Query 001792
Match_columns 1012
No_of_seqs 249 out of 442
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 09:26:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001792.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001792hhsearch_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 8E-244 2E-248 2082.8 76.5 857 140-1012 202-1088(1088)
2 PHA00452 T3/T7-like RNA polyme 100.0 4E-208 8E-213 1856.4 86.5 787 176-1012 3-807 (807)
3 COG5108 RPO41 Mitochondrial DN 100.0 2E-196 4E-201 1644.6 60.1 803 180-1012 251-1117(1117)
4 PF00940 RNA_pol: DNA-dependen 100.0 7E-123 2E-127 1055.9 20.0 388 620-1012 1-405 (405)
5 PF14700 RPOL_N: DNA-directed 100.0 1.5E-47 3.2E-52 423.1 23.8 305 180-498 1-318 (318)
6 smart00482 POLAc DNA polymeras 90.8 0.33 7.2E-06 51.9 5.0 192 691-950 3-202 (206)
7 COG5108 RPO41 Mitochondrial DN 88.4 0.31 6.8E-06 59.3 2.9 75 779-857 860-934 (1117)
8 cd08637 DNA_pol_A_pol_I_C Poly 84.4 4.9 0.00011 47.0 9.9 209 691-967 140-358 (377)
9 cd08638 DNA_pol_A_theta DNA po 83.4 4.5 9.7E-05 47.3 9.0 211 691-969 129-354 (373)
10 PRK14975 bifunctional 3'-5' ex 81.7 3.3 7.1E-05 50.8 7.3 192 708-966 326-527 (553)
11 TIGR00593 pola DNA polymerase 76.6 11 0.00025 48.8 10.1 196 708-967 659-865 (887)
12 cd08642 DNA_pol_A_pol_I_A Poly 76.1 15 0.00031 43.4 10.0 186 691-955 159-345 (378)
13 cd08640 DNA_pol_A_plastid_like 74.7 8.7 0.00019 45.0 7.7 212 708-967 120-349 (371)
14 cd08643 DNA_pol_A_pol_I_B Poly 73.2 11 0.00024 45.0 8.2 198 708-969 188-406 (429)
15 cd08639 DNA_pol_A_Aquificae_li 68.4 25 0.00055 40.5 9.5 188 708-965 104-300 (324)
16 PRK05755 DNA polymerase I; Pro 68.2 16 0.00035 47.3 8.8 209 691-967 640-858 (880)
17 PLN03188 kinesin-12 family pro 47.8 7.2E+02 0.016 34.1 18.0 45 220-264 1126-1170(1320)
18 PF00476 DNA_pol_A: DNA polyme 39.2 22 0.00047 41.7 2.8 196 707-967 155-362 (383)
19 PF07739 TipAS: TipAS antibiot 30.9 78 0.0017 30.1 4.7 56 173-228 13-71 (118)
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=7.8e-244 Score=2082.84 Aligned_cols=857 Identities=58% Similarity=0.973 Sum_probs=797.8
Q ss_pred cceeecCCCchhHHHhh-----hhhhhhh---HHHHhhhhHH-HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHccc
Q 001792 140 RRIFVQDPPWFSSIFLK-----GLYKRIK---LQEYREMKKR-KFNLLRRRQVKQETEAWERMVDEYK-ELEAKMIEKRL 209 (1012)
Q Consensus 140 ~~~~~~~~~~~~~~~~~-----~~~~~~~---~~~~~~~~~~-~~~~l~eRQ~~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 77779999999
Q ss_pred CCCChh-HHHHHHHHHHHHHHHHHHHHHHHhhc--cCccchhhhhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHH
Q 001792 210 APNLPH-IKGLFLGWFGPLSEAIEREQKMQRTK--KQKAAYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAA 286 (1012)
Q Consensus 210 a~~~~~-~~~ll~~w~~~L~~~I~~e~~~~~~~--~~r~~y~p~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~a 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 001792 287 VHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVNSLIKSKRVMEAQKLLKN-EETKPWGRDTQAKL 365 (1012)
Q Consensus 287 ~~IG~aVe~E~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~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 999999999999999988654322211 111124556667778888877776666655555 56789999999999
Q ss_pred HHHHHHHHHHHccccCCCCCCCCCCCCccCceeEeeeeeecCCCCCcceeEEEEecCHHHHHHHHhhhhcccCCCCceee
Q 001792 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 999999999999999999988778889999999999965 44434789999999999999999988888999999999
Q ss_pred CCCCCcCCCCceecccCccceecCCcHHHHHHH-HhccccChHHHHHHHHhhcCceeEEcHHHHHHHHHHHHcCCCCCCC
Q 001792 446 PPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEAL-KSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGL 524 (1012)
Q Consensus 446 pPkpW~~~~~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 4456889999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCC
Q 001792 525 VDRNDVLIPEKP-LSEDMTEVQKWKWSVRKAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHL 603 (1012)
Q Consensus 525 ~~~~~~p~P~~p-~~~d~~~~~~wk~~~~~~~~~~~~~~S~R~~~~~~L~iA~~f~~~~~fYfP~nlDFRGR~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 CCCCccchhhhhhcccCccCCcchhHHHHHHHHHhhCCCCCCCCHHHHHHHHHHhHHHHHHhhcCCCCCchhhhcCCChH
Q 001792 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 HHHHHHHHHHHHHhcCCCCcceeccccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcC
Q 001792 684 QCLAACINLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSN 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 001792 764 KDPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFE 843 (1012)
Q Consensus 764 ~d~~~~~~~~~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-CCccchhhhhccCCCcchhhh
Q 001792 844 AARSIMGWLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQ-RE-GNLVEIRKQRTAFPPNFVHSL 921 (1012)
Q Consensus 844 ~A~~im~WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~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 44 789999999999999999999
Q ss_pred hhHHHHHHHHHHhhcCCcEEEeeccccCCCCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHh------------CCCCC
Q 001792 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 55678
Q ss_pred CCCCCCCCCCChhhhccCCCCCC
Q 001792 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=3.5e-208 Score=1856.36 Aligned_cols=787 Identities=33% Similarity=0.549 Sum_probs=703.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCccchhhhhccCC
Q 001792 176 NLLRRRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQRTKKQKAAYAPHIELLP 255 (1012)
Q Consensus 176 ~~l~eRQ~~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 35889999999999999999999999999999999999999999999999999999999999877888999999999999
Q ss_pred hhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHHHH
Q 001792 256 ADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVNS 335 (1012)
Q Consensus 256 ~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~a~~IG~aVe~E~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 4569999999999999999999999877665433211 0112222333
Q ss_pred HHHHHH-HHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHc-cccCCCCCCCCCCCCccCceeEeeeeeecCCCCCcc
Q 001792 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 222333333334889999999999999999999996 55542111 0111 3
Q ss_pred eeEEEEecCHHHHHHHHhhhhc---ccCCCCceeeCCCCCcCCCCceecccC---ccceecCCcHHHHHHHHhccccChH
Q 001792 414 KRYGVVECDPLVLEGLDRSAKH---MLIPYVPMLVPPKKWKGYNKGGYLFLP---SYVMRTHGSRKQQEALKSVTGNCMK 487 (1012)
Q Consensus 414 k~~gvi~~~~~~~~~l~~~~~~---~~~~~lPMlvpPkpW~~~~~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 567888776555433 348999
Q ss_pred HHHHHHHhhcCceeEEcHHHHHHHHHHHHcCCCCCCCCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHHHhhhhh
Q 001792 488 KVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRNDVLIPEKPLS--EDMTEVQKWKWSVRKAKKINQERHSQR 565 (1012)
Q Consensus 488 ~v~~aLN~Lqst~wrIN~~VL~vi~~~w~~g~~i~~l~~~~~~p~P~~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 hhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCccchhhhhhcccCccCCcchhHHHHHHHHHhhCCCCCC
Q 001792 566 CDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANLFSGGVEK 645 (1012)
Q Consensus 566 ~~~~~~L~iA~~f~~~~~fYfP~nlDFRGR~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 CCHHHHHHHHHHhHHHHHHhhcCCCCCchhhhcCCChHHHHHHHHHHHHHHhcCCCCcceeccccccCCCCchhhHHHHh
Q 001792 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 99999999999999999999999887 99999999999999999999999
Q ss_pred cCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccccccceeeecccchhhHHH
Q 001792 726 GRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGARE 805 (1012)
Q Consensus 726 ~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~~~~~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 1223345678889999999999999999999999999
Q ss_pred HHHHHHHHcCCCCChhhH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCcEEEEcCCCCeEEEeecc
Q 001792 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---EEEEecCCCccchhhhhccCCCcchhhhhhHHHHHHHHHHhhcCC-cEEEeeccccCCCCChhHHH
Q 001792 883 NERHLIRTSLQ---VLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAVACRDAGL-HFAGVHDSFWTHACDVDEMN 958 (1012)
Q Consensus 883 ~~~~~I~t~lq---~l~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 001792 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=1.9e-196 Score=1644.64 Aligned_cols=803 Identities=38% Similarity=0.632 Sum_probs=715.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHH-Hh---------hccCccchhh
Q 001792 180 RRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKM-QR---------TKKQKAAYAP 249 (1012)
Q Consensus 180 eRQ~~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 7899999999999999999999999998865444457889999999999999988874 22 2457899999
Q ss_pred hhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHH
Q 001792 250 HIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELL 329 (1012)
Q Consensus 250 ~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~a~~IG~aVe~E~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~ 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 999999999999999999999999888999999999999999999999999987665543321111 001112
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCC--CCCccCceeEeeeeeecC
Q 001792 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 ----HNAVHNKRSMTRHAKHKGAEWQDWPQDIKAKVGSVALCLLLSVAKIEVKLIDIATEQTLKGEFEAFRHSYQYH--- 475 (1117)
T ss_pred ----HHHHHHHHhhhhhhhhcCcchhcChHHHHHHhhHHHHHHHHHhhhheeEeeechhhchhhhhHHHHHHhhhhc---
Confidence 22222222111123455678999999999999999999999999999876654332 234679999999986
Q ss_pred CCCCcceeEEEEecCHHHHHHHHhhhh--cccCCCCceeeCCCCCcCCCCceecccCccceecCCcHHHHHHHHhcc-cc
Q 001792 408 PGQKTTKRYGVVECDPLVLEGLDRSAK--HMLIPYVPMLVPPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEALKSVT-GN 484 (1012)
Q Consensus 408 ~g~~~~k~~gvi~~~~~~~~~l~~~~~--~~~~~~lPMlvpPkpW~~~~~GGYl~~~~~~~R~~~s~~q~~~l~~~~-~~ 484 (1012)
+ ++++|||.+|..+...+.+... .+.+-+|||||||+||+++.+|||++....++|..++.+|-+|+..++ .+
T Consensus 476 N----g~kigvv~~h~tl~~ll~~~~~~a~l~PqlLPmLV~PkPWtsw~~GGY~y~r~~llRlk~t~eqv~yl~~aseng 551 (1117)
T COG5108 476 N----GTKIGVVATHETLDWLLTENSRLAPLSPQLLPMLVPPKPWTSWFRGGYWYGRVRLLRLKKTGEQVRYLLMASENG 551 (1117)
T ss_pred C----CceeEEEeeHHHHHHHhhcccccCCCChhhhccccCCCCCcCcccCceeeccceeeeecCcHHHHHHHHHhhhcC
Confidence 4 4689999999998887766543 233348999999999999999999999999999999999999987764 78
Q ss_pred ChHHHHHHHHhhcCceeEEcHHHHHHHHHHHHcCCCCCCCCCCCC-CCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHhh
Q 001792 485 CMKKVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRND-VLIPEKP-LSEDMTEVQKWKWSVRKAKKINQERH 562 (1012)
Q Consensus 485 ~l~~v~~aLN~Lqst~wrIN~~VL~vi~~~w~~g~~i~~l~~~~~-~p~P~~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 3345544 56789999999999999999999999
Q ss_pred hhhhhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCccchhhhhhcccCccCCcchhHHHHHHHHHhhCCC
Q 001792 563 SQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANLFSGG 642 (1012)
Q Consensus 563 S~R~~~~~~L~iA~~f~~~~~fYfP~nlDFRGR~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 CCCCCHHHHHHHHHHhHHHHHHhhcCCCCCchhhhcCCChHHHHHHHHHHHHHHhcCCCCcceeccccccCCCCchhhHH
Q 001792 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 HHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccccccceeeecccchhh
Q 001792 723 AALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVG 802 (1012)
Q Consensus 723 AAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~~~~~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 001792 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 22221 2334578999999999999999999999999999998854 24
Q ss_pred CcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecC--CCccchhhhhccCCCcchhhhhhHHHHHHHHHHhhcCCcEE
Q 001792 864 QPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE--GNLVEIRKQRTAFPPNFVHSLDGSHMMMTAVACRDAGLHFA 941 (1012)
Q Consensus 864 ~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~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 7999999999999999999999999999999888764 56899999999999999999999999999999999999999
Q ss_pred EeeccccCCCCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHhCCC--------------------------CCCCCCCC
Q 001792 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 001792 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=7.2e-123 Score=1055.92 Aligned_cols=388 Identities=55% Similarity=0.975 Sum_probs=339.3
Q ss_pred CccCCcchhHHHHHHHHHhhCCCCCCCCHHHHHHHHHHhHHHHHHhhcCCCCCchhhhcCCChHHHHHHHHHHHHHHhcC
Q 001792 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 CCCcceeccccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhh
Q 001792 700 SPHSVISHLPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILI 779 (1012)
Q Consensus 700 ~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~~~~~ak~l~ 779 (1012)
+|++|+||+||||||||||||||||||||.+||++|||+|+++|+|||+.|++.|.+.+.+++... +....+++++.
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 cccccccccccceeeecccchhhHHHHHHHHHHHcCCCC-ChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001792 780 DQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHIT-DDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKV 858 (1012)
Q Consensus 780 ~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~-d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~WL~~~A~~ 858 (1012)
.+|+||+|||+|||+|||||.+|+++||+++|++.+... +....++++.|||+.|+++|+++|++|+.+|+||++||++
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 001792 859 IASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE--GNLVEIRKQRTAFPPNFVHSLDGSHMMMTAVACRDA 936 (1012)
Q Consensus 859 i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~l~~~--~d~vd~rKq~~Af~PNFIHSLDAsHmmlta~~~~~~ 936 (1012)
+++++.||.|+||+||||+|+|++.++++|+|.++....... .+.+|++||++||||||||||||||||||+.+|.+.
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 999999999999999999999999999999998753322221 234599999999999999999999999999999999
Q ss_pred CCcEEEeeccccCCCCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHhCCC--------------CCCCCCCCCCCCChh
Q 001792 937 GLHFAGVHDSFWTHACDVDEMNQILRKKFVELYNMPMLENLLESFQTSYPT--------------LSFPPLPERGNFDLE 1002 (1012)
Q Consensus 937 Gi~FasVHDSFwThA~dvd~M~~ilRe~FV~Lys~~il~~l~e~f~~~~~~--------------~~~p~~P~~G~LDL~ 1002 (1012)
|++|++||||||||||||+.|+++||++||+||++++|++|+++|..+++. +.+|++|++|+|||+
T Consensus 316 ~~~f~~VHDsf~tha~~~~~L~~~lRe~Fv~lys~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~P~~G~ldl~ 395 (405)
T PF00940_consen 316 GIPFATVHDSFWTHACDVDTLNEILREQFVELYSPDILEDFAEDFKARLPDSYQNIWEKKNEFVPIKFPPLPERGDLDLN 395 (405)
T ss_dssp T--EEECTTEEEEEHHHHHHHHHHHHHHHHHHHHCTHHHHHHHHHHCCCTGGTTSHHHHH--HHCCCCHS-----S-SGG
T ss_pred CCeEEEEehhhhcCHHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHhhhhhccccccchhhhhccCCCCCCCCCccHH
Confidence 999999999999999999999999999999999999999999999999986 789999999999999
Q ss_pred hhccCCCCCC
Q 001792 1003 EVLESPYFFN 1012 (1012)
Q Consensus 1003 ~Vl~S~YFF~ 1012 (1012)
+|++|+||||
T Consensus 396 ~V~~S~YfFs 405 (405)
T PF00940_consen 396 EVLKSEYFFS 405 (405)
T ss_dssp GGGG-TTTBB
T ss_pred HHhCCCCCCC
Confidence 9999999997
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=1.5e-47 Score=423.11 Aligned_cols=305 Identities=32% Similarity=0.559 Sum_probs=219.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHHh----hccCccchhhhhccCC
Q 001792 180 RRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQR----TKKQKAAYAPHIELLP 255 (1012)
Q Consensus 180 eRQ~~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 3577899999999999
Q ss_pred hhHHHHHHHHHHHHHHhcC-CCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHHH
Q 001792 256 ADKVAVIVMHKMMGLVMAG-HEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVN 334 (1012)
Q Consensus 256 ~e~lA~Iti~~~l~~~~~~-~~~~~~~~~~~a~~IG~aVe~E~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 9999999999999999844 455678999999999999999999998776644332211110000000000 001111
Q ss_pred HHHHHHHHHHHHHhhcCCCCCC--CCHHHHHHHHHHHHHHHHHHccccCCCCCCCCCCCCccCceeEeeeeeecCCCCCc
Q 001792 335 SLIKSKRVMEAQKLLKNEETKP--WGRDTQAKLGSRLVELLIETAYVQHPVNPADYSPPDVRPAFRHRFKTILKHPGQKT 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 111110000000000 123444 99999999999999999999999987754322 56799999999875 3
Q ss_pred ceeEEEEecCHHHHHHHHhhhhcc-----cCCCCceeeCCCCCcCCCCceecccCccceecCCcHHHHHHHH-hccccCh
Q 001792 413 TKRYGVVECDPLVLEGLDRSAKHM-----LIPYVPMLVPPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEALK-SVTGNCM 486 (1012)
Q Consensus 413 ~k~~gvi~~~~~~~~~l~~~~~~~-----~~~~lPMlvpPkpW~~~~~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 357899999999999998875421 25599999999999999999999999999999887 5545554 4467899
Q ss_pred HHHHHHHHhhcC
Q 001792 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=90.77 E-value=0.33 Score=51.87 Aligned_cols=192 Identities=20% Similarity=0.213 Sum_probs=115.2
Q ss_pred HHHHHHhcCCCCcceeccccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001792 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (1012)
Q Consensus 691 El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~ 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 34455442 2344 47889999988999999999998877766 3569999998765322110
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001792 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 235566666777777 667
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCcchhhhhhHHHHHHH
Q 001792 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 930 (1012)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~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 256666433211100 111222222223367876665666544433
Q ss_pred H-H----HhhcCC--c-EEEeeccccCC
Q 001792 931 V-A----CRDAGL--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 2 223333 3 45699998654
No 7
>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]
Probab=88.45 E-value=0.31 Score=59.27 Aligned_cols=75 Identities=28% Similarity=0.414 Sum_probs=58.9
Q ss_pred hcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001792 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 12455556889999999999999999999999999999997765
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=84.38 E-value=4.9 Score=46.99 Aligned_cols=209 Identities=15% Similarity=0.221 Sum_probs=122.3
Q ss_pred HHHHHHhcCCCCcceeccccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001792 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (1012)
Q Consensus 691 El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~ 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 57889998888889999999999888876 3579999988765321 00
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001792 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 135566666777777 555
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCcchhhhhhHHHHHHH
Q 001792 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 930 (1012)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~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--c-EEEeeccccCC--CCChhHHHHHHHHHHHH
Q 001792 931 V-A----CRDAGL--H-FAGVHDSFWTH--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 333343 3 55699998755 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=83.40 E-value=4.5 Score=47.28 Aligned_cols=211 Identities=19% Similarity=0.201 Sum_probs=126.4
Q ss_pred HHHHHHhcCCCCcceeccccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001792 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (1012)
Q Consensus 691 El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~ 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-----SGGDVFKMIAAQWLGKPV----------- 187 (373)
T ss_pred hhhheeeCC--CCC---EEEEechhhhHHHHHHHHhCCHHHHHHHh-----cCCCHHHHHHHHHhCCCh-----------
Confidence 455555422 343 57899999999999999999999888775 257999998876532100
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001792 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 2455666677788874 55
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCcchhhhhhHHHHHHH
Q 001792 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 930 (1012)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~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 255554332221111 01111112223566877666666555443
Q ss_pred H-HHh----h-------cCCc-EEEeeccccC--CCCChhHHHHHHHHHHHHhc
Q 001792 931 V-ACR----D-------AGLH-FAGVHDSFWT--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 1233 5569999764 55667777788888774443
No 10
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=81.74 E-value=3.3 Score=50.79 Aligned_cols=192 Identities=19% Similarity=0.154 Sum_probs=119.6
Q ss_pred cccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccc
Q 001792 708 LPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 787 (1012)
Q Consensus 708 lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~~~~~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 47889999999999999999999988887 3679999998877211 100 0 3459999
Q ss_pred cccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcEE
Q 001792 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 134555666677776 6677777776655442 12
Q ss_pred EEcCCCCeEEEeeccCcceeEEeeeEEEEEecC-CCccchhhhhccCCCcchhhhhhHHHHHHHH-HHhh-----cCCc-
Q 001792 868 WTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE-GNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-ACRD-----AGLH- 939 (1012)
Q Consensus 868 WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~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 244443211 1110 1111222223334679966555555554432 2222 2333
Q ss_pred EEEeeccccCCC--CChhHHHHHHHHHHH
Q 001792 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 445666677776663
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=76.61 E-value=11 Score=48.78 Aligned_cols=196 Identities=17% Similarity=0.207 Sum_probs=120.4
Q ss_pred cccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccc
Q 001792 708 LPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 787 (1012)
Q Consensus 708 lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~~~~~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 012249999
Q ss_pred cccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcEE
Q 001792 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 33 221 134455555667776 67787777766655541 2
Q ss_pred EEcCCCCeEEEeeccCcceeEEeeeEEEEEecC-CCccchhhhhccCCCcchhhhhhHHHHHHHH-----HHhhcCC--c
Q 001792 868 WTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE-GNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-----ACRDAGL--H 939 (1012)
Q Consensus 868 WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~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 35555210 11110 1111122222235678877766665554432 2445674 3
Q ss_pred -EEEeeccccC--CCCChhHHHHHHHHHHHH
Q 001792 940 -FAGVHDSFWT--HACDVDEMNQILRKKFVE 967 (1012)
Q Consensus 940 -FasVHDSFwT--hA~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 4459999765 446677788888887754
No 12
>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=76.15 E-value=15 Score=43.36 Aligned_cols=186 Identities=15% Similarity=0.050 Sum_probs=109.1
Q ss_pred HHHHHHhcCCCCcceeccccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001792 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (1012)
Q Consensus 691 El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~ 770 (1012)
+++.++.. |.++ .-|..|-|.==|-.+|.|.+|...-++-| ...|||+..|..+-..=.++.
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 34555542 2343 35889999999999999999999877765 578999999887742210000
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001792 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 2343 221 1 23445555677777554333
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCcchhhhhhHHHHHHH
Q 001792 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 930 (1012)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~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 33333544434432 2211 0111 11445544344344444
Q ss_pred HHHhhcCCc-EEEeeccccCCCCChh
Q 001792 931 VACRDAGLH-FAGVHDSFWTHACDVD 955 (1012)
Q Consensus 931 ~~~~~~Gi~-FasVHDSFwThA~dvd 955 (1012)
+.+.+.|.. +..|||..-.+..+.+
T Consensus 320 i~l~~~g~~ivLqVHDElv~Evp~~~ 345 (378)
T cd08642 320 LRLEKAGYDIVMHVHDEVVIEVPEGE 345 (378)
T ss_pred HHHHhcCCeEEEEECceeEEeeccch
Confidence 456667775 4469999999988743
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=74.72 E-value=8.7 Score=45.03 Aligned_cols=212 Identities=20% Similarity=0.127 Sum_probs=120.5
Q ss_pred cccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCC--------CCCCChhHHHHHHhh
Q 001792 708 LPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNK--------DPSKHPQALLAKILI 779 (1012)
Q Consensus 708 lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~--------d~~~~~~~~~ak~l~ 779 (1012)
.-|..|-|-==|-.+|.|.+|....++.| .-.|||+..|..+-....++..+ +.+.++....+. .
T Consensus 120 ~lv~aDySQiElRvlA~lS~D~~Li~af~-----~g~DiH~~tA~~if~~~~e~v~~~~~~~~~~~~~~~~~~~~~~--~ 192 (371)
T cd08640 120 TLIVADYSQLELRLLAHMTRCKSMIEAFN-----AGGDFHSRTASGMYPHVAEAVANGEVLLEWKSEGKPPAPLLKD--K 192 (371)
T ss_pred EEEEechhhhhHHHHHHHcCCHHHHHHHH-----cCCCHHHHHHHHHhCCCHHHhcccccccccccccccccccccc--c
Confidence 35889999999999999999999888776 34699999887654332211110 000000000000 0
Q ss_pred cccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001792 780 DQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVI 859 (1012)
Q Consensus 780 ~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~ylak~v~~ai~e~f~~A~~im~WL~~~A~~i 859 (1012)
..-.|+..|...--.+||.+..|...++ |+ +.+ -|+.+.+...+.||+ +..|.+++....
T Consensus 193 ~~~~R~~AK~infGi~YG~g~~~La~~l-------gi-s~~---------eA~~~i~~f~~~fP~---v~~~~~~~~~~a 252 (371)
T cd08640 193 FKSERRKAKVLNFSIAYGKTAHGLAKDW-------KV-KLK---------EAERTVDAWYSDRPE---VEQWQKKTKKEA 252 (371)
T ss_pred cHHHHHHHHHHHHHHHhccchhHHHHHc-------CC-CHH---------HHHHHHHHHHHHCcc---HHHHHHHHHHHH
Confidence 1345999999999999999999887643 33 221 135566666777877 567777766655
Q ss_pred HcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCcchhhhhhHHHHHHHH-HHh----
Q 001792 860 ASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-ACR---- 934 (1012)
Q Consensus 860 ~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~l~~~~d~vd~rKq~~Af~PNFIHSLDAsHmmlta~-~~~---- 934 (1012)
.+.| .| +|++|-...=|--.+ .+ ...+.+.--.+-|++=+==|+=++..|. .+.
T Consensus 253 ~~~G-yv--~T~~GRrr~lp~i~s-----------------~~-~~~~~~~eR~avN~~IQGsAADI~K~Ami~i~~~l~ 311 (371)
T cd08640 253 RERG-YT--RTLLGRYRYLPDIKS-----------------RN-RKKRGHAERAAINTPIQGSAADIAMKAMLRIYRNLR 311 (371)
T ss_pred HHcC-cE--EccCCCEEECCCccc-----------------cc-HhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHHHHh
Confidence 4443 22 256554322110000 00 0001111112557766666666655442 221
Q ss_pred --hcCCc-EEEeeccccCC--CCChhHHHHHHHHHHHH
Q 001792 935 --DAGLH-FAGVHDSFWTH--ACDVDEMNQILRKKFVE 967 (1012)
Q Consensus 935 --~~Gi~-FasVHDSFwTh--A~dvd~M~~ilRe~FV~ 967 (1012)
..|.. ...|||+.+.. ...++....+|++.+.+
T Consensus 312 ~~~~~~~lvlqVHDElv~evp~~~~~~~~~~v~~~Me~ 349 (371)
T cd08640 312 LKRLGWKLLLQIHDEVILEGPEEKADEALKIVKDCMEN 349 (371)
T ss_pred hccCCceEEEEEcceeEEEcCHHHHHHHHHHHHHHHHh
Confidence 23444 45699998864 44555666777776644
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=73.21 E-value=11 Score=45.03 Aligned_cols=198 Identities=14% Similarity=0.009 Sum_probs=116.7
Q ss_pred cccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccc
Q 001792 708 LPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 787 (1012)
Q Consensus 708 lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~~~~~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 47888998888888999999876666655332 358877655431 11469999
Q ss_pred cccceeeecccchhhHHHHHHHHHHHcC-C---CC---ChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001792 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 KTFIYAFLYGAGDEKLGQIVGDDLRTAKNLNAEWPQTKKGTIKKIADKAKGRVVRANFLKGLPALG---KLIKKVKEAAK 316 (429)
T ss_pred HHHHHHHHHCCChhHHHHHhCCCHHHHHhhhhcccccccchhhhhhhhhhHHHHHHHHHHhCccHH---HHHHHHHHHHH
Confidence 9999999999999999887643222110 0 00 0000111223344555566666677754 45555444433
Q ss_pred cCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCcchhhhhhHHHHHHHH-----HHhh
Q 001792 861 SENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-----ACRD 935 (1012)
Q Consensus 861 ~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~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 2455552211 00 011 1456665555665554432 2333
Q ss_pred cC----C--c-EEEeeccc--cCCCCChhHHHHHHHHHHHHhc
Q 001792 936 AG----L--H-FAGVHDSF--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 2 45699998 7788889999999999886653
No 15
>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=68.41 E-value=25 Score=40.47 Aligned_cols=188 Identities=20% Similarity=0.190 Sum_probs=109.4
Q ss_pred cccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccc
Q 001792 708 LPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 787 (1012)
Q Consensus 708 lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~~~~~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 57899999999999999999999888765 356999999876522100 000 12259999
Q ss_pred cccceeeecccchhhHHHHHHHHHHHcCC-CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcE
Q 001792 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 999999999999999988775322 22 2211 1 23333444555555 456655422 211 12
Q ss_pred EEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCcchhhhhhHHHHHHHH-HHh----hcCCc-E
Q 001792 867 RWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-ACR----DAGLH-F 940 (1012)
Q Consensus 867 ~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~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 000111556655555555554432 222 23554 4
Q ss_pred EEeeccccCCC--CChhHHHHHHHHHH
Q 001792 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 46999988664 33444445555544
No 16
>PRK05755 DNA polymerase I; Provisional
Probab=68.19 E-value=16 Score=47.34 Aligned_cols=209 Identities=17% Similarity=0.207 Sum_probs=123.4
Q ss_pred HHHHHHhcCCCCcceeccccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001792 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (1012)
Q Consensus 691 El~~a~~~~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~ 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 001792 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 245566666777777 566
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhhhccCCCcchhhhhhHHHHHHH
Q 001792 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 930 (1012)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~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 001111111122356777554444444332
Q ss_pred H-----HHhhcCC---cEEEeeccccCC--CCChhHHHHHHHHHHHH
Q 001792 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 2334454 356799998754 45567777777776543
No 17
>PLN03188 kinesin-12 family protein; Provisional
Probab=47.76 E-value=7.2e+02 Score=34.06 Aligned_cols=45 Identities=22% Similarity=0.234 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccCccchhhhhccCChhHHHHHHH
Q 001792 220 FLGWFGPLSEAIEREQKMQRTKKQKAAYAPHIELLPADKVAVIVM 264 (1012)
Q Consensus 220 l~~w~~~L~~~I~~e~~~~~~~~~r~~y~p~L~~l~~e~lA~Iti 264 (1012)
|..-+..+.+.|++-.++..+.|.+..-..|+..|-+|--|.=+=
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 344455666677765555556666666678888876665444333
No 18
>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=39.24 E-value=22 Score=41.70 Aligned_cols=196 Identities=21% Similarity=0.230 Sum_probs=117.6
Q ss_pred ccccccCCCCchhhHHHHhcCChhhhhhcccCCCCCccchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhccccccc
Q 001792 707 HLPIHQDGSCNGLQHYAALGRNTVEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKL 786 (1012)
Q Consensus 707 ~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~d~~~~~~~~~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 457888998888889999999998766655 45799998877653221110 23468999
Q ss_pred ccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcE
Q 001792 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 245566777778887 4555555544333222 12
Q ss_pred EEEcCCCCeEEEeeccCcceeEEeeeEEEEEecCCCccchhhh--hccCCCcchhhhhhHHHHHHH---H--HHhhcCC-
Q 001792 867 RWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQ--RTAFPPNFVHSLDGSHMMMTA---V--ACRDAGL- 938 (1012)
Q Consensus 867 ~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~l~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 111266776655555444332 2 2444444
Q ss_pred --cEEEeeccccC--CCCChhHHHHHHHHHHHH
Q 001792 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 456678888888887654
No 19
>PF07739 TipAS: TipAS antibiotic-recognition domain; InterPro: IPR012925 TipAL is a bacterial transcriptional regulator of the MerR family. The tipA gene can be expressed as a long form, TipAL, and a short form, TipAS, which constitutes the C-terminal part of TipAL. TipAS forms the antibiotic-recognition domain []. This domain, which has an alpha-helical globin-like fold, is also found at the C terminus of other MerR family transcription factors, including Mta, a central regulator of multidrug resistance in Bacillus subtilis [], and SkgA from Caulobacter crescentus []. ; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1NY9_A 3HH0_A 3QAO_A.
Probab=30.90 E-value=78 Score=30.09 Aligned_cols=56 Identities=21% Similarity=0.483 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HcccCCCChhHHHHHHHHHHHHH
Q 001792 173 RKFNLLRRRQVKQETEAWERMVDEYKELEAKMI---EKRLAPNLPHIKGLFLGWFGPLS 228 (1012)
Q Consensus 173 ~~~~~l~eRQ~~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 666666666667777777777777777766554 57888999999999999999665
Done!