Query 001982
Match_columns 986
No_of_seqs 254 out of 439
Neff 5.1
Searched_HMMs 46136
Date Thu Mar 28 13:50:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001982.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001982hhsearch_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 5E-236 1E-240 2013.3 74.2 832 140-986 202-1088(1088)
2 PHA00452 T3/T7-like RNA polyme 100.0 2E-200 4E-205 1784.2 83.7 763 176-986 3-807 (807)
3 COG5108 RPO41 Mitochondrial DN 100.0 1E-190 3E-195 1594.1 57.7 779 180-986 251-1117(1117)
4 PF00940 RNA_pol: DNA-dependen 100.0 2E-114 4E-119 984.2 17.2 364 620-986 1-405 (405)
5 PF14700 RPOL_N: DNA-directed 100.0 6E-48 1.3E-52 424.7 23.7 305 180-498 1-318 (318)
6 smart00482 POLAc DNA polymeras 91.7 0.26 5.6E-06 52.5 5.3 192 665-924 3-202 (206)
7 COG5108 RPO41 Mitochondrial DN 88.1 0.34 7.4E-06 58.8 2.9 76 753-832 860-935 (1117)
8 cd08637 DNA_pol_A_pol_I_C Poly 85.7 4.3 9.2E-05 47.4 10.1 209 665-941 140-358 (377)
9 cd08638 DNA_pol_A_theta DNA po 84.5 4 8.6E-05 47.5 9.1 212 664-943 128-354 (373)
10 PRK14975 bifunctional 3'-5' ex 84.1 2.6 5.6E-05 51.5 7.7 203 666-940 315-527 (553)
11 cd08642 DNA_pol_A_pol_I_A Poly 77.0 14 0.00031 43.3 10.2 185 665-928 159-344 (378)
12 cd08643 DNA_pol_A_pol_I_B Poly 76.6 4.4 9.6E-05 48.1 6.0 210 665-943 176-406 (429)
13 cd08640 DNA_pol_A_plastid_like 76.6 7.7 0.00017 45.3 7.9 223 666-941 109-349 (371)
14 TIGR00593 pola DNA polymerase 76.0 14 0.00031 47.8 10.7 208 665-941 647-865 (887)
15 PRK05755 DNA polymerase I; Pro 75.4 12 0.00026 48.4 9.9 209 665-941 640-858 (880)
16 cd08639 DNA_pol_A_Aquificae_li 71.4 22 0.00048 40.8 9.8 90 666-782 93-182 (324)
17 PF00476 DNA_pol_A: DNA polyme 43.4 19 0.0004 42.1 3.1 207 665-941 144-362 (383)
18 PF07739 TipAS: TipAS antibiot 33.7 67 0.0014 30.5 4.7 56 173-228 13-71 (118)
19 PLN03188 kinesin-12 family pro 20.9 2.3E+03 0.051 29.5 18.3 45 220-264 1126-1170(1320)
20 PF14554 VEGF_C: VEGF heparin- 20.0 53 0.0011 28.2 1.0 18 131-148 6-23 (55)
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=5e-236 Score=2013.30 Aligned_cols=832 Identities=58% Similarity=0.973 Sum_probs=770.4
Q ss_pred cceeecCCCchhHHHhh-----hhhhhhh---HHHHhhhhHH-HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHccc
Q 001982 140 RRIFVQDPPWFSSIFLK-----GLYKRIK---LQEYREMKKR-KFNLLRRRQVKQETEAWERMVDEYK-ELEAKMIEKRL 209 (986)
Q Consensus 140 ~~~~~~~~~~~~~~~~~-----~~~~~~~---~~~~~~~~~~-~~~~l~~RQ~~lE~~~~~~a~~r~~-~~~~~~~~~g~ 209 (986)
..-......|.++.+.. .....++ +...++.+.. +|-.+.+||..+|.++|++|+++|+ +...+|++..+
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 5666777766 8899999999999999999999999 77778999999
Q ss_pred CCCChh-HHHHHHHHHHHHHHHHHHHHHHHhhc--cCccchhhhhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHH
Q 001982 210 APNLPH-IKGLFLGWFGPLSEAIEREQKMQRTK--KQKAAYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAA 286 (986)
Q Consensus 210 a~~~~~-~~~ll~~w~~~L~~~I~~e~~~~~~~--~~r~~y~p~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~~ 286 (986)
++++|| +++++++||++|.++|++|++.++.. +.|..|+|||++||++++|+|||+++|+++++|++.+|+++++++
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 001982 287 VHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVNSLIKSKRVMEAQKLLKN-EETKPWGRDTQAKL 365 (986)
Q Consensus 287 ~~IG~aVe~E~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~W~~~~~~kv 365 (986)
.+||++||+|+|++.++++..+++.-. ..-.-++....++.++.++++.++.+.+..... +...+|+..++++|
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 999999999999999987654322111 111124455666777777777766655555554 56789999999999
Q ss_pred HHHHHHHHHHHccccCCCCCCCCCCCCccCceeEeeeeeecCCCCCcceeEEEEecCHHHHHHHHhhhhcccCCCCccee
Q 001982 366 GSRLVELLIETAYVQHPVNPADYSPPDVRPAFRHRFKTILKHPGQKTTKRYGVVECDPLVLEGLDRSAKHMLIPYVPMLV 445 (986)
Q Consensus 366 G~~Li~~L~e~~~i~~~~~~~~~~~~~~~paF~h~~~~~~~~~g~~~~k~~gvi~~~~~~~~~l~~~~~~~~~~~lPMlv 445 (986)
|++|+++||++++|+++.+++.++.++..|||.|+|++. +|+..+++||+|+|||.+..+|++.+.++.++++||||
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 CCCCCcCCCCcccccCCccceecCCcHHHHHHH-HhccccChHHHHHHHHhhcCcceEEcHHHHHHHHHHHHcCCCCCCC
Q 001982 446 PPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEAL-KSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGL 524 (986)
Q Consensus 446 pP~pW~~~~~GGYl~~~s~l~R~~~~~~q~~~l-~~~~~~~l~~v~~aLN~Lqst~wrIN~~VL~vi~~~w~~g~~i~~l 524 (986)
||+||++++.||||++++++||++++++|.+++ ++.+.++++.||+|||.||+||||||++||||+.++|++|+.+.++
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 5556889999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCC
Q 001982 525 VDRNDVLIPEKP-LSEDMTEVQKWKWSVRKAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHL 603 (986)
Q Consensus 525 ~~~~~~p~P~~p-~~~d~~~~~~wk~~~~~~~~~~~~~~S~R~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~L 603 (986)
+++.+.++|++| ..+|+++++.|+++.+++.+.++++||+|||++|+|+||++|+|+ .||||||||||||+||+||||
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 CCCCchhhhhhhhcccCccCCcchhhHHHHHHHhhcC-------------------------CCCCCCchhhhcCCChHH
Q 001982 604 NHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANLFS-------------------------ENPINGSRWWLTAEDPFQ 658 (986)
Q Consensus 604 n~qGsDl~RsLL~FaegkpLG~~Gl~WLKIhlANl~G-------------------------~dPl~~~~wW~~AD~PwQ 658 (986)
||.|||+|||||+||+|+|||.+||+|||||+||+|| ++||+|++||++||||||
T Consensus 673 NHLgsDlcRglLeF~~GkPLG~sGL~WLKIHlaNL~~g~~kl~~~~RlAF~E~hl~DI~DSAd~PLtG~rWW~~AedPfQ 752 (1088)
T KOG1038|consen 673 NHLGSDLCRGLLEFAEGKPLGPSGLRWLKIHLANLYAGVDKLSLRDRLAFTEEHLDDIFDSADRPLTGRRWWLKAEDPFQ 752 (1088)
T ss_pred cccchHHHHHHHHHhcCCcCCccchhHHHHHHHHHhcccccccHHHHHHHHHHHHHHHhhcccCCCcccchhhcCCChHH
Confidence 9999999999999999999999999999999999995 789999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCC
Q 001982 659 CLAACINLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNK 738 (986)
Q Consensus 659 fLA~C~El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~ 738 (986)
|||+|||+++|++++||+.|+||+||||||||||||||||||||..||++|||+|+|+|||||++||..|.+.+++||++
T Consensus 753 ~LA~C~elaea~RspdPeayiSH~PIHQDGSCNGLQHYAALGrD~~GA~~VNLvpsdkPqDVYs~VA~~V~~~~k~DAe~ 832 (1088)
T KOG1038|consen 753 CLAACMELAEALRSPDPEAYISHIPIHQDGSCNGLQHYAALGRDSEGAAAVNLVPSDKPQDVYSAVAARVEKIMKQDAEK 832 (1088)
T ss_pred HHHHHHHHHHHHcCCCHHHHHhcCCcccCCCcchHHHHHHhcCccccchhccccCCCCchhHHHHHHHHHHHHHHHhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCChhHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHH
Q 001982 739 DPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEA 818 (986)
Q Consensus 739 ~~~~~~~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~ 818 (986)
|+ .+|++|.+.||||||||||||+|||||++|||+||.++|++++.++|+.++|.+|+|+++++|+||+|||.+
T Consensus 833 g~------e~Ak~L~~~V~RKvVKQTVMT~VYGVTyvGAR~QI~krL~e~~~f~d~~~v~~as~Yltk~tf~aLrEmF~~ 906 (1088)
T KOG1038|consen 833 GP------EVAKILKDQVTRKVVKQTVMTSVYGVTYVGARLQIKKRLKEIDDFPDEKEVFDASCYLTKKTFEALREMFTA 906 (1088)
T ss_pred Ch------HHHHHHHHHHhHHHhhhheeeeeeeeeEecHHHHHHHHhhhccCcchhHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 85 589999999999999999999999999999999999999999999999889999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEe-cC-CCcCchhhhhccCCCcchhhhh
Q 001982 819 ARSIMGWLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQ-RE-GNLVEIRKQRTAFPPNFVHSLD 896 (986)
Q Consensus 819 A~~im~WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~-~~-~d~vd~rKQ~~Af~PNFIHSLD 896 (986)
|++||+||++||++|++++.+|+||||+||||||||++.++++|+|.+|++++. .+ +++||.|||++|||||||||||
T Consensus 907 araIq~WlgecAklIs~~~~~V~WtTPLGLPVVQPYr~~~~~qirt~lQt~~~~~~d~~~~vn~rkQktaFPPNFIHSLD 986 (1088)
T KOG1038|consen 907 ARAIQDWLGECAKLISSENSPVEWTTPLGLPVVQPYRQEKKKQIRTGLQTLFLSPRDLTNKVNARKQKTAFPPNFIHSLD 986 (1088)
T ss_pred HHHHHHHHHHHHHHHhcCCCceEEecCCCCcccchhhhhhhhcccccceEEeecchhhccccchhhhhccCCCchhhccc
Confidence 999999999999999999999999999999999999999999999999999998 34 7899999999999999999999
Q ss_pred hHHHHHHHHHHhhcCCcEEEeeccccCCCCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHh------------CCCCCC
Q 001982 897 GSHMMMTAVACRDAGLHFAGVHDSFWTHACDVDEMNQILRKKFVELYNMPMLENLLESFQTS------------YPTLSF 964 (986)
Q Consensus 897 AsHmmlta~~~~~~Gi~FasVHDSFwThA~dvd~m~~ilRe~FV~Lys~~il~~l~e~f~~~------------~~~~~~ 964 (986)
||||||||++|.++||+||+|||||||||||||+||++|||+||+|||+|||++|+|+|++| |+.+.|
T Consensus 987 ~SHMmmTal~C~rqGl~FasVHDsyWTHAcDVd~MN~ilREqFV~Lhs~pIle~L~e~f~~ry~~~~~~~~~~s~l~l~f 1066 (1088)
T KOG1038|consen 987 GSHMMMTALACERQGLTFASVHDSYWTHACDVDVMNRILREQFVELHSQPILERLLESFEKRYKFKDSDFKNDSQLPLIF 1066 (1088)
T ss_pred chHHHHHHHHHHhcCCceeeeecchhccccchHHHHHHHHHHHHHHcccHHHHHHHHHHHHHhccccchhhhhccCCccC
Confidence 99999999999999999999999999999999999999999999999999999999999994 456789
Q ss_pred CCCCCCCCCChhhhccCCCCCC
Q 001982 965 PPLPERGNFDLEEVLESPYFFN 986 (986)
Q Consensus 965 p~~P~~G~LDL~~Vl~S~YFF~ 986 (986)
|++|++|+|||+.||+|+||||
T Consensus 1067 pplP~rGdfDLk~Vl~S~YFFs 1088 (1088)
T KOG1038|consen 1067 PPLPKRGDFDLKKVLDSTYFFS 1088 (1088)
T ss_pred CCCCCCCCccHHHHhccccccC
Confidence 9999999999999999999997
No 2
>PHA00452 T3/T7-like RNA polymerase
Probab=100.00 E-value=2e-200 Score=1784.16 Aligned_cols=763 Identities=33% Similarity=0.550 Sum_probs=679.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCccchhhhhccCC
Q 001982 176 NLLRRRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQRTKKQKAAYAPHIELLP 255 (986)
Q Consensus 176 ~~l~~RQ~~lE~~~~~~a~~r~~~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~~~~~~r~~y~p~L~~l~ 255 (986)
..|.+||++||++++++|++||++++++++++|+++++|++++++.+|+++|+++|+++++.++++|.++.|+|||++++
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 001982 256 ADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVNS 335 (986)
Q Consensus 256 ~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~~~~IG~aVe~E~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 335 (986)
||+||+|||+++|++++++ ++.++++++++||++||+|++++.+++++++..++.. ....+++.+.
T Consensus 83 ~d~lA~Iti~~~l~~l~~~---~~~~~~~~~~~iG~aie~E~r~~~~~~~~~~~~~~~~-----------~~~~~~~~~~ 148 (807)
T PHA00452 83 PEVLAVITLKVTLDMLLSK---ETPTAQAVATAIGRAIEDEIRFGRIEDLNPKYFKKVV-----------EYLKRSRTGS 148 (807)
T ss_pred HHHHHHHHHHHHHHHHhcC---CCchHHHHHHHHHHHHHHHHHHHHHHHhChHHHHHHH-----------HHHHhcccch
Confidence 9999999999999999873 4569999999999999999999999877655433211 0112223333
Q ss_pred HHHHHH-HHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHc-cccCCCCCCCCCCCCccCceeEeeeeeecCCCCCcc
Q 001982 336 LIKSKR-VMEAQKLLKNEETKPWGRDTQAKLGSRLVELLIETA-YVQHPVNPADYSPPDVRPAFRHRFKTILKHPGQKTT 413 (986)
Q Consensus 336 ~~~~~~-~~~~~~~~~~~~~~~W~~~~~~kvG~~Li~~L~e~~-~i~~~~~~~~~~~~~~~paF~h~~~~~~~~~g~~~~ 413 (986)
..++.+ .+.++..+...++.+|+.+++++||++|+++|++++ .++++... ..++ +
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 122333333335889999999999999999999996 55442110 0111 3
Q ss_pred eeEEEEecCHHHHHHHHhhhhc--ccCC-CCcceeCCCCCcCCCCcccccCC---ccceecCCcHHHHHHHHhccccChH
Q 001982 414 KRYGVVECDPLVLEGLDRSAKH--MLIP-YVPMLVPPKKWKGYNKGGYLFLP---SYVMRTHGSRKQQEALKSVTGNCMK 487 (986)
Q Consensus 414 k~~gvi~~~~~~~~~l~~~~~~--~~~~-~lPMlvpP~pW~~~~~GGYl~~~---s~l~R~~~~~~q~~~l~~~~~~~l~ 487 (986)
+++|+|++||++++.+++.... .+.| +|||||||+||+++.+||||+.+ +..+|+++...+..+ .+++|+
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 6789999999999999886543 2344 99999999999999999999853 567888776555433 347999
Q ss_pred HHHHHHHhhcCcceEEcHHHHHHHHHHHHcCCCCCCCCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHHHhhhhh
Q 001982 488 KVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRNDVLIPEKPLS--EDMTEVQKWKWSVRKAKKINQERHSQR 565 (986)
Q Consensus 488 ~v~~aLN~Lqst~wrIN~~VL~vi~~~w~~g~~i~~l~~~~~~p~P~~p~~--~d~~~~~~wk~~~~~~~~~~~~~~S~R 565 (986)
.||++||+||+|||+||++||+||+++|++| .++++++..+.|+|++|+. .+++++++|++++++++++++++||+|
T Consensus 282 ~v~~aLN~Lg~t~w~IN~~vl~v~~~~~~~~-~~~~~~~~~~~~~P~~P~~~~~~~~~~~~wk~~~~~~~~~~~~~~S~r 360 (807)
T PHA00452 282 EVYKAVNALQNTAWRINKDVLAVVNEVVNWG-PVGDVLGIPRRPLPPKPEFLDENEEAFKAWKRAAAAWYTKEKERVSKR 360 (807)
T ss_pred HHHHHHHHHhcCCceecHHHHHHHHHHHhcC-CcccCCCCCCCCCCCCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999 8888888878888888864 456889999999999999999999999
Q ss_pred hhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCchhhhhhhhcccCccCCcchhhHHHHHHHhhcC-----
Q 001982 566 CDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANLFS----- 640 (986)
Q Consensus 566 ~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL~FaegkpLG~~Gl~WLKIhlANl~G----- 640 (986)
|+++++|++|++|+|++.||||||+|||||+|| +|||||||+|+|||||+||+|+|||++|++|||||+||+||
T Consensus 361 ~~~~~~l~iA~~f~~~~~fYfP~n~DfRGR~Yp-~~~ln~qg~Dl~RsLL~Fa~gkpLG~~Gl~WLkih~AN~~G~dK~s 439 (807)
T PHA00452 361 RRLEFMLRVANKFADYKAIYFPYNMDWRGRVYA-VSMLNPQGSDLQKALLRFAEGKPLGKRGLYWLKVHGANCYGVDKVT 439 (807)
T ss_pred HHHHHHHHHHHHhcCCCceeccccccCCCCCCC-CCCCCCCCchHHHHHHHhcCCCCCChhHHHHHHHHHHHHhCCCcCC
Confidence 999999999999999889999999999999999 99999999999999999999999999999999999999999
Q ss_pred -------------------CCCCCCchhhhcCCChHHHHHHHHHHHHHHhcCCCCcceecccccccCCcchhHHHHHhcC
Q 001982 641 -------------------ENPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGR 701 (986)
Q Consensus 641 -------------------~dPl~~~~wW~~AD~PwQfLA~C~El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~r 701 (986)
+||+++. ||++||+||||||+|+||++|+++|+ +|+||||||||||||||||||||||
T Consensus 440 ~~eR~~wv~~n~~~I~~~A~dPl~~~-ww~~Ad~P~qfLA~c~El~~a~~~~~--~~~s~lPI~qDgSCnGlQHyAAL~r 516 (807)
T PHA00452 440 FDERAAWVDENHDNILAAAEDPLNNT-WWAEADSPLCFLAACFEYAAAVHSGT--SYVSGLPVAMDGTCSGLQHFSAMLR 516 (807)
T ss_pred HHHHHHHHHHHHHHHHHHHhCcCCch-hhhcCCCHHHHHHHHHHHHHHHhCCC--ccccccccccCCcccHHHHHHHHhC
Confidence 7899987 99999999999999999999999887 9999999999999999999999999
Q ss_pred ChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccccccceeeecccchhhHHHHH
Q 001982 702 NTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQI 781 (986)
Q Consensus 702 D~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI 781 (986)
|.+||++|||+|+|+|||||+.|++.|.+.+++|+.++.+ ......+++|..+|+||+|||||||+|||||++|+++||
T Consensus 517 D~~ga~~VNL~p~d~p~DvY~~Va~~v~~~i~~d~~~~~~-~~~~~~~~~l~~~i~RkvvKqtVMT~vYGvT~~g~~~qI 595 (807)
T PHA00452 517 DEVGGRAVNLLPSDKPQDIYGIVAEVVNEKLERDAINGTD-NTRALARLWLAYGITRSLTKRPVMTLPYGSTRFSCRDYI 595 (807)
T ss_pred CHHhHHHhCCCCCCCCccHHHHHHHHHHHHHHHHHhCCCc-chHHHHHHHHhCCCChhhcccccccceeCCchhhhHHHH
Confidence 9999999999999999999999999999999999876432 123334567888999999999999999999999999999
Q ss_pred HHHHHHcCCCCChhhH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCcEEEEcCCCCeEEEeeccCC
Q 001982 782 KRRLEEKGHITDDRQL--FAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIA-SENQPVRWTTPLGLPVVQPYCKNE 858 (986)
Q Consensus 782 ~~~L~~~~~~~d~~~~--~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~-~~~~pV~WtTPlGlpVvQ~Y~k~~ 858 (986)
.++|+++|+..++... +.+++|+|++||+||+++|++|+.||+||++||++|+ +.+.||.|+||+||||+|||++.+
T Consensus 596 ~~~l~~~~~~~~~~~~~~~~~~~yla~~i~~ai~~~f~~a~~im~wL~~~a~~i~~~~~~pv~W~TP~GlpV~Q~Y~k~~ 675 (807)
T PHA00452 596 LEDLLQPGIDEGDGAMFTNQAASYMAKLIWDAISETVPAAVEAMNWLQQAAKLLAAKGAEALHWTTPTGFPVWQEYRKPE 675 (807)
T ss_pred HHHHHhcCCCcccchhhhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCCEEEECCCCCEEEeeecCCC
Confidence 9999998876544333 7899999999999999999999999999999999999 999999999999999999999999
Q ss_pred ceeEEeeeE---EEEEecCCCcCchhhhhccCCCcchhhhhhHHHHHHHHHHhhcCC-cEEEeeccccCCCCChhHHHHH
Q 001982 859 RHLIRTSLQ---VLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAVACRDAGL-HFAGVHDSFWTHACDVDEMNQI 934 (986)
Q Consensus 859 ~~~I~t~lq---~~~l~~~~d~vd~rKQ~~Af~PNFIHSLDAsHmmlta~~~~~~Gi-~FasVHDSFwThA~dvd~m~~i 934 (986)
+++|+|.+| .+++..+++++|++||++|||||||||||||||||||++|.+.|+ +|++|||||||||||||.|+++
T Consensus 676 ~~~v~t~~~~~~~i~~~~~~~~~d~~Kq~~a~~PNFIHSLDAsHm~~t~~~~~~~g~~~fa~VHDsfwTha~dvd~m~~~ 755 (807)
T PHA00452 676 EKRVRLRLMGVARVQLYVNTDTIDARKHASGIAPNFVHSLDASHLRLTVVACAEKGIESFAVIHDSFGTHAADADNLHRA 755 (807)
T ss_pred cEEEEEeeccceeEEeccCCCCCCHHHHhcccCCchhhhhhHHHHHHHHHHHHhcCCCcEEEeccCcccChhhHHHHHHH
Confidence 999999987 477777788999999999999999999999999999999999986 8999999999999999999999
Q ss_pred HHHHHHHhcCc-chHHHHHHHHHHhCCCCCCCCCCCCCCCChhhhccCCCCCC
Q 001982 935 LRKKFVELYNM-PMLENLLESFQTSYPTLSFPPLPERGNFDLEEVLESPYFFN 986 (986)
Q Consensus 935 lRe~FV~Lys~-~il~~l~e~f~~~~~~~~~p~~P~~G~LDL~~Vl~S~YFF~ 986 (986)
|||+||+|||+ |+|++|+++|..+| .+++|++|++|+|||++||+|+|||+
T Consensus 756 lRe~FV~lys~~~~L~~l~~~~~~~~-~~~~p~~P~~G~lDL~~Vl~S~yfF~ 807 (807)
T PHA00452 756 IRETFVEMYEENDVLADFADQFGDQL-QLKMPELPEKGSLDLEEVLDSDFFFC 807 (807)
T ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHh-hccCCCCCCCCCCCHHHHhCCCCCCC
Confidence 99999999999 99999999999999 67999999999999999999999996
No 3
>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]
Probab=100.00 E-value=1.3e-190 Score=1594.13 Aligned_cols=779 Identities=37% Similarity=0.628 Sum_probs=692.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHH-Hh---------hccCccchhh
Q 001982 180 RRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKM-QR---------TKKQKAAYAP 249 (986)
Q Consensus 180 ~RQ~~lE~~~~~~a~~r~~~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~-~~---------~~~~r~~y~p 249 (986)
+||..||.+++..|.|+|+..+++..++|-..--.-+.+.++.||..|..+.++|+.. .. +.+.|..|+|
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 7899999999999999999999999999875444457889999999999999998873 22 2457899999
Q ss_pred hhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHH
Q 001982 250 HIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELL 329 (986)
Q Consensus 250 ~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~~~~IG~aVe~E~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~ 329 (986)
||++++++++|+|||+++++++.+++.+.||+++.+...+|++||+|++.+++...+++.++-..+ +.-+.+
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 999999999999999999999999888999999999999999999999999987655443221100 011222
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCC--CCCccCceeEeeeeeecC
Q 001982 330 RKRVNSLIKSKRVMEAQKLLKNEETKPWGRDTQAKLGSRLVELLIETAYVQHPVNPADYS--PPDVRPAFRHRFKTILKH 407 (986)
Q Consensus 330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~~~~kvG~~Li~~L~e~~~i~~~~~~~~~~--~~~~~paF~h~~~~~~~~ 407 (986)
++.+.+ .+..+-.+..++..|.+|+++++++||++++.+|+++++|++...+...+ .....|||.|+|+|.
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 11111123345678899999999999999999999999999876654432 235679999999986
Q ss_pred CCCCcceeEEEEecCHHHHHHHHhhhh--cccCCCCcceeCCCCCcCCCCcccccCCccceecCCcHHHHHHHHhc-ccc
Q 001982 408 PGQKTTKRYGVVECDPLVLEGLDRSAK--HMLIPYVPMLVPPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEALKSV-TGN 484 (986)
Q Consensus 408 ~g~~~~k~~gvi~~~~~~~~~l~~~~~--~~~~~~lPMlvpP~pW~~~~~GGYl~~~s~l~R~~~~~~q~~~l~~~-~~~ 484 (986)
+| +++|||.+|..+...+.+... .+.+.+|||||||+||+++.+|||++....+.|..++.+|-+|+..+ ..+
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 689999999998887765543 22333899999999999999999999999999999999999998766 468
Q ss_pred ChHHHHHHHHhhcCcceEEcHHHHHHHHHHHHcCCCCCCCCCCCC-CCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHhh
Q 001982 485 CMKKVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRND-VLIPEK-PLSEDMTEVQKWKWSVRKAKKINQERH 562 (986)
Q Consensus 485 ~l~~v~~aLN~Lqst~wrIN~~VL~vi~~~w~~g~~i~~l~~~~~-~p~P~~-p~~~d~~~~~~wk~~~~~~~~~~~~~~ 562 (986)
+|++||++||.||+|||+||.+|++|+.++|++|+.+..||.+.+ .-+|+. +.+.+|+++..|+-+.+.+...+...+
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 334554 457789999999999999999999999
Q ss_pred hhhhhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCchhhhhhhhcccCccCCcchhhHHHHHHHhhcC--
Q 001982 563 SQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANLFS-- 640 (986)
Q Consensus 563 S~R~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL~FaegkpLG~~Gl~WLKIhlANl~G-- 640 (986)
|+||+++|+|+||++|.|+ +|||||+||||||+||+|+||||||+|.|||||.||.|+|||++|++|||||+||+||
T Consensus 632 S~RcdfnykLeiAraFl~E-kfYFPH~lDFRGRaYpls~hlnh~gnD~srGLL~F~~gkplgp~Gl~WLkiHlanLfGvd 710 (1117)
T COG5108 632 SKRCDFNYKLEIARAFLDE-KFYFPHQLDFRGRAYPLSLHLNHQGNDASRGLLQFANGKPLGPEGLDWLKIHLANLFGVD 710 (1117)
T ss_pred hhhcchHHHHHHHHHhccC-ccccccccccCcccccCccccccccchhhhhHHHhhcCCcCCcchhhHHHHHhhcccCcc
Confidence 9999999999999999996 8999999999999999999999999999999999999999999999999999999999
Q ss_pred ----------------------CCCCCCchhhhcCCChHHHHHHHHHHHHHHhcCCCCcceecccccccCCcchhHHHHH
Q 001982 641 ----------------------ENPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAA 698 (986)
Q Consensus 641 ----------------------~dPl~~~~wW~~AD~PwQfLA~C~El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAA 698 (986)
+||++|++||..||+|||.||+||||.+++++|||++|+||+||||||||||||||||
T Consensus 711 K~~~~~Rvafv~~n~qei~dSAenPldgnrwW~tAdkPwQALA~CFE~~e~v~~gd~e~fiSH~PvqqDGTCNGLQhyaA 790 (1117)
T COG5108 711 KCSMNERVAFVMANQQEILDSAENPLDGNRWWLTADKPWQALAFCFEWQEYVAEGDHEAFISHLPVQQDGTCNGLQHYAA 790 (1117)
T ss_pred cCcHHHHHHHHHhhHHHHHhhccCCCCCCcchhcCCChHHHHHHHHHHHHHHhcCChHHhhhcCcccccCccchHHHHHH
Confidence 8999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccccccceeeecccchhhHH
Q 001982 699 LGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAR 778 (986)
Q Consensus 699 L~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar 778 (986)
||+|++||+||||+|+|+|+|||..||..|...++.+|+++ +..|+.|++++||+|||+||||+|||||++|++
T Consensus 791 lggD~eGa~qVNLvPSDkP~DvYa~VA~vv~~~L~~~Aeag------De~ak~lKDK~Tr~vVk~tvmtnvygvtyvGat 864 (1117)
T COG5108 791 LGGDEEGAAQVNLVPSDKPNDVYATVASVVIAKLRDIAEAG------DETAKELKDKETRTVVKETVMTNVYGVTYVGAT 864 (1117)
T ss_pred hcCccccceeeeccCCCCchhHHHHHHHHHHHHHHHHHHhh------hhHHHHHhhhhhhhhhhhccccceeeeEEeehH
Confidence 99999999999999999999999999999999999999887 467999999999999999999999999999999
Q ss_pred HHHHHHHHHcCCCCChh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC------------------CCc
Q 001982 779 EQIKRRLEEKGHITDDR-QLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIASE------------------NQP 839 (986)
Q Consensus 779 ~QI~~~L~~~~~~~d~~-~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~~------------------~~p 839 (986)
.||-++|.-. ..+.+ +....+.|+++.+|.++++.|..|+.|++||.+|++.|..+ -.|
T Consensus 865 ~qitk~l~~i--~g~~k~~~~d~~kyltk~vF~a~r~lF~~Ah~iqdwl~~c~~~i~~s~~~d~d~~~~k~gik~de~~p 942 (1117)
T COG5108 865 RQITKRLTLI--YGASKFDTVDPWKYLTKEVFPAERTLFAAAHFIQDWLWDCVGEIVVSAAGDMDWLQKKAGIKADESLP 942 (1117)
T ss_pred HHHHHhcccc--cCchhccccCHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHHhHHHHhcccchhHHHHHhccCcccccc
Confidence 9999998642 22221 23345789999999999999999999999999999988542 479
Q ss_pred EEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecC--CCcCchhhhhccCCCcchhhhhhHHHHHHHHHHhhcCCcEEEe
Q 001982 840 VRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE--GNLVEIRKQRTAFPPNFVHSLDGSHMMMTAVACRDAGLHFAGV 917 (986)
Q Consensus 840 V~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~--~d~vd~rKQ~~Af~PNFIHSLDAsHmmlta~~~~~~Gi~FasV 917 (986)
|+||||+||||+||||..+.++|.|.+|+|.|..+ +.+||+|||.+||||||||||||+||.|||.+|.++||.|++|
T Consensus 943 ViWtTplgLpivQpYr~~~~kq~etnlQtVfi~~~~a~~~v~~rkQ~sg~pPNfiHSlDA~HM~lt~~~C~~qgi~Fa~v 1022 (1117)
T COG5108 943 VIWTTPLGLPIVQPYRTSEQKQLETNLQTVFIQLDVASKKVDKRKQGSGIPPNFIHSLDAAHMQLTVSRCHDQGIRFALV 1022 (1117)
T ss_pred eeeccCCCCcccccchhhHHHHHHhhhheEEEeccccccccChhhccCCCCcchhhhccHHHHHHhHHHhhhcCCceeee
Confidence 99999999999999999999999999999988864 5689999999999999999999999999999999999999999
Q ss_pred eccccCCCCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHhCCC--------------------------CCCCCCCCCC
Q 001982 918 HDSFWTHACDVDEMNQILRKKFVELYNMPMLENLLESFQTSYPT--------------------------LSFPPLPERG 971 (986)
Q Consensus 918 HDSFwThA~dvd~m~~ilRe~FV~Lys~~il~~l~e~f~~~~~~--------------------------~~~p~~P~~G 971 (986)
||||||||||+|.||.+|||+||+||+.+++.+|.++|.+||.+ +++||+|++|
T Consensus 1023 HDSYwTHA~d~d~Mn~~LRE~Fvklh~~~~vlrlk~EF~~ryk~~l~~~k~~ka~dedl~aklg~~t~ipl~lPplP~kG 1102 (1117)
T COG5108 1023 HDSYWTHAGDADAMNQFLREEFVKLHGDHDVLRLKAEFGRRYKGFLVSKKAIKANDEDLTAKLGEGTYIPLELPPLPEKG 1102 (1117)
T ss_pred ecchhccccCHHHHHHHHHHHHHHHhcchHHHHHHHHHhHHhhchhhhhhhhccchHHHHhhcCCCCcccccCCCCCCCC
Confidence 99999999999999999999999999999999999999998842 3589999999
Q ss_pred CCChhhhccCCCCCC
Q 001982 972 NFDLEEVLESPYFFN 986 (986)
Q Consensus 972 ~LDL~~Vl~S~YFF~ 986 (986)
+|||..||+|.||||
T Consensus 1103 ~lDls~vleS~yFFs 1117 (1117)
T COG5108 1103 SLDLSQVLESAYFFS 1117 (1117)
T ss_pred CccHHHHHhhhhccC
Confidence 999999999999997
No 4
>PF00940 RNA_pol: DNA-dependent RNA polymerase; InterPro: IPR002092 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The phage-type enzymes are family of single chain polymerases found in bacteriophages and mitochondria [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3SPA_A 1CEZ_A 1H38_B 1S77_D 1QLN_A 1S0V_D 3E2E_A 2PI4_A 3E3J_B 1S76_D ....
Probab=100.00 E-value=1.7e-114 Score=984.24 Aligned_cols=364 Identities=55% Similarity=0.980 Sum_probs=316.4
Q ss_pred CccCCcchhhHHHHHHHhhcC------------------------CCCCCCchhhhcCCChHHHHHHHHHHHHHHhcCCC
Q 001982 620 GRPLGKSGLRWLKIHLANLFS------------------------ENPINGSRWWLTAEDPFQCLAACINLSEALKSSSP 675 (986)
Q Consensus 620 gkpLG~~Gl~WLKIhlANl~G------------------------~dPl~~~~wW~~AD~PwQfLA~C~El~~a~~s~~P 675 (986)
|||||++|++|||||+||+|| +||+++..||.+||+||||||+|+||++|+++|||
T Consensus 1 ~kpLg~~gl~wLki~~An~~G~dK~s~~eR~~wv~~n~~~I~~~a~~P~~~~~~w~~Ad~P~qfLA~c~e~~~~~~~~~~ 80 (405)
T PF00940_consen 1 GKPLGERGLDWLKIHGANLFGLDKLSFDERIKWVDDNLDDILDSAEDPLDGEEWWLKADKPWQFLAACFELAKALRSGNP 80 (405)
T ss_dssp -EE-CCCHHHHHHHHHHHHCT-TTSTHHHHHHHHHHCHHHHHHHHHTTTTC-TGGGGSSSHHHHHHHHHHHHHHHCCCSG
T ss_pred CCCCcHhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHhhCcccchHHHhcCCcHHHHHHHHHHHHHHHhcCCc
Confidence 799999999999999999999 78999999999999999999999999999999999
Q ss_pred CcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcc
Q 001982 676 HSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQ 755 (986)
Q Consensus 676 ~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~ 755 (986)
++|+||+||||||||||||||||||||.+||++|||+|+++|+|||+.|++.|.+.+.+++... +....+++++..+
T Consensus 81 ~~~~s~lPV~~DgSCsGlQH~sal~rD~~ga~~vNLip~~~p~DiY~~V~~~v~~~l~~~~~~~---~~~~~~~~~l~~~ 157 (405)
T PF00940_consen 81 EEFVSHLPVHQDGSCSGLQHYSALLRDEVGAKAVNLIPSDKPQDIYSEVAEEVKKRLEEDADDA---EEDNSLAKWLKGG 157 (405)
T ss_dssp CCSEE-SEEEEEBSTHHHHHHHHHTT-HHHHHHTTSSSSSS---HHHHHHHHHHHHHHHHHHEH---HCCHHHHHHCCCT
T ss_pred hheeecceeeecCcccHHHHHHHHccCHhhChhcCCCCCCCCCchHHHHHHHHHHHHHHhhccc---ccchHHHHHhcCC
Confidence 9999999999999999999999999999999999999999999999999999999999883100 1126889999999
Q ss_pred cccccccccceeeecccchhhHHHHHHHHHHHcCCCC-ChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 756 VDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHIT-DDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIA 834 (986)
Q Consensus 756 i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~-d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~ 834 (986)
|+||+|||+|||+|||||.+|+++||+++|++.+... +....++++.|||+.|+++|+++|++|+.+|+||++||++++
T Consensus 158 i~Rk~vK~~vMT~~YG~T~~g~~~qi~~~l~~~~~~~~~~~~~~~~~~~la~~i~~~i~~~~~~a~~~m~wL~~~a~~~~ 237 (405)
T PF00940_consen 158 ITRKLVKRPVMTIVYGVTFYGARDQIKEQLKEKGDEEEDKIESYKAAMYLAKIIFEAIKEVFPGARNIMDWLQEIAKIIA 237 (405)
T ss_dssp --HHHHHHHHHHHHHT-TCCHHHHHHHHHCHCHCCCTTTTTTHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHH
T ss_pred CChhhcccceEEeeeCcchhhHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999886544 345788999999999999999999999999999999999999
Q ss_pred cCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecC--CCcCchhhhhccCCCcchhhhhhHHHHHHHHHHhhcCC
Q 001982 835 SENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE--GNLVEIRKQRTAFPPNFVHSLDGSHMMMTAVACRDAGL 912 (986)
Q Consensus 835 ~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~--~d~vd~rKQ~~Af~PNFIHSLDAsHmmlta~~~~~~Gi 912 (986)
+++.||.|+||+||||+|+|++.+.++|+|.++....... .+.+|++||++||||||||||||||||||+.+|.+.|+
T Consensus 238 ~~~~pv~W~tP~Gl~V~Q~Y~~~~~~~i~~~~~~~~~~~~~~~~~~d~~Kq~~a~~PNFIHSlDAshl~~t~~~~~~~~~ 317 (405)
T PF00940_consen 238 KLNKPVSWTTPLGLPVVQPYRKSKKKRIKTYLQGVSRRRVIREDPVDKRKQKNAFAPNFIHSLDASHLMLTANACNKEGI 317 (405)
T ss_dssp CTCB-EEEEETTSEEEEE--EEESEEEEESSSTTTEEE--EEEEES-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred ccCCcEEEECCCCCEEEecccccCceeeEeecceeEEeccCCCCCCCHHHHhcccCCchHhhHHHHHHHHHHHHHHhcCC
Confidence 9999999999999999999999999999998764333221 23459999999999999999999999999999999999
Q ss_pred cEEEeeccccCCCCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHhCCC--------------CCCCCCCCCCCCChhhh
Q 001982 913 HFAGVHDSFWTHACDVDEMNQILRKKFVELYNMPMLENLLESFQTSYPT--------------LSFPPLPERGNFDLEEV 978 (986)
Q Consensus 913 ~FasVHDSFwThA~dvd~m~~ilRe~FV~Lys~~il~~l~e~f~~~~~~--------------~~~p~~P~~G~LDL~~V 978 (986)
+|++||||||||||||+.|+++|||+||+||++++|++++++|..+++. +.+|++|++|+|||++|
T Consensus 318 ~f~~VHDsf~tha~~~~~L~~~lRe~Fv~lys~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~P~~G~ldl~~V 397 (405)
T PF00940_consen 318 PFATVHDSFWTHACDVDTLNEILREQFVELYSPDILEDFAEDFKARLPDSYQNIWEKKNEFVPIKFPPLPERGDLDLNEV 397 (405)
T ss_dssp -EEECTTEEEEEHHHHHHHHHHHHHHHHHHHHCTHHHHHHHHHHCCCTGGTTSHHHHH--HHCCCCHS-----S-SGGGG
T ss_pred eEEEEehhhhcCHHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHhhhhhccccccchhhhhccCCCCCCCCCccHHHH
Confidence 9999999999999999999999999999999999999999999999986 78999999999999999
Q ss_pred ccCCCCCC
Q 001982 979 LESPYFFN 986 (986)
Q Consensus 979 l~S~YFF~ 986 (986)
++|+||||
T Consensus 398 ~~S~YfFs 405 (405)
T PF00940_consen 398 LKSEYFFS 405 (405)
T ss_dssp GG-TTTBB
T ss_pred hCCCCCCC
Confidence 99999997
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=6e-48 Score=424.75 Aligned_cols=305 Identities=32% Similarity=0.553 Sum_probs=219.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHHh----hccCccchhhhhccCC
Q 001982 180 RRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQR----TKKQKAAYAPHIELLP 255 (986)
Q Consensus 180 ~RQ~~lE~~~~~~a~~r~~~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~~----~~~~r~~y~p~L~~l~ 255 (986)
|||++||+++++.|++||++..+++.++|.+++++++++++++|+++|.++|+++++.+. ..++++.|+|||+.||
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 001982 256 ADKVAVIVMHKMMGLVMAG-HEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVN 334 (986)
Q Consensus 256 ~e~lA~Iti~~~l~~~~~~-~~~~~~~~~~~~~~IG~aVe~E~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 (986)
||++|+|||+++|++++++ +..+|+++++++.+||++||+|++++++.+...+.+.+............. .++.+.
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 455778999999999999999999998876644322211110000000000 001111
Q ss_pred HHHHHHHHHHHHHhhcCCCCCC--CCHHHHHHHHHHHHHHHHHHccccCCCCCCCCCCCCccCceeEeeeeeecCCCCCc
Q 001982 335 SLIKSKRVMEAQKLLKNEETKP--WGRDTQAKLGSRLVELLIETAYVQHPVNPADYSPPDVRPAFRHRFKTILKHPGQKT 412 (986)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~--W~~~~~~kvG~~Li~~L~e~~~i~~~~~~~~~~~~~~~paF~h~~~~~~~~~g~~~ 412 (986)
..++.......... -+..+.. |+..++++||++|+++|+++++|++...++.+ ...+|||+|+|++. +
T Consensus 158 ~~~~~~~~~~~~~~-~~~~~~~~~W~~~~~~~vG~~Ll~~l~~~~~i~~~~~~~~~--~~~~paf~~~~~~~---~---- 227 (318)
T PF14700_consen 158 QLLKNRKDSSGKPS-LEEEWSDSPWPSDIRAKVGSFLLELLMETAKIPVERKDPET--SEEQPAFYHSYRYR---K---- 227 (318)
T ss_dssp HHHHHHHSHSS-ST-TT-TCCC--SCHHHHHHHHHHHHHHHHHCTCEEEEEESTT-------BSEEEEE------T----
T ss_pred HHHHHHHHhccccc-cccccccCCCCHHHHHHHHHHHHHHHHhheeeccccCCccc--cccccchhhhhccc---c----
Confidence 11110000000000 0123444 99999999999999999999999987744322 56799999999875 3
Q ss_pred ceeEEEEecCHHHHHHHHhhhhc-----ccCCCCcceeCCCCCcCCCCcccccCCccceecCCcHHHHHHH-HhccccCh
Q 001982 413 TKRYGVVECDPLVLEGLDRSAKH-----MLIPYVPMLVPPKKWKGYNKGGYLFLPSYVMRTHGSRKQQEAL-KSVTGNCM 486 (986)
Q Consensus 413 ~k~~gvi~~~~~~~~~l~~~~~~-----~~~~~lPMlvpP~pW~~~~~GGYl~~~s~l~R~~~~~~q~~~l-~~~~~~~l 486 (986)
++++|+|++||.+.+.++..... .++.+|||||||+||+++++||||..++.+||++++ .|..++ ++...++|
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 35789999999999999876542 125599999999999999999999999999999887 555555 44567899
Q ss_pred HHHHHHHHhhcC
Q 001982 487 KKVFEALDTLGS 498 (986)
Q Consensus 487 ~~v~~aLN~Lqs 498 (986)
+.||+|||+||+
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=91.68 E-value=0.26 Score=52.51 Aligned_cols=192 Identities=20% Similarity=0.212 Sum_probs=115.6
Q ss_pred HHHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001982 665 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 744 (986)
Q Consensus 665 El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 744 (986)
++++++.. |++| +-|..|-|.==|=.+|.|.+|......-| ...|+|+.+|..+...-.+
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 47889999999999999999988877765 3569999998765321110
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 745 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 824 (986)
Q Consensus 745 ~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~ 824 (986)
. .....|+..|+.+--..||.+..|..+++ | ++.+ -|+.+.++..+.||+ +..
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 12346999999999999999987776553 3 2222 245566667777777 667
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecCCCcCchhhhhccCCCcchhhhhhHHHHHHH
Q 001982 825 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 904 (986)
Q Consensus 825 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~Af~PNFIHSLDAsHmmlta 904 (986)
|.+++.....+.+. .+|+.|-...-|-.. +.....+.+..-.+.|++=+=-|+=++..|
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 111222222223367876655555444433
Q ss_pred H-H----HhhcCC--c-EEEeeccccCC
Q 001982 905 V-A----CRDAGL--H-FAGVHDSFWTH 924 (986)
Q Consensus 905 ~-~----~~~~Gi--~-FasVHDSFwTh 924 (986)
. . ..+.|+ . .+.|||+....
T Consensus 175 m~~~~~~~~~~~~~~~~vl~vHDElv~e 202 (206)
T smart00482 175 MIKMDEALKEKGLRARLLLQVHDELVFE 202 (206)
T ss_pred HHHHHHHHHhcCCCceEEEeeceeEEee
Confidence 2 2 233333 3 55699998654
No 7
>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]
Probab=88.10 E-value=0.34 Score=58.85 Aligned_cols=76 Identities=28% Similarity=0.422 Sum_probs=59.6
Q ss_pred hcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 753 IDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKV 832 (986)
Q Consensus 753 ~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~ 832 (986)
.-+++|++.|| ||.+||...+-..+.- ++|- +.+++-..++|.+|.++...+|++.+++...+..-|+|++..+++
T Consensus 860 yvGat~qitk~--l~~i~g~~k~~~~d~~-kylt-k~vF~a~r~lF~~Ah~iqdwl~~c~~~i~~s~~~d~d~~~~k~gi 935 (1117)
T COG5108 860 YVGATRQITKR--LTLIYGASKFDTVDPW-KYLT-KEVFPAERTLFAAAHFIQDWLWDCVGEIVVSAAGDMDWLQKKAGI 935 (1117)
T ss_pred EeehHHHHHHh--cccccCchhccccCHH-HHHH-HhHhHHHHHHHHHHHHHHHHHHHHHhHHHHhcccchhHHHHHhcc
Confidence 44899999999 9999999765333322 2222 224555568899999999999999999999999999999987764
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=85.70 E-value=4.3 Score=47.36 Aligned_cols=209 Identities=15% Similarity=0.216 Sum_probs=122.8
Q ss_pred HHHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001982 665 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 744 (986)
Q Consensus 665 El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 744 (986)
+++.++..+ .+| .-|..|-|-==|=.+|.|.+|....+..| ...|+|+.+|..+... ..
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 567776633 344 57899999888899999999999888876 3579999988765321 00
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 745 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 824 (986)
Q Consensus 745 ~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~ 824 (986)
+.. ..-.|+..|..+--..||.+..|..+++ |+ +.+ -|+.+.+...+.||+ +..
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 HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecCCCcCchhhhhccCCCcchhhhhhHHHHHHH
Q 001982 825 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 904 (986)
Q Consensus 825 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~Af~PNFIHSLDAsHmmlta 904 (986)
|.+++...+...+- .+|+.|-...-|--. +.....+-+..-.+.|++=+=-|+=+|..+
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 245555422211000 001111111112356777665555444433
Q ss_pred H-H----HhhcCC---cEEEeeccccCCC--CChhHHHHHHHHHHHH
Q 001982 905 V-A----CRDAGL---HFAGVHDSFWTHA--CDVDEMNQILRKKFVE 941 (986)
Q Consensus 905 ~-~----~~~~Gi---~FasVHDSFwThA--~dvd~m~~ilRe~FV~ 941 (986)
. . +.+.|+ -+..|||+..... .+++...+++++.+-+
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 3556999987553 4566666777776533
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=84.54 E-value=4 Score=47.54 Aligned_cols=212 Identities=19% Similarity=0.201 Sum_probs=127.0
Q ss_pred HHHHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCC
Q 001982 664 INLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKH 743 (986)
Q Consensus 664 ~El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~ 743 (986)
..+++++..+ .+| +-|..|-|-==|=.+|.|.+|.....+.| .-.|||+.+|..+-..-.
T Consensus 128 ~~iR~~f~a~--~G~---~lv~~DysqiElRvlA~ls~D~~l~~~~~-----~g~Dih~~~A~~~~g~~~---------- 187 (373)
T cd08638 128 ISLRHAFIPP--PGR---VLLSADYSQLELRILAHLSGDPALIELLN-----SGGDVFKMIAAQWLGKPV---------- 187 (373)
T ss_pred hhhhheeeCC--CCC---EEEEechhhhHHHHHHHHhCCHHHHHHHh-----cCCCHHHHHHHHHhCCCh----------
Confidence 3456666532 344 57899999999999999999999888775 257999998876532100
Q ss_pred hhHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 744 PQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIM 823 (986)
Q Consensus 744 ~~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im 823 (986)
.. ...-.|+..|..+--..||.+..|...++ |+ +.+ -|+.+.+...+.||+. .
T Consensus 188 --~~-----v~~~~R~~aK~~~fg~~YG~g~~~La~~l-------~~-s~~---------eA~~~i~~f~~~~p~v---~ 240 (373)
T cd08638 188 --EE-----VTDEERQQAKQLVYGILYGMGAKSLAEQL-------GV-SEE---------EAKQFIESFKNAYPGV---R 240 (373)
T ss_pred --hh-----CCHHHHHHHhHHHHhhHhCCcHHHHHHHh-------CC-CHH---------HHHHHHHHHHHHCccH---H
Confidence 00 11246999999999999999999887654 32 221 2455666777788874 5
Q ss_pred HHHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecCCCcCchhhhhccCCCcchhhhhhHHHHHH
Q 001982 824 GWLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMT 903 (986)
Q Consensus 824 ~WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~Af~PNFIHSLDAsHmmlt 903 (986)
.|.+++.....+.| .| +|+.|-...-|--.. .....+-..--.+.|++=+==|+=+|..
T Consensus 241 ~~~~~~~~~a~~~g-~v--~T~~GRrr~~p~~~~------------------~~~~~~~~~~r~a~N~~iQGsaAdi~K~ 299 (373)
T cd08638 241 RFIRETIERARRNG-FV--ETLTGRRRYLPEINS------------------GNSSERAQAERQAVNTVIQGSAADIMKI 299 (373)
T ss_pred HHHHHHHHHHHHcC-cE--EccCCCEEeCCCCCC------------------CCHHHHHHHHHHHhchhhhhHHHHHHHH
Confidence 56665555444332 22 355554332221111 0011111222356677766666655544
Q ss_pred HH-HHh----h-------cCC-cEEEeeccccC--CCCChhHHHHHHHHHHHHhc
Q 001982 904 AV-ACR----D-------AGL-HFAGVHDSFWT--HACDVDEMNQILRKKFVELY 943 (986)
Q Consensus 904 a~-~~~----~-------~Gi-~FasVHDSFwT--hA~dvd~m~~ilRe~FV~Ly 943 (986)
|. .+. . .+. -...|||+... +..+++.+.+++++.+-.-.
T Consensus 300 ami~i~~~l~~~~~~~~~~~~~lvl~VHDEl~~ev~~~~~~~~~~~i~~~Me~~~ 354 (373)
T cd08638 300 AMINIHEKLHSLLPNLPAGRARLVLQIHDELLFEVPESDVDEVARIIKRSMENAA 354 (373)
T ss_pred HHHHHHHHHHhhcccccCCCeEEEEEEccEEEEEeCHHHHHHHHHHHHHHHhCcc
Confidence 32 221 2 123 35569999774 45667777788887774443
No 10
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=84.10 E-value=2.6 Score=51.47 Aligned_cols=203 Identities=19% Similarity=0.150 Sum_probs=124.9
Q ss_pred HHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChh
Q 001982 666 LSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQ 745 (986)
Q Consensus 666 l~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~ 745 (986)
++.++.. |+++ .-|..|-|.==|=.+|.|.+|....++.| .-.|+|+.+|..+-.. + .+
T Consensus 315 iR~~f~a--~~G~---~lv~aDysqiElRvlA~ls~D~~l~~~~~-----~g~Dih~~~A~~~~~~---~----~~---- 373 (553)
T PRK14975 315 IRSAFVA--DPGW---KLVVADASQIELRVLAAYSGDERMIEAFR-----TGGDLHRLTASVGFGK---P----EE---- 373 (553)
T ss_pred HhceEEc--CCCC---EEEEechhhhHHHHHHHHcCCHHHHHHHh-----cCCCHHHHHHHHHhCC---C----cc----
Confidence 5666552 2344 47899999999999999999999988877 3679999998877211 1 00
Q ss_pred HHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 746 ALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGW 825 (986)
Q Consensus 746 ~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~W 825 (986)
. .-.|+..|..+.-.+||.+..|..+++. .. + -|+.+.+...+.||+ +..|
T Consensus 374 -~-------~~~R~~aK~~~~g~~YG~g~~~l~~~~~-~~--------~---------ea~~~~~~~~~~~p~---v~~~ 424 (553)
T PRK14975 374 -E-------KEERALAKAANFGAIYGATSKGLQEYAK-NY--------G---------EAARLLERLRRAYPR---AVGW 424 (553)
T ss_pred -c-------hhHHHHHHHHHHHhhhCCcHHHHHHHcC-CH--------H---------HHHHHHHHHHHHCcc---HHHH
Confidence 0 3459999999999999999998887653 11 1 134555666677776 6677
Q ss_pred HHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecC-CCcCchhhhhccCCCcchhhhhhHHHHHHH
Q 001982 826 LGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE-GNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 904 (986)
Q Consensus 826 L~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~-~d~vd~rKQ~~Af~PNFIHSLDAsHmmlta 904 (986)
++++.+...+.| .| +|.+|=... +... +.....+.+..-++.|++=+==|+=++..|
T Consensus 425 ~~~~~~~a~~~g-~v--~T~~GR~~~-------------------~~~~~~~~~~~~~~~~r~a~N~~iQGsaAdi~k~a 482 (553)
T PRK14975 425 VERAAREGERGG-VV--RTLLGRTSP-------------------PPGFAWRARRRARSRGRFTRNFPVQGTAADWAKLA 482 (553)
T ss_pred HHHHHHHHHHCC-eE--ECCCCCeec-------------------CCCccccChhHHhHhhhhhcCccchhHHHHHHHHH
Confidence 777776655442 12 245543211 1110 011122222233467996555555555443
Q ss_pred H-HHhh-----cCCc-EEEeeccccCCC--CChhHHHHHHHHHHH
Q 001982 905 V-ACRD-----AGLH-FAGVHDSFWTHA--CDVDEMNQILRKKFV 940 (986)
Q Consensus 905 ~-~~~~-----~Gi~-FasVHDSFwThA--~dvd~m~~ilRe~FV 940 (986)
. .+.+ .+.. +..|||....+. .+++.+.+++++.+-
T Consensus 483 m~~~~~~l~~~~~~~lvl~vHDEl~~e~~~~~~~~~~~~i~~~M~ 527 (553)
T PRK14975 483 LALLRRRLAEGLDAELVFFVHDEVVVECPEEEAEEVAAAIEEAME 527 (553)
T ss_pred HHHHHHHHhhcCCcEEEEEecceeEEEecHHHHHHHHHHHHHHHH
Confidence 2 2222 2333 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=76.97 E-value=14 Score=43.26 Aligned_cols=185 Identities=16% Similarity=0.052 Sum_probs=109.3
Q ss_pred HHHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001982 665 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 744 (986)
Q Consensus 665 El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 744 (986)
+++.++..+ .++ .-|..|-|.==|-.+|.|.+|...-++-| ...|||...|..+-..=.++.
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 456665532 344 35889999999999999999999877765 568999999887742110000
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 745 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 824 (986)
Q Consensus 745 ~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~ 824 (986)
-...--|...|...--++||.+.+|.+..-.+ +.|+ +.+ + |+.+.++..+.||+.+..|.
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 222 1 23445555677777554333
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecCCCcCchhhhhccCCCcchhhhhhHHHHHHH
Q 001982 825 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 904 (986)
Q Consensus 825 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~Af~PNFIHSLDAsHmmlta 904 (986)
=.++.++...+.+. +... .+|. .=|-|..-=|--|-+.-
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 11445544344343444
Q ss_pred HHHhhcCCc-EEEeeccccCCCCCh
Q 001982 905 VACRDAGLH-FAGVHDSFWTHACDV 928 (986)
Q Consensus 905 ~~~~~~Gi~-FasVHDSFwThA~dv 928 (986)
+.+.+.|.. +..|||..-.+..+.
T Consensus 320 i~l~~~g~~ivLqVHDElv~Evp~~ 344 (378)
T cd08642 320 LRLEKAGYDIVMHVHDEVVIEVPEG 344 (378)
T ss_pred HHHHhcCCeEEEEECceeEEeeccc
Confidence 456667774 556999999998874
No 12
>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=76.60 E-value=4.4 Score=48.15 Aligned_cols=210 Identities=13% Similarity=0.002 Sum_probs=122.3
Q ss_pred HHHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001982 665 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 744 (986)
Q Consensus 665 El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 744 (986)
+++.++..+ .++ +-|.-|.|.==|-.+|.|.+|..++..+.... -.|+++..|..+
T Consensus 176 ~iR~~Fva~--~G~---~lv~aDySQiELRiLAhls~d~~~~~l~~~~~---~~DiH~~ta~~~---------------- 231 (429)
T cd08643 176 ECRELFGVP--PGW---SLVGADASGLELRCLAHYLARYDGGAYTRKVL---GGDIHWANAQAM---------------- 231 (429)
T ss_pred hhhheEecC--CCC---EEEEecHHHHHHHHHHHHhcccchHHHHhhhc---ccchhHHHHHHh----------------
Confidence 556665432 343 47889999888889999999876666555332 358877655431
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcC-C---CC---ChhhHHHHHHHHHHHHHHHHHHHHH
Q 001982 745 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKG-H---IT---DDRQLFAAACYAAKVTLTALGEIFE 817 (986)
Q Consensus 745 ~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~-~---~~---d~~~~~~~a~Ylak~v~~ai~e~f~ 817 (986)
+...|+..|...--.+||.+..|..+++.-..++-. + ++ +......++..-++.+.+...+.||
T Consensus 232 ---------g~~~R~~AK~i~fGiiYG~g~~~La~~lg~~~~eA~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~f~~~~P 302 (429)
T cd08643 232 ---------GLLSRDGAKTFIYAFLYGAGDEKLGQIVGDDLRTAKNLNAEWPQTKKGTIKKIADKAKGRVVRANFLKGLP 302 (429)
T ss_pred ---------ChHHHhhhHHHHHHHHHCCChhHHHHHhCCCHHHHHhhhhcccccccchhhhhhhhhhHHHHHHHHHHhCc
Confidence 115699999999999999999999887643222110 0 00 0000111223344556666666677
Q ss_pred HHHHHHHHHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecCCCcCchhhhhccCCCcchhhhhh
Q 001982 818 AARSIMGWLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDG 897 (986)
Q Consensus 818 ~A~~im~WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~Af~PNFIHSLDA 897 (986)
+.+ .|++++-....+.| . ..|..|-... + .. .+ .+-|++=+==|
T Consensus 303 ~v~---~~~~~~~~~a~~~G-y--v~tl~GRrr~----------~---------~~------~r-----~A~Nt~iQGsA 346 (429)
T cd08643 303 ALG---KLIKKVKEAAKKRG-H--LVGLDGRRIR----------V---------RS------AH-----AALNTLLQSAG 346 (429)
T ss_pred cHH---HHHHHHHHHHHhCC-c--eeCCCCCccc----------C---------ch------HH-----HHhChhhhhHH
Confidence 754 45555444433332 1 2455553211 0 00 01 14566555555
Q ss_pred HHHHHHHH-----HHhhcC----C---cEEEeeccc--cCCCCChhHHHHHHHHHHHHhc
Q 001982 898 SHMMMTAV-----ACRDAG----L---HFAGVHDSF--WTHACDVDEMNQILRKKFVELY 943 (986)
Q Consensus 898 sHmmlta~-----~~~~~G----i---~FasVHDSF--wThA~dvd~m~~ilRe~FV~Ly 943 (986)
+-+|..|. .+.+.| . -++.|||.. =++..+++.+.+++++++..-.
T Consensus 347 ADi~K~Ami~i~~~l~~~g~~~~~~~~lvlqVHDElv~ev~~~~ae~v~~~v~~~Me~a~ 406 (429)
T cd08643 347 AILMKKWLVLLDDELTAKGGVWGGDFEYCAWVHDEVQIECRKGIAEEVGKIAVEAAEKAG 406 (429)
T ss_pred HHHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEccceEEEeCHHHHHHHHHHHHHHHHHhh
Confidence 55554432 233344 3 246699998 7788889999999999886653
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=76.59 E-value=7.7 Score=45.32 Aligned_cols=223 Identities=20% Similarity=0.129 Sum_probs=125.6
Q ss_pred HHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCC-------
Q 001982 666 LSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNK------- 738 (986)
Q Consensus 666 l~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~------- 738 (986)
+++++..+ +++ .-|..|-|-==|-.+|.|.+|....++.| .-.|+|+..|..+-....++..+
T Consensus 109 iR~~Fva~--~G~---~lv~aDySQiElRvlA~lS~D~~Li~af~-----~g~DiH~~tA~~if~~~~e~v~~~~~~~~~ 178 (371)
T cd08640 109 IRKAFIAS--PGN---TLIVADYSQLELRLLAHMTRCKSMIEAFN-----AGGDFHSRTASGMYPHVAEAVANGEVLLEW 178 (371)
T ss_pred hhheEecC--CCC---EEEEechhhhhHHHHHHHcCCHHHHHHHH-----cCCCHHHHHHHHHhCCCHHHhccccccccc
Confidence 56665532 344 35889999999999999999999888776 34699999887654322211110
Q ss_pred -CCCCChhHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHH
Q 001982 739 -DPSKHPQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFE 817 (986)
Q Consensus 739 -~~~~~~~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~ 817 (986)
+.+.++....+. ...-.|+..|...--.+||.+..|...++ |+ +.+ -|+.+.+...+.||
T Consensus 179 ~~~~~~~~~~~~~--~~~~~R~~AK~infGi~YG~g~~~La~~l-------gi-s~~---------eA~~~i~~f~~~fP 239 (371)
T cd08640 179 KSEGKPPAPLLKD--KFKSERRKAKVLNFSIAYGKTAHGLAKDW-------KV-KLK---------EAERTVDAWYSDRP 239 (371)
T ss_pred ccccccccccccc--ccHHHHHHHHHHHHHHHhccchhHHHHHc-------CC-CHH---------HHHHHHHHHHHHCc
Confidence 000000000000 01345999999999999999999887644 33 222 13556666777788
Q ss_pred HHHHHHHHHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecCCCcCchhhhhccCCCcchhhhhh
Q 001982 818 AARSIMGWLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDG 897 (986)
Q Consensus 818 ~A~~im~WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~Af~PNFIHSLDA 897 (986)
+ +..|.+++.....+.| .| +|++|-...=|--.+ .+ -..+.+.--.+-|++=+==|
T Consensus 240 ~---v~~~~~~~~~~a~~~G-yv--~T~~GRrr~lp~i~s-----------------~~-~~~~~~~eR~avN~~IQGsA 295 (371)
T cd08640 240 E---VEQWQKKTKKEARERG-YT--RTLLGRYRYLPDIKS-----------------RN-RKKRGHAERAAINTPIQGSA 295 (371)
T ss_pred c---HHHHHHHHHHHHHHcC-cE--EccCCCEEECCCccc-----------------cc-HhhhhhhHHHHHhhhhhHHH
Confidence 7 5677777666554443 22 256654322110000 00 00010111124566666666
Q ss_pred HHHHHHHH-HHh------hcCCc-EEEeeccccCC--CCChhHHHHHHHHHHHH
Q 001982 898 SHMMMTAV-ACR------DAGLH-FAGVHDSFWTH--ACDVDEMNQILRKKFVE 941 (986)
Q Consensus 898 sHmmlta~-~~~------~~Gi~-FasVHDSFwTh--A~dvd~m~~ilRe~FV~ 941 (986)
+=++..|. .+. +.|.. +..|||+.+.. ...++....+|++.+.+
T Consensus 296 ADI~K~Ami~i~~~l~~~~~~~~lvlqVHDElv~evp~~~~~~~~~~v~~~Me~ 349 (371)
T cd08640 296 ADIAMKAMLRIYRNLRLKRLGWKLLLQIHDEVILEGPEEKADEALKIVKDCMEN 349 (371)
T ss_pred HHHHHHHHHHHHHHHhhccCCceEEEEEcceeEEEcCHHHHHHHHHHHHHHHHh
Confidence 65555442 221 23444 46699998864 44555566777776644
No 14
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.04 E-value=14 Score=47.82 Aligned_cols=208 Identities=16% Similarity=0.206 Sum_probs=126.7
Q ss_pred HHHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001982 665 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 744 (986)
Q Consensus 665 El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 744 (986)
++++++.. |++| .-|..|-|-==|-.+|.|.+|....++.| .-.|||+..|..+-..-.+
T Consensus 647 ~iR~~Fia--~~G~---~lv~aDySQIELRilAhls~D~~Li~af~-----~g~DiH~~tA~~~fg~~~e---------- 706 (887)
T TIGR00593 647 KIRKAFVA--EKGW---LLISADYSQIELRVLAHLSQDENLIEAFQ-----NGEDIHTETASRLFGVEIE---------- 706 (887)
T ss_pred hhhheEec--CCCC---eEEEechhHhHHHHHHHHcCCHHHHHHHh-----cCCChHHHHHHHHhCCChh----------
Confidence 35555543 2344 37888988888999999999999877765 3469999998876321100
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 745 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 824 (986)
Q Consensus 745 ~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~ 824 (986)
. ...-.|...|...--.+||.+.+|..+++ |+ +.+ -|+.+.+...+.||+ +..
T Consensus 707 --~-----vt~~~R~~AK~infGiiYG~g~~~La~~l-------~i-s~~---------eA~~~i~~yf~~yp~---v~~ 759 (887)
T TIGR00593 707 --D-----VTPNMRRIAKTINFGVVYGMSAFGLAQEL-------GI-SRK---------EAKEFIERYFARYPG---VKD 759 (887)
T ss_pred --h-----CCHHHHhhhhHhhcCcccccchhHHHHHc-------CC-CHH---------HHHHHHHHHHHHCcc---HHH
Confidence 0 01234999999999999999999887654 33 221 234455555667776 677
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecC-CCcCchhhhhccCCCcchhhhhhHHHHHH
Q 001982 825 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE-GNLVEIRKQRTAFPPNFVHSLDGSHMMMT 903 (986)
Q Consensus 825 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~-~d~vd~rKQ~~Af~PNFIHSLDAsHmmlt 903 (986)
|+.++.....+.|- | +|..|-.- .+..- +.....|.+.--.+.|.+=+==|+=+|..
T Consensus 760 ~~~~~~~~a~~~Gy-v--~Tl~GRrr-------------------~lp~i~s~n~~~r~~aeR~A~N~~iQGsAADi~K~ 817 (887)
T TIGR00593 760 YIENTVEEARKKGY-V--ETLFGRRR-------------------YIPDINSRNRNVREAAERMAINAPIQGSAADIMKI 817 (887)
T ss_pred HHHHHHHHHHHcCc-E--EecCCCEe-------------------eCCCccccchhhHhHHHhhhhhhhhhhHHHHHHHH
Confidence 88777766655541 2 45555210 11110 11111222222356787766666655544
Q ss_pred HH-----HHhhcCC--c-EEEeeccccCC--CCChhHHHHHHHHHHHH
Q 001982 904 AV-----ACRDAGL--H-FAGVHDSFWTH--ACDVDEMNQILRKKFVE 941 (986)
Q Consensus 904 a~-----~~~~~Gi--~-FasVHDSFwTh--A~dvd~m~~ilRe~FV~ 941 (986)
|. ++.+.|+ . +..|||..... ...++.+..++++.+-.
T Consensus 818 Ami~v~~~l~~~~~~~~lvlqVHDElv~Evp~~~~~~v~~~l~~~Me~ 865 (887)
T TIGR00593 818 AMIKLDKRLKERKLKARLLLQVHDELIFEAPEEEAEEVAALVKEVMEH 865 (887)
T ss_pred HHHHHHHHHHhcCCCeEEEeeEceEeeeecCHHHHHHHHHHHHHHHHh
Confidence 32 2445664 3 45699997754 46677778888887754
No 15
>PRK05755 DNA polymerase I; Provisional
Probab=75.44 E-value=12 Score=48.36 Aligned_cols=209 Identities=17% Similarity=0.206 Sum_probs=123.8
Q ss_pred HHHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001982 665 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 744 (986)
Q Consensus 665 El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 744 (986)
++++++.. |++| .-|..|-|.==|-.+|.|.+|.....+.| .-.|+|+.+|..+-..-.++
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 46666653 3455 47899999999999999999999887765 34699999887653221000
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 745 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 824 (986)
Q Consensus 745 ~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~ 824 (986)
...-.|+..|..+--..||.+..|...++ |+ +.+ -|+.+.+...+.||+ +..
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 33 222 245566666777777 566
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecCCCcCchhhhhccCCCcchhhhhhHHHHHHH
Q 001982 825 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTA 904 (986)
Q Consensus 825 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~Af~PNFIHSLDAsHmmlta 904 (986)
|++++.......| .| .|..|-...=|- + . +.....+.+.--.+.|++=+==|+=++..|
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 001111111122356776554444443332
Q ss_pred H-----HHhhcCC---cEEEeeccccCC--CCChhHHHHHHHHHHHH
Q 001982 905 V-----ACRDAGL---HFAGVHDSFWTH--ACDVDEMNQILRKKFVE 941 (986)
Q Consensus 905 ~-----~~~~~Gi---~FasVHDSFwTh--A~dvd~m~~ilRe~FV~ 941 (986)
. ...+.|+ -...|||+..-. ...++.+.+++++.+-.
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 366799998754 45566777777776543
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=71.36 E-value=22 Score=40.81 Aligned_cols=90 Identities=19% Similarity=0.159 Sum_probs=66.5
Q ss_pred HHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChh
Q 001982 666 LSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQ 745 (986)
Q Consensus 666 l~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~ 745 (986)
++.++..+ .+| .-|..|-|.==+=.+|.|.+|.....+.| ...|+|+.+|..+...-.
T Consensus 93 iR~~f~a~--~G~---~lv~aDysqiElRilA~ls~D~~l~~~~~-----~g~Dih~~~A~~~~g~~~------------ 150 (324)
T cd08639 93 FRRCFVAP--EGN---KLIIADYSQIELRIAAEISGDERMISAYQ-----KGEDLHRLTASLITGKPI------------ 150 (324)
T ss_pred cceeEEcC--CCC---EEEEechhhhHHHHHHHHhCCHHHHHHHh-----cCCCHhHHHHHHHhCCCh------------
Confidence 45555532 344 47899999999999999999999887765 356999999876522100
Q ss_pred HHHHHHhhcccccccccccceeeecccchhhHHHHHH
Q 001982 746 ALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIK 782 (986)
Q Consensus 746 ~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~ 782 (986)
... ..-.|+..|..+--..||.+..|..+++.
T Consensus 151 ~~v-----~~~~R~~aK~~~fg~~YG~g~~~L~~~l~ 182 (324)
T cd08639 151 EEI-----TKEERQLAKAVNFGLIYGMSAKGLREYAR 182 (324)
T ss_pred hhC-----CHHHHHHhhhHHHHHHhCCchHHHHHHHh
Confidence 000 12359999999999999999999988775
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=43.44 E-value=19 Score=42.11 Aligned_cols=207 Identities=20% Similarity=0.231 Sum_probs=123.4
Q ss_pred HHHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 001982 665 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 744 (986)
Q Consensus 665 El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 744 (986)
+++.++..+ .+ ++-|..|.|-==|=.+|.|.+|.....+.+ ...|+|..+|..+...-.++
T Consensus 144 ~~R~~f~a~--~G---~~lv~aD~sqiElRvlA~ls~D~~l~~~~~-----~g~D~h~~~a~~~~~~~~~~--------- 204 (383)
T PF00476_consen 144 EIRSAFVAP--PG---YVLVSADYSQIELRVLAHLSGDENLIEAFR-----NGEDIHTETASDIFGKPYEE--------- 204 (383)
T ss_dssp GGGGGEEGS--ST---EEEEEEEESSHHHHHHHHHHTHHHHHHHHH-----TTCCHHHHHHHHHTTCHGGG---------
T ss_pred ccceeEecC--cc---ceeeeeehhhhhHHHHHHhcccHHHHHhhc-----ccccHHHHHHHHhcCCCccc---------
Confidence 456665533 34 457889999888899999999998766665 45799999877653221110
Q ss_pred hHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 745 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 824 (986)
Q Consensus 745 ~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~ 824 (986)
.....|+..|..+--..||.+..|..+++. ++.+ -|+.+.++..+.||+ +..
T Consensus 205 --------v~~~~R~~aK~~~~g~~YG~g~~~la~~l~--------~s~~---------eA~~~~~~f~~~~p~---v~~ 256 (383)
T PF00476_consen 205 --------VTKEERQKAKTVNFGLIYGMGAKGLAEQLG--------ISEE---------EAKELIDAFFEAFPG---VKK 256 (383)
T ss_dssp --------TTHHHHHHHHHHHHHHHTT-THHHHHHHHT--------SCHH---------HHHHHHHHHHHHSHH---HHH
T ss_pred --------cchhhHHHHhHHHHhhhhccCHHHHHHHcc--------CCHH---------HHHHHHHHHHHhCch---HHH
Confidence 234689999999999999999988887763 3322 245566777778888 455
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecCCCcCchhhhh--ccCCCcchhhhhhHHHHH
Q 001982 825 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQR--TAFPPNFVHSLDGSHMMM 902 (986)
Q Consensus 825 WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~--~Af~PNFIHSLDAsHmml 902 (986)
|..++.......+ .| +|..|-.- .+.. .+..+..... --.+.|++=+-=|+=++.
T Consensus 257 ~~~~~~~~a~~~g-~v--~t~~gr~r-------------------~~p~-~~~~~~~~~~~~~r~a~N~~iQgsaAdi~k 313 (383)
T PF00476_consen 257 WMERVKKRARENG-YV--ETLFGRRR-------------------YLPN-IDSRNKSLRASAERQAVNTPIQGSAADIMK 313 (383)
T ss_dssp HHHHHHHHHHHHS-EE--ECTTSSEE-------------------ECGG-GGSSSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCC-eE--EEeccccc-------------------cCCc-hhcccchhhhHHHHHHHhHHHHHHHHHHHH
Confidence 5555544333221 11 34444322 1111 0111221111 112567665555554443
Q ss_pred HH---H--HHhhcCC---cEEEeeccccCC--CCChhHHHHHHHHHHHH
Q 001982 903 TA---V--ACRDAGL---HFAGVHDSFWTH--ACDVDEMNQILRKKFVE 941 (986)
Q Consensus 903 ta---~--~~~~~Gi---~FasVHDSFwTh--A~dvd~m~~ilRe~FV~ 941 (986)
.+ + .+.+.|+ -+..|||+++.. ...++.+.++|++.+..
T Consensus 314 ~am~~i~~~l~~~~~~~~l~l~VHDEli~ev~~~~~~~v~~~l~~~M~~ 362 (383)
T PF00476_consen 314 LAMIRIHEALREKGLGARLVLQVHDELIFEVPEDEAEEVAEILKEIMEN 362 (383)
T ss_dssp HHHHHHHHHHHHTT-SEEEEEEESSEEEEEEEGGGHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhcCcCceeEEEEcCeeheeecHhHHHHHHHHHHHHHHh
Confidence 32 2 2344444 356799998854 46678888888877654
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=33.67 E-value=67 Score=30.46 Aligned_cols=56 Identities=21% Similarity=0.483 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HcccCCCChhHHHHHHHHHHHHH
Q 001982 173 RKFNLLRRRQVKQETEAWERMVDEYKELEAKMI---EKRLAPNLPHIKGLFLGWFGPLS 228 (986)
Q Consensus 173 ~~~~~l~~RQ~~lE~~~~~~a~~r~~~~~~~~~---~~g~a~~~~~~~~ll~~w~~~L~ 228 (986)
..|.+..+|...|..+.++....+|.+.++++. +.|..++.+-++.++.+|+..+.
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 666666666667777777777777777766655 57888999999999999999665
No 19
>PLN03188 kinesin-12 family protein; Provisional
Probab=20.91 E-value=2.3e+03 Score=29.50 Aligned_cols=45 Identities=22% Similarity=0.234 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccCccchhhhhccCChhHHHHHHH
Q 001982 220 FLGWFGPLSEAIEREQKMQRTKKQKAAYAPHIELLPADKVAVIVM 264 (986)
Q Consensus 220 l~~w~~~L~~~I~~e~~~~~~~~~r~~y~p~L~~l~~e~lA~Iti 264 (986)
|..-+..+.+.|++-.++..+.|.+..-..|++.|-+|--|+=+=
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 334455566666665555555566666678888876665444333
No 20
>PF14554 VEGF_C: VEGF heparin-binding domain; PDB: 2VGH_A 4DEQ_A 1VGH_A 1KMX_A.
Probab=20.02 E-value=53 Score=28.15 Aligned_cols=18 Identities=56% Similarity=0.898 Sum_probs=11.6
Q ss_pred cccccCCcccceeecCCC
Q 001982 131 HQLMCLEPRRRIFVQDPP 148 (986)
Q Consensus 131 ~~~~~~~~~~~~~~~~~~ 148 (986)
|=.-+.|.++++|||||-
T Consensus 6 ~C~PCSErRk~Lfvqdp~ 23 (55)
T PF14554_consen 6 HCEPCSERRKRLFVQDPL 23 (55)
T ss_dssp ----SSSSSCTTEEE-TT
T ss_pred cccccHhHhhhhcccCcc
Confidence 334458999999999995
Done!