~AK~infGi~YG~g~~~La~~l-------gi-s~~---------eA~~~i~~f~~~fP~---v~~~~~~~~~~a~ 253 (371)
T cd08640 194 KSERRKAKVLNFSIAYGKTAHGLAKDW-------KV-KLK---------EAERTVDAWYSDRPE---VEQWQKKTKKEAR 253 (371)
T ss_pred HHHHHHHHHHHHHHHhccchhHHHHHc-------CC-CHH---------HHHHHHHHHHHHCcc---HHHHHHHHHHHHH
Confidence 345999999999999999999887643 32 221 235566677778887 5677777666554
Q ss_pred cCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCccchhhhhHHHHHHHH-HHh-----
Q 001795 861 SENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-ACR----- 934 (1012)
Q Consensus 861 ~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~af~PNFIHSLDAsHmmlta~-~~~----- 934 (1012)
+.| .| +|++|-...=|--.. .+ ...+.+.--.+-|++=+==|+=++..|. .+.
T Consensus 254 ~~G-yv--~T~~GRrr~lp~i~s-----------------~~-~~~~~~~eR~avN~~IQGsAADI~K~Ami~i~~~l~~ 312 (371)
T cd08640 254 ERG-YT--RTLLGRYRYLPDIKS-----------------RN-RKKRGHAERAAINTPIQGSAADIAMKAMLRIYRNLRL 312 (371)
T ss_pred HcC-cE--EccCCCEEECCCccc-----------------cc-HhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHHHHhh
Confidence 443 22 256554322110000 00 0001111112557766666666655442 222
Q ss_pred -hcCCc-EEEeeccccCC--CCChhHHHHHHHHHHHH
Q 001795 935 -DAGLH-FAGVHDSFWTH--ACDVDEMNQILRKKFVE 967 (1012)
Q Consensus 935 -~~Gi~-FasVHDSFwTh--A~dvd~M~~ilRe~FV~ 967 (1012)
..|.. +..|||+.+.. ...++....+|++.+.+
T Consensus 313 ~~~~~~lvlqVHDElv~evp~~~~~~~~~~v~~~Me~ 349 (371)
T cd08640 313 KRLGWKLLLQIHDEVILEGPEEKADEALKIVKDCMEN 349 (371)
T ss_pred ccCCceEEEEEcceeEEEcCHHHHHHHHHHHHHHHHh
Confidence 23444 45699998864 44555566777776644
No 13
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=73.50 E-value=12 Score=48.67 Aligned_cols=196 Identities=17% Similarity=0.208 Sum_probs=120.4
Q ss_pred cccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccc
Q 001795 708 LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 787 (1012)
Q Consensus 708 lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~i~RKvV 787 (1012)
.-|..|-|-==|-.+|.|.+|....++.| .-.|||+..|..+-..-.+ . ...-.|...
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 36778888888889999999998877765 3469999988876321100 0 012349999
Q ss_pred cccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcEE
Q 001795 788 KQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIASENQPVR 867 (1012)
Q Consensus 788 KqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~~~~pV~ 867 (1012)
|...--.+||.+.+|..+++ |+ +.+ -|+.+.+...+.||+ +..|+.++.....+.|- |
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 234555556667776 67787777766655541 2
Q ss_pred EEcCCCCeEEEeeccCcceeEEeeeEEEEEecC-CCccchhhhhccCCCccchhhhhHHHHHHHH-----HHhhcCC--c
Q 001795 868 WTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE-GNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-----ACRDAGL--H 939 (1012)
Q Consensus 868 WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~-~d~vd~rKQ~~af~PNFIHSLDAsHmmlta~-----~~~~~Gi--~ 939 (1012)
+|..|-.- .+..- +.....|.+.--.+.|.+=+==|+=+|..|. ++.+.|+ .
T Consensus 775 -~Tl~GRrr-------------------~lp~i~s~n~~~r~~aeR~A~N~~iQGsAADi~K~Ami~v~~~l~~~~~~~~ 834 (887)
T TIGR00593 775 -ETLFGRRR-------------------YIPDINSRNRNVREAAERMAINAPIQGSAADIMKIAMIKLDKRLKERKLKAR 834 (887)
T ss_pred -EecCCCEe-------------------eCCCccccchhhHhHHHhhhhhhhhhhHHHHHHHHHHHHHHHHHHhcCCCeE
Confidence 45555210 11110 1111122222235678877666665554432 2445564 3
Q ss_pred -EEEeeccccCC--CCChhHHHHHHHHHHHH
Q 001795 940 -FAGVHDSFWTH--ACDVDEMNQILRKKFVE 967 (1012)
Q Consensus 940 -FasVHDSFwTh--A~dvd~M~~ilRe~FV~ 967 (1012)
+..|||..... ...++.+..++++.+-.
T Consensus 835 lvlqVHDElv~Evp~~~~~~v~~~l~~~Me~ 865 (887)
T TIGR00593 835 LLLQVHDELIFEAPEEEAEEVAALVKEVMEH 865 (887)
T ss_pred EEeeEceEeeeecCHHHHHHHHHHHHHHHHh
Confidence 45699997754 46677778888887754
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=72.36 E-value=11 Score=45.00 Aligned_cols=198 Identities=14% Similarity=0.005 Sum_probs=116.5
Q ss_pred cccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccc
Q 001795 708 LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 787 (1012)
Q Consensus 708 lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~i~RKvV 787 (1012)
+-|.-|.|.==|-.+|.|.+|..++..+.... -.|+++..|..+ +...|+..
T Consensus 188 ~lv~aDySQiELRiLAhls~d~~~~~l~~~~~---~~DiH~~ta~~~-------------------------g~~~R~~A 239 (429)
T cd08643 188 SLVGADASGLELRCLAHYLARYDGGAYTRKVL---GGDIHWANAQAM-------------------------GLLSRDGA 239 (429)
T ss_pred EEEEecHHHHHHHHHHHHhcccchHHHHhhhc---ccchhHHHHHHh-------------------------ChHHHhhh
Confidence 46888998888889999999876666555332 358887655431 11469999
Q ss_pred cccceeeecccchhhHHHHHHHHHHHcC-C---CC---ChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001795 788 KQTVMTSVYGVTFVGAREQIKRRLEEKG-H---IT---DDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIA 860 (1012)
Q Consensus 788 KqtVMT~vYGvT~~Gar~QI~~~L~~~~-~---~~---d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~ 860 (1012)
|...--.+||.+..|..+++.-..++-. . ++ +......++..-++.+.+...+.||+.+. |++++-....
T Consensus 240 K~i~fGiiYG~g~~~La~~lg~~~~eA~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~f~~~~P~v~~---~~~~~~~~a~ 316 (429)
T cd08643 240 KTFIYAFLYGAGDEKLGQIVGDDLRTAKNLNAEWPQTKKGTIKKIADKAKGRVVRANFLKGLPALGK---LIKKVKEAAK 316 (429)
T ss_pred HHHHHHHHHCCChhHHHHHhCCCHHHHHhhhhcccccccchhhhhhhhhhHHHHHHHHHHhCccHHH---HHHHHHHHHH
Confidence 9999999999999999887643222110 0 00 00001112233455566666666777554 5555444433
Q ss_pred cCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCccchhhhhHHHHHHHH-----HHhh
Q 001795 861 SENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-----ACRD 935 (1012)
Q Consensus 861 ~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~af~PNFIHSLDAsHmmlta~-----~~~~ 935 (1012)
+.| . .+|..|-... +. +.+ .+-|++=+==|+-+|..|. ...+
T Consensus 317 ~~G-y--v~tl~GRrr~-------------------~~------~~r-----~A~Nt~iQGsAADi~K~Ami~i~~~l~~ 363 (429)
T cd08643 317 KRG-H--LVGLDGRRIR-------------------VR------SAH-----AALNTLLQSAGAILMKKWLVLLDDELTA 363 (429)
T ss_pred hCC-c--eeCCCCCccc-------------------Cc------hHH-----HHhChhhhhHHHHHHHHHHHHHHHHHHh
Confidence 332 1 2455553211 00 011 1456665555555554432 2333
Q ss_pred cC----C---cEEEeeccc--cCCCCChhHHHHHHHHHHHHhc
Q 001795 936 AG----L---HFAGVHDSF--WTHACDVDEMNQILRKKFVELY 969 (1012)
Q Consensus 936 ~G----i---~FasVHDSF--wThA~dvd~M~~ilRe~FV~Ly 969 (1012)
.| . -++.|||.. =++..+++.+.+++++++..-.
T Consensus 364 ~g~~~~~~~~lvlqVHDElv~ev~~~~ae~v~~~v~~~Me~a~ 406 (429)
T cd08643 364 KGGVWGGDFEYCAWVHDEVQIECRKGIAEEVGKIAVEAAEKAG 406 (429)
T ss_pred cCCCcCCCeEEEEEEccceEEEeCHHHHHHHHHHHHHHHHHhh
Confidence 44 3 246699998 7788889999999999886653
No 15
>PRK05755 DNA polymerase I; Provisional
Probab=68.27 E-value=15 Score=47.58 Aligned_cols=209 Identities=17% Similarity=0.206 Sum_probs=123.5
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001795 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (1012)
Q Consensus 691 El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 770 (1012)
++++++.. |++| .-|..|-|+==|-.+|.|.+|.....+.| .-.|+|+.+|..+-..-.++
T Consensus 640 ~iR~~f~~--~~G~---~lv~~DysqiElRilA~ls~D~~l~~~~~-----~g~Dih~~~A~~~~~~~~~~--------- 700 (880)
T PRK05755 640 RIRKAFVA--PEGY---KLLSADYSQIELRILAHLSGDEGLIEAFA-----EGEDIHTATASEVFGVPLEE--------- 700 (880)
T ss_pred hhhheEec--CCCC---EEEEechhhhHHHHHHHHcCCHHHHHHHh-----cCCCHHHHHHHHHhCCChhh---------
Confidence 45666553 3455 47889999999999999999999887765 34699999887653221000
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001795 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 850 (1012)
Q Consensus 771 ~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~ 850 (1012)
...-.|+..|..+--..||.+..|...++ |+ +.+ -|+.+.+...+.||+ +..
T Consensus 701 --------v~~~~R~~aK~~~fg~~YG~g~~~la~~l-------~i-s~~---------eA~~~~~~~~~~~p~---v~~ 752 (880)
T PRK05755 701 --------VTSEQRRRAKAINFGIIYGMSAFGLAQQL-------GI-SRK---------EAKEYIDRYFERYPG---VKE 752 (880)
T ss_pred --------CCHHHHHHHHHHhcchhhCCChHHHHHHc-------CC-CHH---------HHHHHHHHHHHHCcc---HHH
Confidence 01124999999999999999988776543 32 221 245566667777777 566
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCccchhhhhHHHHHHH
Q 001795 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 930 (1012)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~af~PNFIHSLDAsHmmlta 930 (1012)
|++++.......| .| .|..|-...=|- + . +.....+.+.--.+.|++=+==|+=++..|
T Consensus 753 ~~~~~~~~a~~~g-~v--~t~~GR~r~~p~--------------~--~--~~~~~~~~~~~r~a~N~~iQgsaAdi~k~a 811 (880)
T PRK05755 753 YMERTVEQAREKG-YV--ETLFGRRRYLPD--------------I--N--SRNGNRRAFAERAAINAPIQGSAADIIKLA 811 (880)
T ss_pred HHHHHHHHHHHcC-CE--ECCCCCeEeCCc--------------c--c--CCCHHHHHHHHHHHhhhhhhhHHHHHHHHH
Confidence 7777766655443 22 355554221110 0 0 001111111122356776554444444332
Q ss_pred H-----HHhhcCC---cEEEeeccccCC--CCChhHHHHHHHHHHHH
Q 001795 931 V-----ACRDAGL---HFAGVHDSFWTH--ACDVDEMNQILRKKFVE 967 (1012)
Q Consensus 931 ~-----~~~~~Gi---~FasVHDSFwTh--A~dvd~M~~ilRe~FV~ 967 (1012)
. ...+.|+ -...|||+..-. ...++.+.+++++.+-.
T Consensus 812 m~~~~~~l~~~~~~~~l~l~vHDel~~ev~~~~~~~~~~~~~~~me~ 858 (880)
T PRK05755 812 MIRVDKALKEEGLKSRMLLQVHDELVFEVPEDELEEVKKLVKEVMEN 858 (880)
T ss_pred HHHHHHHHHhcCCCceEEEEEcceeEEEeCHHHHHHHHHHHHHHHhC
Confidence 1 1333454 366799998754 45566777777776533
No 16
>cd08639 DNA_pol_A_Aquificae_like Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences. 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' nucleas
Probab=67.96 E-value=24 Score=40.63 Aligned_cols=188 Identities=20% Similarity=0.190 Sum_probs=109.4
Q ss_pred cccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccc
Q 001795 708 LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 787 (1012)
Q Consensus 708 lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~i~RKvV 787 (1012)
.-|..|-|.==+=.+|.|.+|.....+.| ...|+|+.+|..+...-. ... ..-.|+..
T Consensus 104 ~lv~aDysqiElRilA~ls~D~~l~~~~~-----~g~Dih~~~A~~~~g~~~------------~~v-----~~~~R~~a 161 (324)
T cd08639 104 KLIIADYSQIELRIAAEISGDERMISAYQ-----KGEDLHRLTASLITGKPI------------EEI-----TKEERQLA 161 (324)
T ss_pred EEEEechhhhHHHHHHHHhCCHHHHHHHh-----cCCCHhHHHHHHHhCCCh------------hhC-----CHHHHHHh
Confidence 47899999999999999999999887765 346999999876522100 000 12359999
Q ss_pred cccceeeecccchhhHHHHHHHHHHHcCC-CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcE
Q 001795 788 KQTVMTSVYGVTFVGAREQIKRRLEEKGH-ITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIASENQPV 866 (1012)
Q Consensus 788 KqtVMT~vYGvT~~Gar~QI~~~L~~~~~-~~d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~~~~pV 866 (1012)
|..+--..||.+..|..+++.... |. ++.+ + |+.+.+...+.||+ +..|..+.- +.. ..
T Consensus 162 K~~~fg~~YG~g~~~L~~~l~~~~---g~~~s~~-e--------A~~~~~~f~~~~p~---v~~~~~~~~---a~~--~g 221 (324)
T cd08639 162 KAVNFGLIYGMSAKGLREYARTNY---GVEMSLE-E--------AEKFRESFFFFYKG---ILRWHHRLK---AKG--PI 221 (324)
T ss_pred hhHHHHHHhCCchHHHHHHHhhhc---CcCCCHH-H--------HHHHHHHHHHhChh---HHHHHHHHH---Hhh--cC
Confidence 999999999999999988774322 22 2211 1 23344444556665 456665422 211 12
Q ss_pred EEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCccchhhhhHHHHHHHH-HHh----hcCCc-E
Q 001795 867 RWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-ACR----DAGLH-F 940 (1012)
Q Consensus 867 ~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~af~PNFIHSLDAsHmmlta~-~~~----~~Gi~-F 940 (1012)
..+|+.|-...-+ ....--+.|++=+=-|+=++..|. .+. ..+.. .
T Consensus 222 ~v~Tl~GRrr~~~----------------------------~~~~r~avN~~IQGsaADi~K~ami~i~~~l~~~~~~lv 273 (324)
T cd08639 222 EVRTLLGRRRVFE----------------------------YFTFTEALNYPIQGTGADILKLALALLVDRLKDLDAKIV 273 (324)
T ss_pred eEECCCCCeeccc----------------------------chhhhhHhhhhhhhHHHHHHHHHHHHHHHHHhcCCCeEE
Confidence 3467777422210 000111556655555555544432 222 23554 4
Q ss_pred EEeeccccCCC--CChhHHHHHHHHHH
Q 001795 941 AGVHDSFWTHA--CDVDEMNQILRKKF 965 (1012)
Q Consensus 941 asVHDSFwThA--~dvd~M~~ilRe~F 965 (1012)
..|||++.... ..++...+++++.+
T Consensus 274 l~VHDElv~ev~~~~~~~~~~~i~~~M 300 (324)
T cd08639 274 LCVHDEIVLEVPEDEAEEAKKILESSM 300 (324)
T ss_pred eeeceeeeeecCHHHHHHHHHHHHHHH
Confidence 56999988764 33444445555544
No 17
>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=39.03 E-value=21 Score=41.88 Aligned_cols=196 Identities=21% Similarity=0.229 Sum_probs=117.4
Q ss_pred ccccccCCCcchhhHHHHhhCChhhhcccCcCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhccccccc
Q 001795 707 HLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKL 786 (1012)
Q Consensus 707 ~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~i~RKv 786 (1012)
+.-|..|.|-==|=.+|.|.+|....++.+ ...|+|..+|..+...-.++ .....|+.
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 346888999888889999999998766654 45799999877653221110 23468999
Q ss_pred ccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcE
Q 001795 787 VKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIASENQPV 866 (1012)
Q Consensus 787 VKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~~~~pV 866 (1012)
.|..+--..||.+..|..+++. ++.+ -|+.+.++..+.||+ +..|..++.......+ .|
T Consensus 213 aK~~~~g~~YG~g~~~la~~l~--------~s~~---------eA~~~~~~f~~~~p~---v~~~~~~~~~~a~~~g-~v 271 (383)
T PF00476_consen 213 AKTVNFGLIYGMGAKGLAEQLG--------ISEE---------EAKELIDAFFEAFPG---VKKWMERVKKRARENG-YV 271 (383)
T ss_dssp HHHHHHHHHTT-THHHHHHHHT--------SCHH---------HHHHHHHHHHHHSHH---HHHHHHHHHHHHHHHS-EE
T ss_pred HhHHHHhhhhccCHHHHHHHcc--------CCHH---------HHHHHHHHHHHhCch---HHHHHHHHHHHHhcCC-eE
Confidence 9999999999999988887663 2222 245667777778888 4555555544333222 12
Q ss_pred EEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhh--hccCCCccchhhhhHHHHHHH---H--HHhhcCC-
Q 001795 867 RWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQ--RTAFPPNFVHSLDGSHMMMTA---V--ACRDAGL- 938 (1012)
Q Consensus 867 ~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ--~~af~PNFIHSLDAsHmmlta---~--~~~~~Gi- 938 (1012)
+|..|-.- .+.. .+..+.... .--.+.|++=+-=|+=++..+ + .+.+.|+
T Consensus 272 --~t~~gr~r-------------------~~p~-~~~~~~~~~~~~~r~a~N~~iQgsaAdi~k~am~~i~~~l~~~~~~ 329 (383)
T PF00476_consen 272 --ETLFGRRR-------------------YLPN-IDSRNKSLRASAERQAVNTPIQGSAADIMKLAMIRIHEALREKGLG 329 (383)
T ss_dssp --ECTTSSEE-------------------ECGG-GGSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-S
T ss_pred --EEeccccc-------------------cCCc-hhcccchhhhHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhcCcC
Confidence 34444322 1111 011121111 111256766555555444332 2 2344444
Q ss_pred --cEEEeeccccC--CCCChhHHHHHHHHHHHH
Q 001795 939 --HFAGVHDSFWT--HACDVDEMNQILRKKFVE 967 (1012)
Q Consensus 939 --~FasVHDSFwT--hA~dvd~M~~ilRe~FV~ 967 (1012)
-+..|||+++. +...++.+..+|++.+..
T Consensus 330 ~~l~l~VHDEli~ev~~~~~~~v~~~l~~~M~~ 362 (383)
T PF00476_consen 330 ARLVLQVHDELIFEVPEDEAEEVAEILKEIMEN 362 (383)
T ss_dssp EEEEEEESSEEEEEEEGGGHHHHHHHHHHHHHT
T ss_pred ceeEEEEcCeeheeecHhHHHHHHHHHHHHHHh
Confidence 35679999875 446678888888877654
No 18
>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=33.02 E-value=69 Score=30.48 Aligned_cols=56 Identities=21% Similarity=0.483 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HcccCCCChhHHHHHHHHHHHHH
Q 001795 173 RKFNLLRRRQVKQETEAWERMVDEYKELEAKMI---EKRLAPNLPHIKGLFLGWFGPLS 228 (1012)
Q Consensus 173 ~~~~~l~~RQ~~lE~~~~~~a~~r~~~~~~~~~---~~g~a~~~~~~~~ll~~w~~~L~ 228 (1012)
..|.+..+|...|..+.++....+|.+.++++. +.|..++.+-++.++.+|+..+.
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 666666667667777777777777777766655 57888999999999999999665
No 19
>PLN03188 kinesin-12 family protein; Provisional
Probab=23.33 E-value=2.1e+03 Score=29.94 Aligned_cols=44 Identities=23% Similarity=0.254 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccCccchhhhhccCChhHHHHHH
Q 001795 220 FLGWFGPLSEAIEREQKMQRTKKQKAAYAPHIELLPADKVAVIV 263 (1012)
Q Consensus 220 l~~w~~~L~~~I~~e~~~~~~~~~r~~y~p~L~~l~~e~lA~It 263 (1012)
|..-+..+.+.|+.-.++..+.|.+..-..|++.|-+|--|.=+
T Consensus 1126 ll~~hr~i~egi~dvkkaaakag~kg~~~~f~~alaae~s~l~~ 1169 (1320)
T PLN03188 1126 LLARHRRIQEGIDDVKKAAARAGVRGAESKFINALAAEISALKV 1169 (1320)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHH
Confidence 33445556666666555555566666667888887666444333
Done!