Query 001555
Match_columns 1055
No_of_seqs 150 out of 311
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 03:42:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001555.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001555hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03813 Nrap: Nrap protein; 100.0 3E-228 7E-233 2125.8 90.0 913 88-1048 1-972 (972)
2 KOG2054 Nucleolar RNA-associat 100.0 2E-197 4E-202 1726.5 67.3 1003 10-1048 81-1121(1121)
3 PTZ00418 Poly(A) polymerase; P 99.6 9E-14 1.9E-18 164.6 25.9 366 82-509 128-515 (593)
4 COG5186 PAP1 Poly(A) polymeras 99.4 1.4E-12 3E-17 142.4 16.3 272 83-396 84-366 (552)
5 KOG2245 Poly(A) polymerase and 99.4 8.8E-12 1.9E-16 142.1 20.3 308 83-441 92-411 (562)
6 PF04928 PAP_central: Poly(A) 99.1 1E-09 2.2E-14 120.1 13.6 147 227-378 96-251 (254)
7 TIGR03671 cca_archaeal CCA-add 98.9 1.6E-06 3.5E-11 100.3 29.7 357 17-498 2-367 (408)
8 PRK13300 tRNA CCA-pyrophosphor 98.8 3.5E-06 7.6E-11 98.9 28.9 357 17-499 3-371 (447)
9 COG1746 CCA1 tRNA nucleotidylt 98.2 0.00087 1.9E-08 77.1 27.9 258 16-376 6-267 (443)
10 PF03813 Nrap: Nrap protein; 98.1 0.00073 1.6E-08 87.8 27.1 342 13-396 478-852 (972)
11 smart00572 DZF domain in DSRM 96.3 0.16 3.4E-06 55.6 16.4 221 82-368 4-231 (246)
12 COG5260 TRF4 DNA polymerase si 96.0 0.089 1.9E-06 61.9 13.7 130 82-270 97-227 (482)
13 smart00572 DZF domain in DSRM 95.8 0.043 9.3E-07 59.9 9.4 98 729-829 114-220 (246)
14 PF04928 PAP_central: Poly(A) 95.6 0.03 6.5E-07 61.9 7.8 154 732-906 96-253 (254)
15 KOG1906 DNA polymerase sigma [ 95.0 1.6 3.5E-05 52.8 19.7 163 79-299 100-269 (514)
16 PRK13300 tRNA CCA-pyrophosphor 94.8 2.9 6.4E-05 50.0 21.3 229 568-886 17-255 (447)
17 KOG2054 Nucleolar RNA-associat 92.8 0.93 2E-05 57.6 12.6 169 223-396 804-987 (1121)
18 PF09249 tRNA_NucTransf2: tRNA 92.5 1.1 2.4E-05 43.3 9.9 108 242-374 1-112 (114)
19 PF07528 DZF: DZF domain; Int 92.3 4 8.7E-05 45.2 15.5 131 218-378 108-240 (248)
20 PTZ00418 Poly(A) polymerase; P 90.8 3.1 6.7E-05 51.2 13.7 173 730-918 238-417 (593)
21 TIGR03671 cca_archaeal CCA-add 90.7 2.1 4.5E-05 50.6 11.9 205 568-859 16-230 (408)
22 cd05400 NT_2-5OAS_ClassI-CCAas 89.3 1.6 3.4E-05 43.8 8.3 83 81-182 28-110 (143)
23 cd05402 NT_PAP_TUTase Nucleoti 89.0 2 4.4E-05 41.2 8.6 79 81-180 20-98 (114)
24 PF07528 DZF: DZF domain; Int 88.4 2.2 4.9E-05 47.2 9.3 101 729-830 114-223 (248)
25 PF10421 OAS1_C: 2'-5'-oligoad 86.4 4.5 9.8E-05 42.8 9.7 125 237-367 41-173 (190)
26 KOG2245 Poly(A) polymerase and 84.4 8.5 0.00018 46.0 11.6 142 744-907 214-360 (562)
27 PF10421 OAS1_C: 2'-5'-oligoad 66.3 7 0.00015 41.4 4.1 59 746-805 45-108 (190)
28 PF09249 tRNA_NucTransf2: tRNA 66.0 9.4 0.0002 37.0 4.6 96 749-886 3-104 (114)
29 COG5186 PAP1 Poly(A) polymeras 50.7 44 0.00095 38.6 7.1 151 732-906 194-351 (552)
30 COG1669 Predicted nucleotidylt 44.7 20 0.00043 34.0 2.8 29 81-110 25-53 (97)
31 KOG0925 mRNA splicing factor A 39.1 1.7E+02 0.0036 35.6 9.7 91 488-597 202-294 (699)
32 cd05397 NT_Pol-beta-like Nucle 36.6 40 0.00087 27.6 3.2 27 79-106 16-42 (49)
33 COG1746 CCA1 tRNA nucleotidylt 30.6 2.3E+02 0.0049 33.9 9.0 228 567-887 20-258 (443)
34 cd05403 NT_KNTase_like Nucleot 30.1 58 0.0013 29.2 3.5 32 79-111 17-48 (93)
35 PF09441 Abp2: ARS binding pro 29.6 24 0.00052 36.2 0.9 27 748-784 100-126 (175)
36 PF01909 NTP_transf_2: Nucleot 25.9 48 0.001 30.0 2.2 32 80-112 14-45 (93)
37 KOG2277 S-M checkpoint control 23.8 4.8E+02 0.01 32.5 11.1 132 234-369 256-431 (596)
No 1
>PF03813 Nrap: Nrap protein; InterPro: IPR005554 Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus []. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [].
Probab=100.00 E-value=3.2e-228 Score=2125.81 Aligned_cols=913 Identities=40% Similarity=0.649 Sum_probs=808.4
Q ss_pred eeccccccC--CCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhh--ccCCCCccEEEeccCCCcceeeEEEE
Q 001555 88 SYSINCVVK--PAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHL--KSSPSFDKVEWSAMQNEARKPVLVVY 163 (1055)
Q Consensus 88 S~~l~t~~k--~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L--~~~~~~~~v~~~~~~~d~~kPil~l~ 163 (1055)
||+++|++| ++.+|||+||||++|||+|||||||||||||+|||+||++| ++.+...+++|+++|||++||||+|+
T Consensus 1 S~~l~t~~k~~~~~~VDl~v~mP~~~fq~KDyln~RY~~KRA~YLa~iA~~L~~~~~~~~~~v~~~~~~gd~~kPil~l~ 80 (972)
T PF03813_consen 1 SYALKTMIKSKPNLTVDLAVEMPKSLFQEKDYLNYRYFHKRALYLAYIAAHLQKKKSKLFVDVSFEYLNGDPLKPILVLR 80 (972)
T ss_pred CcccccccccCCCCeeEEEEeCChhhcCchhhccchHHHHHHHHHHHHHHHHhhhccccceeEEEEeCCCCCCCCeEEEE
Confidence 899999999 88999999999999999999999999999999999999999 55578899999999999999999999
Q ss_pred eCCCCC----CCCCeEEEEeecCC-CcccccccCcccCCccCCCCCC----CCCCCCccchhhhhccChHHHHHHHHHHh
Q 001555 164 PAVKSV----EAPGFFVRIIPTAA-SLFNIAKLNLKRNNVRAFNQDG----IPRATPKYNSSILEDMFLEDNAEYVEKTI 234 (1055)
Q Consensus 164 p~~~~~----~~~~~~IRii~~~~-~~F~~~rl~P~rnnvR~~~~~~----~~~pTP~YNssIl~D~~~~~~l~~l~~~~ 234 (1055)
|+++.. .+++|+||||||++ ++||++||+|+|||||.....+ .++|||+||++||+||++.+|+++|+++.
T Consensus 81 p~~~~~~~~~~~~~~~iRi~~~~~~~~F~~~rl~P~rnnvR~~~~~~~~~~~~~pTP~YNssIL~D~~~~~~l~~l~~~~ 160 (972)
T PF03813_consen 81 PKGKKDSDDFSKTKFRIRIIPSIPSDTFPLSRLAPSRNNVRPSWFDEEDSSSLPPTPHYNSSILEDMLMEEHLKYLHEAS 160 (972)
T ss_pred ECCccccccccCCcEEEEEEecCCcccCCHHhcCCCCCccCcCcccccccCCCCCCCcchHHHHHHHhHHHHHHHHHHHH
Confidence 987543 34679999999964 9999999999999999864322 46999999999999999999999999999
Q ss_pred hChHHHHHHHHHHHHHHHhcCCCcCC--CCchhHHHHHHHHHHhhc------cccCcCCcHHHHHHHHHHHHhcCCCCCC
Q 001555 235 SRWKELGEALILLKVWARQRSSIYVH--DCLNGYLISILLSYLVSL------DKINNSMKALQILRVVLDFIATSKLWNR 306 (1055)
Q Consensus 235 ~~~~~f~dA~~LlkvWl~QRg~~~~~--ggf~gf~~s~lla~Ll~~------~~l~~~~SsyQifr~~l~fLa~~d~~~~ 306 (1055)
++||+|+|||+||||||+|||++++. ||||||+|+|||+||+++ ++++++||||||||++|+|||++||+++
T Consensus 161 ~~~p~f~dA~iLlkvWl~QRg~~~~~~~~Gf~~f~~s~lla~Ll~~g~~~~~~~l~~~mSsyQlFr~~l~fLA~~d~~~~ 240 (972)
T PF03813_consen 161 KSSPAFRDACILLKVWLRQRGFGSGISQGGFGGFEWSMLLAYLLQGGGRNGKKKLSKSMSSYQLFRAVLQFLATTDLSKK 240 (972)
T ss_pred hcCHHHHHHHHHHHHHHhcCCCCcccCCCCcchHHHHHHHHHHHcCCCccCCcccCCCCCHHHHHHHHHHHHhccccccC
Confidence 99999999999999999999999888 999999999999999998 9999999999999999999999999999
Q ss_pred ceeecCCCCCCCChhHHHhhhhcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHhhhhcCCCcccccccccc-ccc
Q 001555 307 GLYFPPKGQIGVSKEEKLQYKEAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGFEETFLTKI-DFP 385 (1055)
Q Consensus 307 ~i~~~~~~~~~~~~~~~~~f~~~f~vvf~D~sg~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~~~~d~F~~lFl~~~-~~~ 385 (1055)
|++|+.+++ +.+...+|++.|++||+|++|++|||++||.|+|++||+||+.|+++||+...|+|+++||+++ ++.
T Consensus 241 ~l~~~~~~~---~~~~~~~~~~~~~~vf~D~sg~~Nl~~~ms~~s~~~L~~eA~~tl~lL~~~~~d~F~~lFl~~~~~~~ 317 (972)
T PF03813_consen 241 PLFFKSSSD---STESLEEFHSAFDPVFVDPSGGLNLLAKMSPSSYEELQHEAKLTLELLDDSSDDGFDSLFLTKVDPPA 317 (972)
T ss_pred ceEEecCCC---ccchhhhhhccCCeEEEeCCCCEEEEEcCCHHHHHHHHHHHHHHHHHhccccccchhhhhcccCCccc
Confidence 999988754 4456788999999999999999999999999999999999999999999999999999999994 666
Q ss_pred ccccEEEEeecCCcccccccccCCchhhHH-HHHHHHHHHHHHhhccccceEEEEecCCCCcccccCCCCcCCCCceEEE
Q 001555 386 AKYDYCVRLNLRGHTEVHALGFCLDDECWR-LYEQKVHSLLNQGLVDRAKSIRVTWRNSPSEWNIENGLAVLDREPLLVG 464 (1055)
Q Consensus 386 ~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~lL~~aLgdR~~~i~~~~~~~~~~w~i~~~~~~~~~~~l~vG 464 (1055)
.+||++++|...............+...+. .+.++|+++|+||||||+++|++. .++.++|++.+.++.....+++||
T Consensus 318 ~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lL~raLgdR~~~i~v~-~~~~~~w~i~~~~~~~~~~~l~vG 396 (972)
T PF03813_consen 318 LRFDHVLRISPDSLLSSFSPDESLDFLSFSNYLLRKIYRLLKRALGDRAKLIRVL-RPSQPPWSISSKPPKSKPKTLTVG 396 (972)
T ss_pred ccCCEEEEEcchhhcccccccccccccchhHHHHHHHHHHHHHHHHHHHHeEEEe-CCCCCCcccCCCCCCCCCceEEEE
Confidence 999999999322111111111111212222 367899999999999999999997 777899999998776555589999
Q ss_pred EEecCccccccccccCCCCCCHHHHHHHHhhhcCcccccccCCCCeEEEEecCCCcccccchHHHHHHHHHHHcCCCCCC
Q 001555 465 ISVSSLEKLFRIVDIGPNAENKEEALRFRKFWGEKAELRRFKDGTIAESTVWESEQWTRHLILKGIIEYVLLRHLSLSKE 544 (1055)
Q Consensus 465 l~l~~~~~~~r~vd~GP~ad~~~ea~~FR~FWG~KsELRRFkDGsI~E~VvW~~~~~~~~~I~~~Iv~yiL~~H~~~~~~ 544 (1055)
++|| |+||+|+||+||+|||++||++||+|||+||||||||||||+|||||+. .+|+.||+|||+|||++|++++.+
T Consensus 397 l~ln-~~~~~r~vd~GP~a~d~~ea~~FR~FWG~KsELRRFkDGsI~EsVvWs~--~~~~~I~~~Iv~yiL~~H~~~~~~ 473 (972)
T PF03813_consen 397 LILN-PENAFRLVDRGPSAEDKEEAAAFREFWGEKSELRRFKDGSICESVVWSS--AERRLIPEQIVRYILQRHLKIPSD 473 (972)
T ss_pred EEEc-hhhceeeeeeCcCCcCcHHHHHHHHHhCchhhhcccCCCCEEEEEecCC--CCCCchHHHHHHHHHHHhcCCccc
Confidence 9995 9999999999999998899999999999999999999999999999955 578999999999999999999999
Q ss_pred cEEEecccchhhhccC----CCCccchHHHHHHHHHHHHHHHhccCCCCeeeeecccCCcccccccCCCCCCCCCccccc
Q 001555 545 NVVQIVDQLDFSLLHG----AKDLVSFSASLLEAFEVLSKRLHLIEDIPLKISSVQPLDSAFRFTSVFPPEPHPLANERH 620 (1055)
Q Consensus 545 ~i~~~~~~~d~~l~~~----~~~~~~~~~~~~~af~~L~k~Lr~L~~LPL~I~~V~p~sp~lRyTsv~pP~p~~~~~~~~ 620 (1055)
+|++.++++|..+... ......+++++++||++|+|.||+|+||||+|++|+|+||+|||||||||.|+.
T Consensus 474 ~i~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~af~~L~k~lr~L~~LPL~I~~v~p~sp~lRyts~~pp~p~~------ 547 (972)
T PF03813_consen 474 SISFIGDQFDSLLPLPGSGSSPTDEESFQSVMRAFDELEKDLRSLEDLPLSITSVQPASPALRYTSVFPPVPHA------ 547 (972)
T ss_pred eEEeehhhhhhhhcCccccCCCCchHHHHHHHHHHHHHHHHHhcCccCCcceeeeccCCHhhhcCCCCCCCCcc------
Confidence 9999999999876421 222346788999999999999999999999999999999999999999999872
Q ss_pred cccccCCCCCCccCceEEEEEeccCCCCCCCHHHHHHHHHHHHHHHHHHHhhccC--C----------eeeecCCceeee
Q 001555 621 TVSRLHKLTPSCIQPLEVMIQLEGSGNWPMDHVAIEKTKSAFLIKIGESLQNRWG--M----------TCSATEDDADIF 688 (1055)
Q Consensus 621 ~~~~~~~~~p~~~~pi~vvlqfE~SgkWPddl~AIq~~K~AF~lkia~~L~~~~~--~----------~~~v~~d~lDV~ 688 (1055)
+|.|++|++|+||||+|||||||++|||++|+||+++|+|.|+++++ + .+.++.++|||+
T Consensus 548 --------~~~~~~p~~vvl~fE~S~kWPddl~AI~~~K~Af~lkiae~L~~~~~~~~~~~v~~~~~~~~~~~~~~ldV~ 619 (972)
T PF03813_consen 548 --------VPRYIPPIEVVLQFESSGKWPDDLEAIQKTKTAFLLKIAEELEKQYGDGIKARVGLDNSLSPIANQAFLDVL 619 (972)
T ss_pred --------ccCCCCCEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHhhCCcceeeecccccccceeccceEEEE
Confidence 47899999999999999999999999999999999999999997766 4 455556679998
Q ss_pred c-cceeEEEEEeccchhhHHhhhc--cccc---c--ccc-cchhhhhhhhhHHHHHHHHHhcCCChhHHHHHHHHHHHhc
Q 001555 689 M-SGYAFRLKILHERGLSLVKSEN--GNKA---K--RVY-STDKILFIRGQHASMINGLQGRYPVFGPVVRVAKRWAASH 759 (1055)
Q Consensus 689 ~-~G~~FRl~I~~~rE~~Ll~~~~--~~k~---~--~~~-~~~~~~~~~p~h~~~i~~l~~r~pafs~tvRLaKrWl~sh 759 (1055)
+ +||+||+||+|+||++||+++. .+.. . ... ..+++.++.|+||++|++||+|||+|||||||+|||++||
T Consensus 620 ~~~G~~FRl~I~~~rE~~Ll~~~~~~~~~~~k~~~~~~~~~~~~~~~~~p~h~~~i~~l~~~~p~fs~tvRL~KrW~~sh 699 (972)
T PF03813_consen 620 YPEGYVFRLRIYHDREETLLKRQLKTEDGQLKQEATEALASLERRFIHLPKHTSAIHGLHTRFPSFSPTVRLAKRWLSSH 699 (972)
T ss_pred ecCccEEEEEEecchhHHHHHHhhcccCcccchhhhHHHHHHHHHHHhhHHHHHHHHHHHhhCCchhHHHHHHHHHHHhc
Confidence 8 9999999999999999999985 2211 1 111 1234455669999999999999999999999999999999
Q ss_pred CCCCCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCCCCCeEEEeCCCCCCHhhHHHHHHHHHHhhhhcc
Q 001555 760 LFSACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDWTFSALVVDINNDFGPEDFKVINDNFMSSRKASE 839 (1055)
Q Consensus 760 lLs~hi~eE~vELLva~vFl~p~p~~~P~S~~~GFlRfL~lLs~~DW~~~PLiVd~~~~lt~~~~~~i~~~F~~~R~~~~ 839 (1055)
||++||+||+||||||++|++|+||++|+||++||+|||+|||+|||+++|||||+|++++++++++|+++|.++|+
T Consensus 700 lLs~~i~~E~vELlva~vfl~~~p~~~P~S~~~GFlRfL~lLs~~dW~~~PLiVd~~~~l~~~~~~~i~~~f~~~R~--- 776 (972)
T PF03813_consen 700 LLSGHISEEAVELLVASVFLSPAPWSPPSSPQTGFLRFLHLLSTWDWREEPLIVDFNNELTEEDRAEIETNFDAWRK--- 776 (972)
T ss_pred cCcccCCHHHHHHHHHHHhcCCCCCCCCCCHhHHHHHHHHHHHhCCCCcCCEEEECCCCCCHHHHHHHHHHHHHhhc---
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCeEEEEecCCCCCCcccCCCCCHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccccccccccCCCCcEEEEecC
Q 001555 840 ENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRLVAYARSSANLLTKLILEDQTDSCRWECLFRTPLNNYDAVVLLHR 919 (1055)
Q Consensus 840 ~dp~~~~p~mfIaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~s~~~l~~~~~~~~~~~~~~~~lF~p~l~~YD~vI~L~~ 919 (1055)
+||++++|+|||||++|++|..||+.+|+++|++||++|||+|+++|+... ....+|+++|+||+++|||||||++
T Consensus 777 ~dp~~~~p~~~IaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~sl~~l~~~~----~~~~~~~~lF~~~l~~YD~vI~L~~ 852 (972)
T PF03813_consen 777 IDPAMNLPAMFIATPYDPEGSLWTRNGPSKVVAKRLTALAKASLKLLEEQG----LSDLDWKSLFRPPLSDYDFVIHLNP 852 (972)
T ss_pred cCccccCCcEEEEeCCCCCCCEeECCCCCHHHHHHHHHHHHHHHHHHHhcC----CCCCCHHHhcCCCccCCCEEEEecC
Confidence 599999999999999999999999999999999999999999999998432 2367999999999999999999999
Q ss_pred CCCCCcccccCCccccccccccccCCccccCCCCCcccccCChhhh-hccCCCCCChHHHHHHHHHHHcCCcEEEeecCC
Q 001555 920 DRLPYPRRLLFPSEVNRGRHVARVNASKAFGPFLVPEEMKGSSEEV-KNKMMVDFDPLRCFVGDVEKEYSKKLKLWYDSL 998 (1055)
Q Consensus 920 ~~lp~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~nl~~~~~~~-~~~~~v~fdPv~~~v~eL~~~yg~~~~FF~d~~ 998 (1055)
+.+|++.+.+. ....| +|+....... ....++|||||++|++||+++|||+++||||++
T Consensus 853 ~~l~~~~~~~~--------------~~~~~------knl~~~~~~~~~~~~~~~fdPv~~~v~eL~~~yg~~~~FF~d~~ 912 (972)
T PF03813_consen 853 KKLPRYSSSIA--------------SSSKF------KNLDSKSINDSLPEPVVGFDPVQLFVDELRRAYGDTALFFYDPY 912 (972)
T ss_pred ccCCchhhhcc--------------ccccc------CCcccccccccCCccccCCChHHHHHHHHHHHcCCcEEEEecCC
Confidence 99998754331 11123 4443321111 112378999999999999999999999999999
Q ss_pred CCcEEEEEEecCCCCccc----------ccCCCccccCHHHHHHHHHHhccccceEEEec
Q 001555 999 GGDAIGLTWERVGSKKRE----------REEAPEEETDSIGVLKAVGELGKGFVRDIYFL 1048 (1055)
Q Consensus 999 gg~vIg~~w~P~~~~~~~----------~~~~~~v~~N~~ail~ei~~lG~gLV~~I~~~ 1048 (1055)
||++|||+|||++.++++ ..+++.|++|++|||+||++||||||++||++
T Consensus 913 gg~vIg~lW~P~~~~p~~fkv~~~~~~~p~~~~~v~lN~~ail~ei~~lG~~LV~~I~~~ 972 (972)
T PF03813_consen 913 GGDVIGVLWNPSAFKPRPFKVSLSYSRKPVSKGKVELNKEAILEEIKRLGGGLVKSIEVK 972 (972)
T ss_pred CCCEEEEEECCCcCCCCcccccCccceeEcCCCeEEECHHHHHHHHHHHHhhhhheEEcC
Confidence 999999999999854332 12356799999999999999999999999985
No 2
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=100.00 E-value=1.7e-197 Score=1726.53 Aligned_cols=1003 Identities=35% Similarity=0.551 Sum_probs=854.5
Q ss_pred cCcccccHHHhhcccccCCCchhhhHHHHHHHHHHHHHhcCCCCCCCCcccCCccccccCCceeEEEEeCCceee-Eeee
Q 001555 10 TDPMDYKVEELLKEVHFARAPAITKLVDDTVSAVRKSISKIPDAFPVTADLAPGFVRDIGADKVEFKFNKPKTFK-IGGS 88 (1055)
Q Consensus 10 ~~~f~LQidELL~ev~~~~~~~~~~~le~~L~~lk~~i~~ip~~~~~~~~~~~~~~~~~~~~~~~f~f~~P~~v~-vvGS 88 (1055)
++.||||++|+++|++++.++ ...+|.+||...+++.+..+.--.+. .++--+++.. -.-+|.|.||.+|. ||||
T Consensus 81 s~~f~lq~~e~l~~~~L~~k~--~~~ie~fl~~~~~~l~~~~D~~~~~~-~~~vp~~~~~-~~~~~~f~~p~~v~~vv~s 156 (1121)
T KOG2054|consen 81 SNLFRLQVEELLKEVRLKQKK--KDRIEAFLESPNKRLVELKDQLNLPY-AVKVPLKDCP-YAVKFRFLPPAQVTKVVGS 156 (1121)
T ss_pred cchhhcchhhhhhhhcccccc--ccHHHHHHHHHHHHHHHhhhhhcccc-cccccccccc-ccccccccCccccceeeee
Confidence 568999999999999999888 55799999999999994433311111 1111111111 12338899999999 8888
Q ss_pred eccccccCCCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhhccCCCCccEEEeccCCCcceeeEEEEeCCCC
Q 001555 89 YSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLVVYPAVKS 168 (1055)
Q Consensus 89 ~~l~t~~k~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~~~~~~~v~~~~~~~d~~kPil~l~p~~~~ 168 (1055)
+..+++.+|+..||++|+||++.|+.|||||.|||+|||.||+|+|+||-....+.+++|.|.|||++||||.|+|.+++
T Consensus 157 al~~~~~~P~i~vDvll~mP~e~~~~kd~ln~Ryf~kra~yla~~~~hl~e~l~~~~~~f~~~n~d~~~pil~i~~~~~~ 236 (1121)
T KOG2054|consen 157 ALLGTCLRPDISVDVLLTMPREILQQKDGLNQRYFRKRALYLAYLAHHLLEDLLFGSLEFSYTNGDHLKPILLIRPRGKD 236 (1121)
T ss_pred cccCcccCCcchhhhhhhhhHHhhcCcccccccccchHHHHHHHHHHHHHhccccceeeecccCCccccchhhccccCCc
Confidence 88899999999999999999999999999999999999999999999999888889999999999999999999999876
Q ss_pred CCC--CCeEEEEeecCCCcccccccCcccCCccCCCCCCCCCCCCccchhhhhccChHHHHHHHHHHhhChHHHHHHHHH
Q 001555 169 VEA--PGFFVRIIPTAASLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKELGEALIL 246 (1055)
Q Consensus 169 ~~~--~~~~IRii~~~~~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssIl~D~~~~~~l~~l~~~~~~~~~f~dA~~L 246 (1055)
... .++..-+|||.--.|+.+||+|.+||+|..++.++++|||.||+++|+|++.++|+++|+++.+..++|+|||.|
T Consensus 237 ~~~~~~~~~~~li~~~~~~f~~~kllp~~~~ir~~~e~~e~ppTP~yN~svL~~~~le~~~q~L~K~~s~~~~f~da~~L 316 (1121)
T KOG2054|consen 237 ERLVTVRPPDFLIPCRLLPFKNNKLLPWYNGIRPAGEGSEEPPTPRYNTSVLEDQVLEEYLQLLSKTLSSAKGFKDALAL 316 (1121)
T ss_pred cccccccCccccccccccccccccccchhcccCccccCCCCCCCCccchhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence 442 245667788877899999999999999999887789999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCcCCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCCChhHHHhh
Q 001555 247 LKVWARQRSSIYVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGVSKEEKLQY 326 (1055)
Q Consensus 247 lkvWl~QRg~~~~~ggf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~~~~~~~~f 326 (1055)
||+|||||.++.+.||||+|+|+|+|+||+.+++|+.+||+||+||.+|+|||++||+.+||.++.++ .+.+...+|
T Consensus 317 lk~WlrqRs~~~~~~gfg~f~~s~lvv~L~s~~ki~~~~S~yqvfR~vl~flat~dlt~~~~~l~~~~---~s~~~~~~f 393 (1121)
T KOG2054|consen 317 LKVWLRQRSLDIGQGGFGGFLLSALVVYLVSTRKIHTTLSAYQVFRSVLQFLATTDLTVNGISLVPSS---PSLPALADF 393 (1121)
T ss_pred HHHHHHhhhhhcccCcchHHHHHHHHHHHHhcCchhhcchHHHHHHHHHHHHhhhhhhccceEeccCC---CCchhhhhh
Confidence 99999999988899999999999999999999999999999999999999999999999999887653 455677889
Q ss_pred hhcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHhhhhcCCCcccccccccccccccccEEEEeecCCcc---ccc
Q 001555 327 KEAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGFEETFLTKIDFPAKYDYCVRLNLRGHT---EVH 403 (1055)
Q Consensus 327 ~~~f~vvf~D~sg~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~~~~d~F~~lFl~~~~~~~~fD~~~~i~~~~~~---~~~ 403 (1055)
++++.++|+|.+|.+|||++||.++|+++|+||+.|+.+||+...|+|+.+||++++.+.+||+++++..-... ...
T Consensus 394 ~e~~~~~f~D~s~~~NLc~~mt~s~y~~~q~ea~ltl~lL~~~~~~~F~~IFmtkip~~~~yDh~l~l~~~~~l~~~~~~ 473 (1121)
T KOG2054|consen 394 HEGQLVTFIDSSGHLNLCANMTASTYEQVQEEARLTLMLLDSRADDGFSLIFMTKIPVFRAYDHVLHLSPLSRLQAAEHL 473 (1121)
T ss_pred hhcceeeEeccCCcchhhhhccHHHHHHHHHHHHHHHHHHhhhhhcCcceeeeecCCchhhhheeeeccccchhhhHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999632211 112
Q ss_pred ccccCCch---hhHHHHHHHHHHHHHHhhccccceEEEEecCCCCcccccCCCCcCCCCceEEEEEecCccccccccccC
Q 001555 404 ALGFCLDD---ECWRLYEQKVHSLLNQGLVDRAKSIRVTWRNSPSEWNIENGLAVLDREPLLVGISVSSLEKLFRIVDIG 480 (1055)
Q Consensus 404 ~~~~~~~~---~~~~~~~~~i~~lL~~aLgdR~~~i~~~~~~~~~~w~i~~~~~~~~~~~l~vGl~l~~~~~~~r~vd~G 480 (1055)
....|... ..|..+...+..+|++|||||++.|.+. ....+.|++++.+++..++.+.+|++++ |+.+.|+||+|
T Consensus 474 ~~~~~~~~d~~~~y~~~lh~~t~ll~~gLgdRv~~I~~~-~~~~~~w~is~~p~~~~~~~i~lglll~-pe~~~~~l~iG 551 (1121)
T KOG2054|consen 474 LSGFCEKQDNGGLYSQLLHPLTTLLEQGLGDRVKSIAIS-RPIVPEWSISEDPPKHGDKTITLGLLLS-PEGLYRVLTIG 551 (1121)
T ss_pred cccchhhhhcccHHHHHHHHHHHHHHHHHHHHHhhhhhc-cCCccccccccCcccccCceEEEEEEec-hHHhcchhhcC
Confidence 22233222 2455667778899999999999999986 5678999999998886568899999995 99999999999
Q ss_pred CCCCCHHHHHHHHhhhcCcccccccCCCCeEEEEecCCCc-ccccchHHHHHHHHHHHcCCCCCCcEEEecccchhhhcc
Q 001555 481 PNAENKEEALRFRKFWGEKAELRRFKDGTIAESTVWESEQ-WTRHLILKGIIEYVLLRHLSLSKENVVQIVDQLDFSLLH 559 (1055)
Q Consensus 481 P~ad~~~ea~~FR~FWG~KsELRRFkDGsI~E~VvW~~~~-~~~~~I~~~Iv~yiL~~H~~~~~~~i~~~~~~~d~~l~~ 559 (1055)
|+|||.+||++||+|||+||||||||||+|+|||||++.+ .+++.|++|||+|+|++|++++..+++++++++|..+..
T Consensus 552 P~aed~~ea~kFR~FWGekSeLRRFkDGsI~E~vVWet~s~~~~~lIp~qIV~h~LqkHlsl~a~~~~~~~~~ld~~~~~ 631 (1121)
T KOG2054|consen 552 PAAEDQEEAAKFREFWGEKSELRRFKDGSITEAVVWETASSSQKRLIPRQIVTHLLQKHLSLPATCVVYVGGELDAVLQL 631 (1121)
T ss_pred CCcccChhHHHHHHHhcchhhhhhhcCCceeEEEEeecCCcccccccHHHHHHHHHHHhcCCCcceeeeeccchHHHHhh
Confidence 9998899999999999999999999999999999999876 568999999999999999999999999999999977543
Q ss_pred CCCC----ccchHHHHHHHHHHHHHHHhccCCCCeeeeecccCCcccccccCCCCCCCCCccccccccccCCCCCCccCc
Q 001555 560 GAKD----LVSFSASLLEAFEVLSKRLHLIEDIPLKISSVQPLDSAFRFTSVFPPEPHPLANERHTVSRLHKLTPSCIQP 635 (1055)
Q Consensus 560 ~~~~----~~~~~~~~~~af~~L~k~Lr~L~~LPL~I~~V~p~sp~lRyTsv~pP~p~~~~~~~~~~~~~~~~~p~~~~p 635 (1055)
.... ....+ ++++|||+|.|.|++|+||||+|++|+|+||+|||||||||.| ..+....... .+-+++
T Consensus 632 lk~~~~t~~~~l~-~v~kaYddLsk~L~gL~gLPLsIssV~g~~~~lRyts~~pp~~-~~~~~~~es~----~~q~~i-- 703 (1121)
T KOG2054|consen 632 LKESSSTSSENLY-AVVKAYDDLSKVLRGLKGLPLSISSVLGASSALRYTSVFPPSV-AVAFSFYESS----RLQSSI-- 703 (1121)
T ss_pred CCCCcccchhhHH-HHHHHHHHHHHHHhcccCCCceeeeeccccchhcccccCCCCC-Ccccccccch----hhhhhh--
Confidence 2211 11223 8999999999999999999999999999999999999999976 3222221111 112222
Q ss_pred eEEEEEeccCCCCCCCHHHHHHHHHHHHHHHHHH-HhhccCCeeeecCCceeeeccceeEEEEEeccchhhHHhhhc---
Q 001555 636 LEVMIQLEGSGNWPMDHVAIEKTKSAFLIKIGES-LQNRWGMTCSATEDDADIFMSGYAFRLKILHERGLSLVKSEN--- 711 (1055)
Q Consensus 636 i~vvlqfE~SgkWPddl~AIq~~K~AF~lkia~~-L~~~~~~~~~v~~d~lDV~~~G~~FRl~I~~~rE~~Ll~~~~--- 711 (1055)
|+||||||+|||||||++||||+|+||++||||+ |++++|+.|+++.|++||+.+||+||+||.|+||..++++..
T Consensus 704 ~~VviqlE~SgKWP~d~eai~r~ksAFlLKIaE~~lr~q~gl~~~~t~d~~~vlk~Gy~Frirv~~dRei~llk~v~~~~ 783 (1121)
T KOG2054|consen 704 MTVVIQLEGSGKWPDDLEAIRRLKSAFLLKIAERNLRAQHGLTCVATADHLDVLKSGYVFRIRVLNDREIILLKDVQSER 783 (1121)
T ss_pred eEEEEEeccCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhCCCcccCccceeeecCccEEEEEEecchhHHHHHHHhhhc
Confidence 7999999999999999999999999999999995 999999999999999999999999999999999999998862
Q ss_pred -ccccc---ccccchhhhhhhhhHHHHHHHHHhcCCChhHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHhhcCCCCCCCC
Q 001555 712 -GNKAK---RVYSTDKILFIRGQHASMINGLQGRYPVFGPVVRVAKRWAASHLFSACLVEEAVELLVAYLFLKPLPFNVP 787 (1055)
Q Consensus 712 -~~k~~---~~~~~~~~~~~~p~h~~~i~~l~~r~pafs~tvRLaKrWl~shlLs~hi~eE~vELLva~vFl~p~p~~~P 787 (1055)
..+.. .....++..++.|+|+++||++||+||+||+||||||||+++|+|++|+.||++|||||++|++|.||.+|
T Consensus 784 ~s~~~~~~a~~~~~e~~~~~~p~ht~aL~~l~qsh~~ys~vvrLaKrWl~shLL~~h~~De~iELLva~lf~~p~p~~~p 863 (1121)
T KOG2054|consen 784 GSTKLRDEAASLSLEKKFIILPLHTLALQSLSQSHPFYSSVVRLAKRWLGSHLLSGHHLDEAIELLVAALFLKPGPLVPP 863 (1121)
T ss_pred cccccchhHHHHHHHHHHhhhHHHHHHHHHHhhcccchhHHHHHHHHHHHHHhhccchHHHHHHHHHHHHhcCccCCCCC
Confidence 22222 22334566777899999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhhHHHHHHHHHhcCCCCCCeEEEeCCCCCCHhhHHHHHHHHHHhhhhccccccCCCCeEEEEecCCCCCCcccCCCC
Q 001555 788 CSRVTGFLRFLRLLAEYDWTFSALVVDINNDFGPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSP 867 (1055)
Q Consensus 788 ~S~~~GFlRfL~lLs~~DW~~~PLiVd~~~~lt~~~~~~i~~~F~~~R~~~~~dp~~~~p~mfIaT~~D~~g~~wT~~~P 867 (1055)
+|+++||+|||+|||+|||+.+|||||+|++++++|+.++.+.|.+.|+ ..|+|+|+|+||..|..||..+|
T Consensus 864 sS~~~gFlRfL~llS~~dW~~~PLIvd~nn~~~ed~~~e~~e~f~s~R~--------~lp~m~vit~yD~~~~~~t~~~P 935 (1121)
T KOG2054|consen 864 SSPENGFLRFLSLLSTWDWKFDPLIVDFNNGFPEDERSELEEKFISARK--------QLPPMVVITPYDHLGSKFTRTSP 935 (1121)
T ss_pred CCcchhHHHHHHHHhcCcccCCceEEEcCCCCcHHHHHHHHHHHhhhcc--------cCCceEEeeccccccccccccCc
Confidence 9999999999999999999999999999999999999999999999999 45899999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccccccccccCCCCcEEEEecCCCCCCcccccCCcccccc----cccccc
Q 001555 868 NFTELKRLVAYARSSANLLTKLILEDQTDSCRWECLFRTPLNNYDAVVLLHRDRLPYPRRLLFPSEVNRG----RHVARV 943 (1055)
Q Consensus 868 s~~v~~Rl~~LAk~s~~~l~~~~~~~~~~~~~~~~lF~p~l~~YD~vI~L~~~~lp~~~~~l~~~~~~~~----~~~~~~ 943 (1055)
+..|+.|++++|+.|++++++.+.++-...+.+.++|+.+|..||.||.+++..+|++....+....+.. ...+.+
T Consensus 936 ~~~v~~r~~alar~sl~ll~k~~p~~~~t~~~~~~lf~~~L~~yd~vi~~~~~~lp~~~~~~~~~~~~~~~p~~~~pv~g 1015 (1121)
T KOG2054|consen 936 NQIVLNRLVALARESLKLLEKQAPGEIKTIVRPTSLFRENLSPYDAVIQLEPNKLPRPRALDLRKPLNSTKPRQLKPVAG 1015 (1121)
T ss_pred hHHHHHHHHHhhhhhHHhhcccccccchhhhhhhhhhhcccccccchhcccccccCCchhhccccccccccccccCcchh
Confidence 9999999999999999999887665433456789999999999999999999999998665443332210 000000
Q ss_pred CCccccC---CCCCcccccCChhhhhccCCCCCChHHHHHHHHHHHcCCcEEEeecCCCCcEEEEEEecCCCCccccc--
Q 001555 944 NASKAFG---PFLVPEEMKGSSEEVKNKMMVDFDPLRCFVGDVEKEYSKKLKLWYDSLGGDAIGLTWERVGSKKRERE-- 1018 (1055)
Q Consensus 944 ~~~~~~~---~~~~~~nl~~~~~~~~~~~~v~fdPv~~~v~eL~~~yg~~~~FF~d~~gg~vIg~~w~P~~~~~~~~~-- 1018 (1055)
.-...|. ++. .++.+ -+-++-+++.|...|-+.|+...-+||. .||.-||..|++..-++..++
T Consensus 1016 ~~~~a~~~~n~f~--~~~pg--------~~~~~~~~~~~~~~l~~~f~~l~~~fy~-~g~~~v~t~~~~~e~~~~~k~n~ 1084 (1121)
T KOG2054|consen 1016 LLRSAYQLFNSFF--YVLPG--------GLWRTSSIHKLKNKLWRNFLFLLSDFYY-KGGGPVGTGWKKPEDKKPAKDNR 1084 (1121)
T ss_pred hhhhhhhhhhhhh--ccCCC--------cccchHHHHHHHHHHHHHHHHHHHHHHh-cCCCceeeeecchhhcccccccc
Confidence 0000000 000 00000 0224788999999999999999988888 588888888888763332221
Q ss_pred -------CCCccccCHHHHHHHHHHhccccceEEEec
Q 001555 1019 -------EAPEEETDSIGVLKAVGELGKGFVRDIYFL 1048 (1055)
Q Consensus 1019 -------~~~~v~~N~~ail~ei~~lG~gLV~~I~~~ 1048 (1055)
++..|++|+++|++||..+|+|||++++++
T Consensus 1085 d~~~k~v~~~~~~Ln~~~i~~ei~~~g~~lv~~~ql~ 1121 (1121)
T KOG2054|consen 1085 DSEEKSVSDPTVRLNRDGILEEILILGQDLVKSVQLK 1121 (1121)
T ss_pred ccccccCCCchheechhhhhhHHHHhccCcccccccC
Confidence 234689999999999999999999999863
No 3
>PTZ00418 Poly(A) polymerase; Provisional
Probab=99.61 E-value=9e-14 Score=164.60 Aligned_cols=366 Identities=13% Similarity=0.209 Sum_probs=236.0
Q ss_pred eeeEeeeeccccccCCCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhhccCCCCccEEEeccCCCcceeeEE
Q 001555 82 TFKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLV 161 (1055)
Q Consensus 82 ~v~vvGS~~l~t~~k~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~~~~~~~v~~~~~~~d~~kPil~ 161 (1055)
.|-.+|||.||. ..|+..||.++..|+.+ .|.-|...+...|++.+...++. ---|+..|+|.
T Consensus 128 ~I~tfGSYrLGV-~~pgSDID~L~V~P~~v-------------tredFF~~f~~~L~~~~~V~eL~---~V~~A~VPiIk 190 (593)
T PTZ00418 128 KLFTFGSYRLGV-VAPGSDIDTLCLAPRHI-------------TRESFFSDFYAKLQQDPNITKLQ---PVPDAYTPVIK 190 (593)
T ss_pred EEEEeccccccC-CCCCCcccEEEECCCCC-------------CHHHHHHHHHHHHhcCCCcceee---ccCccccCeEE
Confidence 466999999994 66788999999999765 35555667888888765444443 45789999999
Q ss_pred EEeCCCCCCCCCeEEEEeec--CCCcccccccCcccC-CccCCCCCCCCCCCCccchhhhhccChHHHHHHHHHHhhChH
Q 001555 162 VYPAVKSVEAPGFFVRIIPT--AASLFNIAKLNLKRN-NVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWK 238 (1055)
Q Consensus 162 l~p~~~~~~~~~~~IRii~~--~~~~F~~~rl~P~rn-nvR~~~~~~~~~pTP~YNssIl~D~~~~~~l~~l~~~~~~~~ 238 (1055)
+.-. ++.|-|..| +...-|..-=.++.+ -+|...+ ..----|.. .-..++-+...+.+
T Consensus 191 ~~~~-------GI~iDL~fa~l~~~~vp~~~~~l~d~~lL~nlde----~s~rSLNG~--------Rvtd~Il~lVPn~~ 251 (593)
T PTZ00418 191 FVYD-------GIDIDLLFANLPLPTIPDCLNSLDDDYILRNVDE----KTVRSLNGC--------RVADLILASVPNKD 251 (593)
T ss_pred EEEC-------CEEEeeeecccCCCCCCccccccCchhhhhcCCH----HHhhhhccH--------HHHHHHHHHCCChH
Confidence 9875 478888887 222332221112222 2222110 000011111 22345555567789
Q ss_pred HHHHHHHHHHHHHHhcCCCcC-CCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCC-
Q 001555 239 ELGEALILLKVWARQRSSIYV-HDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQI- 316 (1055)
Q Consensus 239 ~f~dA~~LlkvWl~QRg~~~~-~ggf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~- 316 (1055)
+|+-|++.+|.||++||.+++ .|.+||..||||+|.+|| +.+.+++-+|+..++...|+++|. +|+.++...+.
T Consensus 252 ~Fr~aLR~IKlWAkrRGIYsNv~GflGGV~wAILvARVCQ---LyPna~~s~Lv~~FF~iys~W~Wp-~PV~L~~i~~~~ 327 (593)
T PTZ00418 252 YFRTTLRFIKLWAKRRGIYSNVLGYLGGVSWAILTARICQ---LYPNFAPSQLIHKFFRVYSIWNWK-NPVLLCKIKEVP 327 (593)
T ss_pred HHHHHHHHHHHHHHHhccccccccccchHHHHHHHHHHHH---hCCCCCHHHHHHHHHHHhhcCCCC-CCeEcccccccc
Confidence 999999999999999998766 566799999999999998 888999999999999999999995 69888754321
Q ss_pred ----CCC------hhHHHhhhhcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHhhhh--c-CCCccccccccccc
Q 001555 317 ----GVS------KEEKLQYKEAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDK--C-GDGGFEETFLTKID 383 (1055)
Q Consensus 317 ----~~~------~~~~~~f~~~f~vvf~D~sg~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~--~-~~d~F~~lFl~~~~ 383 (1055)
... ..+..+-.+.+||+ .-..-.+|.++++|.++.+.|+.|-+++.+++++ . +...+..+| .+.+
T Consensus 328 ~~~g~~~~~VWdPr~~~~dr~h~MPII-TPayP~mNst~nVt~sT~~vI~~Ef~Ra~~i~~~i~~~~~~~W~~Lf-ep~~ 405 (593)
T PTZ00418 328 NIPGLMNFKVWDPRVNPQDRAHLMPII-TPAFPSMNSTHNVTYTTKRVITEEFKRAHEIIKYIEKNSENTWTNVL-EPLD 405 (593)
T ss_pred cCCcccCCcccCCCCCcccccccCCee-cCCCCCccccccccHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHc-CCcc
Confidence 000 00112334556664 6677789999999999999999999999999986 2 446899999 6889
Q ss_pred ccccccEEEEeecCCcccccccccCCchhhHHHH-HHHHHHHHHHhhccccceEEEEecCCCCcccc--cCCCCc-CCCC
Q 001555 384 FPAKYDYCVRLNLRGHTEVHALGFCLDDECWRLY-EQKVHSLLNQGLVDRAKSIRVTWRNSPSEWNI--ENGLAV-LDRE 459 (1055)
Q Consensus 384 ~~~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~i~~lL~~aLgdR~~~i~~~~~~~~~~w~i--~~~~~~-~~~~ 459 (1055)
|..+|-+++.|.+.+... .+...|..+ +.++.. |...|- |...|.+. .|+- ...... .-..
T Consensus 406 Ff~~Yk~yl~V~v~a~~~-------~~~~~w~G~VESRlR~-Lv~~LE-~~~~i~~~------p~P~~f~~~~~~~~~~~ 470 (593)
T PTZ00418 406 FFTSYKHFLVIQVYATNE-------HVHNKWEGWIESKIRF-LIKKLE-TLNNLKIR------PYPKFFKYQDDGWDYAS 470 (593)
T ss_pred hhhhcceEEEEEEEECCH-------HHhhhhhhHHHHHHHH-HHHHhh-ccCCceEe------ecCcccccCCCCceeEE
Confidence 999999999998643211 122335443 455554 666664 45555442 1211 110000 0123
Q ss_pred ceEEEEEecCccccccccccCCCCCCHHHHHHHHhhhcCcccccccCCCC
Q 001555 460 PLLVGISVSSLEKLFRIVDIGPNAENKEEALRFRKFWGEKAELRRFKDGT 509 (1055)
Q Consensus 460 ~l~vGl~l~~~~~~~r~vd~GP~ad~~~ea~~FR~FWG~KsELRRFkDGs 509 (1055)
.+.|||.+. ..+.. .+...|=.....+|.+.=..-.+-..++|+.
T Consensus 471 ~ffIGL~~~-~~~~~----~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~ 515 (593)
T PTZ00418 471 SFFIGLVFF-SKNVY----NNSTFDLRYAIRDFVDIINNWPEMEKYPDQI 515 (593)
T ss_pred EEEEeEeec-cCCCC----CCceEecHHHHHHHHHHHHhhhhcccCCCCc
Confidence 599999995 32211 1112232334567775432222222355654
No 4
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=99.45 E-value=1.4e-12 Score=142.44 Aligned_cols=272 Identities=14% Similarity=0.201 Sum_probs=204.0
Q ss_pred eeEeeeeccccccCCCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhhccCCCCccEEEeccCCCcceeeEEE
Q 001555 83 FKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLVV 162 (1055)
Q Consensus 83 v~vvGS~~l~t~~k~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~~~~~~~v~~~~~~~d~~kPil~l 162 (1055)
|-..|||.|| +..|+..||-.|.+|+.. -|.-|..++...|+..+...++. --.|...|||.+
T Consensus 84 IFTyGSYRLG-VhgpGsDIDtLvvVPkHV-------------sR~dFFt~f~~~Lrer~ei~eva---~vpDAfVPIIK~ 146 (552)
T COG5186 84 IFTYGSYRLG-VHGPGSDIDTLVVVPKHV-------------SRSDFFTHFYEELRERPEIEEVA---KVPDAFVPIIKL 146 (552)
T ss_pred eeeecceeee-ccCCCCCcceEEEecccc-------------cHHHHHHHHHHHhccCcchhhhc---cCCcccceeEEE
Confidence 4467999998 466788999999999875 66777779999998765443333 557899999999
Q ss_pred EeCCCCCCCCCeEEEEeec-CC-CcccccccCcccCCccCCCCCCCCCCCCccchhhhhccChHHHHHHHHHHhhChHHH
Q 001555 163 YPAVKSVEAPGFFVRIIPT-AA-SLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKEL 240 (1055)
Q Consensus 163 ~p~~~~~~~~~~~IRii~~-~~-~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssIl~D~~~~~~l~~l~~~~~~~~~f 240 (1055)
+-.| ..|.+|.+ .+ ..-|.+--+-++|-+|.-.+.. -=--|.+-..| +.|++ ..+-..|
T Consensus 147 KF~G-------IsIDLifARLs~P~Vp~~l~Lsd~nLLk~~dEkc----ilsLNGtRVTD----eiL~L----VP~~~vF 207 (552)
T COG5186 147 KFQG-------ISIDLIFARLSIPVVPDGLNLSDDNLLKSMDEKC----ILSLNGTRVTD----EILNL----VPSVKVF 207 (552)
T ss_pred EecC-------ccceeeeeeccCCcCCCcccccchhhhhcchHHH----HHhhcCceehH----HHHHh----CCchHHH
Confidence 8764 67888876 22 3444444445566566532210 01234444444 44444 4556789
Q ss_pred HHHHHHHHHHHHhcCCCcCCCC-chhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCCC
Q 001555 241 GEALILLKVWARQRSSIYVHDC-LNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGVS 319 (1055)
Q Consensus 241 ~dA~~LlkvWl~QRg~~~~~gg-f~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~~ 319 (1055)
+.|++-+|.|+++|....+.-| +||..|+|++|..|| |.+..+|.-|+-.++..|++++| .+|+.+..-+|++..
T Consensus 208 ~~ALRaIK~WAqRRavYaN~~GfpGGVAwam~VARiCQ---LYPNA~S~vIv~kFF~ils~WnW-PqPviLkPieDgplq 283 (552)
T COG5186 208 HSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVARICQ---LYPNASSFVIVCKFFEILSSWNW-PQPVILKPIEDGPLQ 283 (552)
T ss_pred HHHHHHHHHHHHhhhhhccccCCcchHHHHHHHHHHHh---hccCcchHhHHHHHHHHHHhcCC-CCCeEeeeccCCCee
Confidence 9999999999999997766555 499999999999999 99999999999999999999999 579998876654432
Q ss_pred h------hHHHhhhhcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHhhhhcCCC--cccccccccccccccccEE
Q 001555 320 K------EEKLQYKEAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDKCGDG--GFEETFLTKIDFPAKYDYC 391 (1055)
Q Consensus 320 ~------~~~~~f~~~f~vvf~D~sg~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~~~~d--~F~~lFl~~~~~~~~fD~~ 391 (1055)
. .+.++-.+..||+ .-+--.+....++|.++-.-+-+|--++.++++|.-.+ .|..+| .+.+|..||-++
T Consensus 284 vrvWnPKvYpsDk~HRMPvI-TPAYPSMCATHNit~STq~vIl~EfvRa~~I~~di~~n~~~w~~lF-ek~DFF~RYk~y 361 (552)
T COG5186 284 VRVWNPKVYPSDKYHRMPVI-TPAYPSMCATHNITNSTQHVILMEFVRAHKILSDIERNALDWRRLF-EKSDFFSRYKLY 361 (552)
T ss_pred EEeeCCccCcccccccCccc-cCCchhhhhhccccchhhhhHHHHHHHHHHhhhhHhhccccHHHHH-HhhhHHHHHhHh
Confidence 1 1333333446764 56666777888899999999999999999999996555 899999 689999999999
Q ss_pred EEeec
Q 001555 392 VRLNL 396 (1055)
Q Consensus 392 ~~i~~ 396 (1055)
+.|..
T Consensus 362 leitA 366 (552)
T COG5186 362 LEITA 366 (552)
T ss_pred hhhhh
Confidence 98874
No 5
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=99.41 E-value=8.8e-12 Score=142.06 Aligned_cols=308 Identities=14% Similarity=0.216 Sum_probs=215.0
Q ss_pred eeEeeeeccccccCCCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhhccCCCCccEEEeccCCCcceeeEEE
Q 001555 83 FKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLVV 162 (1055)
Q Consensus 83 v~vvGS~~l~t~~k~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~~~~~~~v~~~~~~~d~~kPil~l 162 (1055)
|-..|||.|| +..++..||-.+.-|+.. -|+=|...+-..|++.+...++. --.|+..||+.+
T Consensus 92 IftfGSYRLG-Vhg~GADIDtLcV~Prhv-------------~R~DFF~sf~~mL~~~~eVteL~---~V~dAfVPiikf 154 (562)
T KOG2245|consen 92 IFTFGSYRLG-VHGPGADIDTLCVGPRHV-------------SRSDFFTSFYDMLKERPEVTELH---AVEDAFVPIIKF 154 (562)
T ss_pred EEeccceeec-ccCCCCCcceeeeccccc-------------cHHHHHHHHHHHHhcCccccccc---cccccccceEEE
Confidence 4477999998 456678999999999654 67777778889998876554444 557899999999
Q ss_pred EeCCCCCCCCCeEEEEeec-CC-CcccccccCcccCCccCCCCCCCCCCCCccchhhhhccChHHHHHHHHHHhhChHHH
Q 001555 163 YPAVKSVEAPGFFVRIIPT-AA-SLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKEL 240 (1055)
Q Consensus 163 ~p~~~~~~~~~~~IRii~~-~~-~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssIl~D~~~~~~l~~l~~~~~~~~~f 240 (1055)
+-. +..|-|+.+ .+ -..|..-=.-+.|-+|...+ ..-=--|.+-..| +.|++ .-+-..|
T Consensus 155 Kf~-------GI~IDllfArL~l~~VP~dldl~ddslLknlDe----~~vrSLNGcRVtd----qiL~L----VPn~~~F 215 (562)
T KOG2245|consen 155 KFD-------GIEIDLLFARLALPVVPEDLDLSDDSLLKNLDE----RCVRSLNGCRVTD----QILKL----VPNQENF 215 (562)
T ss_pred Eec-------CeeeeeeehhcccccCCCcccccchHhhhcccH----HHHHHhcCcCHHH----HHHHh----CCCHHHH
Confidence 765 478888876 11 22222111112222221110 0000123333332 33443 4566799
Q ss_pred HHHHHHHHHHHHhcCCCcCCCC-chhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCCC
Q 001555 241 GEALILLKVWARQRSSIYVHDC-LNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGVS 319 (1055)
Q Consensus 241 ~dA~~LlkvWl~QRg~~~~~gg-f~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~~ 319 (1055)
+-+++-+|.|++.||.+++.-| |||..||||+|..|| +.+..++--|+..++--++++.| .+|+.++..++..+.
T Consensus 216 ~~tLRaiKlWAKrrgVYsN~~GF~GGV~wA~LVARiCQ---LYPNA~~s~Lv~kfF~ifs~W~W-P~PVlL~~ie~~~L~ 291 (562)
T KOG2245|consen 216 RITLRAIKLWAKRRGVYSNVMGFLGGVAWAMLVARICQ---LYPNASPSTLVAKFFRVFSQWNW-PNPVLLKPIEEGNLN 291 (562)
T ss_pred HHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHc---cCCCcchHHHHHHHHHHHhhccC-CCceEeccccccccC
Confidence 9999999999999998777655 599999999999999 99999999999999999999999 579999877544333
Q ss_pred hh------HHHhhhhcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHhhhhcC--CCcccccccccccccccccEE
Q 001555 320 KE------EKLQYKEAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDKCG--DGGFEETFLTKIDFPAKYDYC 391 (1055)
Q Consensus 320 ~~------~~~~f~~~f~vvf~D~sg~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~~~--~d~F~~lFl~~~~~~~~fD~~ 391 (1055)
.+ +..+=-+..|++ .-+--..|-.+++|.|+..-++.|-+.++++.++.. .-.|..|| .+.+|..+|-++
T Consensus 292 ~~VWdPr~n~~DryHlMPII-TPAyP~~nsthNVS~ST~~Vi~~Ef~~g~~I~~~i~~~k~~W~~LF-E~~~FF~rYk~y 369 (562)
T KOG2245|consen 292 LPVWDPRVNPSDRYHLMPII-TPAYPQMNSTHNVSRSTLKVITEEFKRGLEICDDIELNKLDWSDLF-ELYNFFSRYKHY 369 (562)
T ss_pred ccccCCCCCCCCcceecccc-cCCcccccccccccHHHHHHHHHHHHHHHHHHHHHHhccccHHHHh-hhhHHHHHHhhH
Confidence 21 111222346775 667779999999999999999999999999999954 34899999 688999999999
Q ss_pred EEeecCCcccccccccCCchhhHHHHH-HHHHHHHHHhhccccceEEEEec
Q 001555 392 VRLNLRGHTEVHALGFCLDDECWRLYE-QKVHSLLNQGLVDRAKSIRVTWR 441 (1055)
Q Consensus 392 ~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~i~~lL~~aLgdR~~~i~~~~~ 441 (1055)
+.|.+..... .+...|..+. .++. +|..-|. |...|.+.++
T Consensus 370 l~i~~~A~~~-------ed~l~w~G~vESriR-~Lv~klE-~~~~i~~ahp 411 (562)
T KOG2245|consen 370 LQITASAATE-------EDLLKWVGWVESRIR-QLVLKLE-RNQVILIAHP 411 (562)
T ss_pred heeeeeccCh-------HHHhhhhhHHHHHHH-HHHHHHH-hhcceEEecC
Confidence 9998654311 1224465444 4444 4444443 4666666544
No 6
>PF04928 PAP_central: Poly(A) polymerase central domain; InterPro: IPR007012 In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolutio has been determined []. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta-sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.; GO: 0004652 polynucleotide adenylyltransferase activity, 0006351 transcription, DNA-dependent; PDB: 1Q79_A 1Q78_A 1F5A_A 2O1P_A 2HHP_A 3C66_B 1FA0_A 2Q66_A.
Probab=99.08 E-value=1e-09 Score=120.05 Aligned_cols=147 Identities=13% Similarity=0.265 Sum_probs=102.2
Q ss_pred HHHHHHHhhChHHHHHHHHHHHHHHHhcCCCcC-CCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCC
Q 001555 227 AEYVEKTISRWKELGEALILLKVWARQRSSIYV-HDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWN 305 (1055)
Q Consensus 227 l~~l~~~~~~~~~f~dA~~LlkvWl~QRg~~~~-~ggf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~ 305 (1055)
..++-+...+...|+.|++.+|.|+++||.+++ .|-+||..||+|+|+.|| +.+..++-+|+..++.+.|++||.
T Consensus 96 ~~~il~~Vp~~~~Fr~~lR~IK~WAk~RGIYsn~~GylGGI~waILvArvcq---l~Pn~~~~~ll~~FF~~ys~W~W~- 171 (254)
T PF04928_consen 96 TDYILRLVPNQETFRTALRFIKLWAKRRGIYSNVFGYLGGIHWAILVARVCQ---LYPNASPSTLLSRFFQIYSQWDWP- 171 (254)
T ss_dssp HHHHHCTSS-HHHHHHHHHHHHHHHHHTT-B-CCCTSB-HHHHHHHHHHHHH---HSTT--HHHHHHHHHHHHHCS-TT-
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHccccchhhccchHHHHHHHHHHHHH---HCccccccchHHHHHHHhcCCCCC-
Confidence 455556666778999999999999999997665 567799999999999998 888899999999999999999995
Q ss_pred CceeecCCCCCCC------ChhHHHhhhhcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHhhhhc--CCCccccc
Q 001555 306 RGLYFPPKGQIGV------SKEEKLQYKEAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDKC--GDGGFEET 377 (1055)
Q Consensus 306 ~~i~~~~~~~~~~------~~~~~~~f~~~f~vvf~D~sg~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~~--~~d~F~~l 377 (1055)
+|+.+....+... +..+..+-++.+||+ .-..-.+|.++++|.++.+.|+.|-+++.+++++. +...++.|
T Consensus 172 ~PV~l~~~~~~~~~~~~w~p~~~~~~~~~~MpIi-TP~yP~~Nst~nVt~st~~~i~~Ef~ra~~i~~~~~~~~~~W~~L 250 (254)
T PF04928_consen 172 NPVVLDPIEDGPLGFKVWNPRLYPRDRRHLMPII-TPAYPSMNSTYNVTRSTLRIIREEFQRAHEILSEILKGGASWSDL 250 (254)
T ss_dssp S-EESS-----SSSCGS--TTT-HHHHC-SS-EE--SSSS--BTTTT--HHHHHHHHHHHHHHHHHHHHHHTTSS-HHHC
T ss_pred CceeecccccCcccccCCCCCCCCCCcccceeEc-cCCCCccccccccCHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHH
Confidence 5988865432211 111334456667774 44556999999999999999999999999999884 34666666
Q ss_pred c
Q 001555 378 F 378 (1055)
Q Consensus 378 F 378 (1055)
|
T Consensus 251 ~ 251 (254)
T PF04928_consen 251 F 251 (254)
T ss_dssp T
T ss_pred c
Confidence 6
No 7
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=98.87 E-value=1.6e-06 Score=100.27 Aligned_cols=357 Identities=17% Similarity=0.223 Sum_probs=208.4
Q ss_pred HHHhhcccccCCCchhhhHHHHHHHHHHHHHhcCCCCCCCCcccCCccccccCCceeEEEEeCCceeeEeeeeccccccC
Q 001555 17 VEELLKEVHFARAPAITKLVDDTVSAVRKSISKIPDAFPVTADLAPGFVRDIGADKVEFKFNKPKTFKIGGSYSINCVVK 96 (1055)
Q Consensus 17 idELL~ev~~~~~~~~~~~le~~L~~lk~~i~~ip~~~~~~~~~~~~~~~~~~~~~~~f~f~~P~~v~vvGS~~l~t~~k 96 (1055)
++|.|++|+|+... .+.+.+...+|.+.|.+.=... -....|.++||++=+|..+
T Consensus 2 ~~~vl~~i~Ps~eE--~~~~~~~~~~l~~~l~~~~~e~-----------------------~~~~~v~~~GS~ArgT~L~ 56 (408)
T TIGR03671 2 LEEVLERIKPTEEE--REKLKKVADELIARLEEIIEEL-----------------------GVDAEVVLVGSYARGTWLK 56 (408)
T ss_pred hHHHhhhcCCCHHH--HHHHHHHHHHHHHHHHHHHHhc-----------------------CCcceEEEEeeEecCCccC
Confidence 47899999999666 5567676666666555432110 0112577999999999999
Q ss_pred CCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhhccCCCCccEEEeccCCCcceeeEEEEeCCCCCCCCCeEE
Q 001555 97 PAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLVVYPAVKSVEAPGFFV 176 (1055)
Q Consensus 97 ~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~~~~~~~v~~~~~~~d~~kPil~l~p~~~~~~~~~~~I 176 (1055)
.+..|||.|-.|.+.=. ..+.+... .|+..+.+.+......|. -.|-+.+.-. ++.|
T Consensus 57 G~sDIDIfi~f~~~~~~-------e~l~~~gl---~i~~~~~~~~~~~~~~ya------eHpYv~~~~~-------G~~V 113 (408)
T TIGR03671 57 GDRDIDIFILFPKDTSR-------EELEEYGL---EIGHEVLKRGGNYEERYA------EHPYVSGEIE-------GFEV 113 (408)
T ss_pred CCCceeEEEEeCCCCCH-------HHHHHHHH---HHHHHHHhhCCCHhheec------cCceEEEEEc-------cEEE
Confidence 88899999999876532 22333333 344444332222223332 3455555443 5899
Q ss_pred EEeecCCCcccccccCcccCCccCCCCC-CCCCCCCccchhhhhccChHHHHHHHHHHhhChHHHHHHHHHHHHHHHhcC
Q 001555 177 RIIPTAASLFNIAKLNLKRNNVRAFNQD-GIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKELGEALILLKVWARQRS 255 (1055)
Q Consensus 177 Rii~~~~~~F~~~rl~P~rnnvR~~~~~-~~~~pTP~YNssIl~D~~~~~~l~~l~~~~~~~~~f~dA~~LlkvWl~QRg 255 (1055)
-|-||.. ++....- +.-=.|| -|.+++.+-.+. .++|=++|+|-|++.=|
T Consensus 114 DiVPcy~--------------v~~g~~~~taVDRtp-------------~H~~fv~~rl~~--~~~d~VRLlK~f~k~ig 164 (408)
T TIGR03671 114 DVVPCYK--------------VESGEEIISAVDRTP-------------FHTRYVLERLDG--KLRDDVRLLKQFLKGIG 164 (408)
T ss_pred EEEeeEE--------------ccCcCeeeccccCch-------------HHHHHHHHhhhh--hHHHHHHHHHHHHHhCC
Confidence 9999843 1110000 0001366 567777666654 49999999999999987
Q ss_pred C---CcCCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCCChhHHHhhhhcCCE
Q 001555 256 S---IYVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGVSKEEKLQYKEAFPV 332 (1055)
Q Consensus 256 ~---~~~~ggf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~~~~~~~~f~~~f~v 332 (1055)
. ....+||+||+.=+|++| |.-|.++++-.+++ +.++.+...+. . . ..| .-|+
T Consensus 165 vYGsE~~~~GFSGYl~ELLv~~-------------yG~F~~~l~~a~~w---k~~~~id~~~~-~--~---~~f--~~Pl 220 (408)
T TIGR03671 165 VYGSELKTRGFSGYLCELLVIH-------------YGSFENVLKAASKW---KPGVVIDIEEH-G--T---KKF--DDPL 220 (408)
T ss_pred ccchhhccCCccHHHHHHHHHH-------------hCCHHHHHHHHHhc---CCCeEEecCcc-c--c---ccC--CCCE
Confidence 4 445789999999999998 66788888888754 34666632211 0 0 122 3488
Q ss_pred EEeCCCC-ceeeccCCCHHHHHHHHHHHHHHHHhhhhcCCCcccccccccccc----cccccEEEEeecCCccccccccc
Q 001555 333 VICDPSA-QVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGFEETFLTKIDF----PAKYDYCVRLNLRGHTEVHALGF 407 (1055)
Q Consensus 333 vf~D~sg-~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~~~~d~F~~lFl~~~~~----~~~fD~~~~i~~~~~~~~~~~~~ 407 (1055)
|++||.- .-|+++.+|...+.++.+.|+..++ +++.+-|.+-=+.+.++ ..+=..++.+..+.. .
T Consensus 221 vViDPvDp~RNVAaalS~~~~~~fv~aar~fl~---~Ps~~fF~p~~~~~~~~~~~l~~r~t~~~~~~f~~p-------~ 290 (408)
T TIGR03671 221 VVIDPVDPKRNVAAALSLENLARFILAARMFLK---NPSLEFFFPPEIEPEEFLERLERRGTTLLAIVFRTP-------D 290 (408)
T ss_pred EEeCCCCCcchHHHHcCHHHHHHHHHHHHHHHH---CCCHHHcCCCCCChHHHHHHHhhcCcEEEEEEeCCC-------C
Confidence 8899954 8899999999999999999988764 45555553320111111 122223333332211 0
Q ss_pred CCchhhHHHHHHHHHHHHHHhhccccceEEEEecCCCCcccccCCCCcCCCCceEEEEEecCccccccccccCCCCCCHH
Q 001555 408 CLDDECWRLYEQKVHSLLNQGLVDRAKSIRVTWRNSPSEWNIENGLAVLDREPLLVGISVSSLEKLFRIVDIGPNAENKE 487 (1055)
Q Consensus 408 ~~~~~~~~~~~~~i~~lL~~aLgdR~~~i~~~~~~~~~~w~i~~~~~~~~~~~l~vGl~l~~~~~~~r~vd~GP~ad~~~ 487 (1055)
.-++..|-++. +..+-|.+.|..+ -..+. +. ..|. +.....+-+.|...+--.=.+-.||+..+.+
T Consensus 291 ~v~Dil~pQl~-r~~~~i~~~L~~~--gF~v~-r~--~~~~--------~~~~~~l~~el~~~~lp~~~~h~GPpv~~~~ 356 (408)
T TIGR03671 291 VVDDILYPQLE-RSGRSLVKLLERE--GFEVL-RY--GVWA--------DENTCYLLLELESAELPRVKLHVGPPVWVRD 356 (408)
T ss_pred CCccchhHHHH-HHHHHHHHHHHHC--CCEEE-Ee--eeec--------CCCeEEEEEEeeccccCCceeeeCCCccchh
Confidence 11224454443 2333334444321 12222 10 1232 1122344444432222222456899998767
Q ss_pred HHHHHHhhhcC
Q 001555 488 EALRFRKFWGE 498 (1055)
Q Consensus 488 ea~~FR~FWG~ 498 (1055)
.|.+|.+=|.+
T Consensus 357 ~a~~F~~k~~~ 367 (408)
T TIGR03671 357 HAEKFIEKYED 367 (408)
T ss_pred HHHHHHHHhcc
Confidence 89999988844
No 8
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=98.78 E-value=3.5e-06 Score=98.90 Aligned_cols=357 Identities=16% Similarity=0.199 Sum_probs=212.5
Q ss_pred HHHhhcccccCCCchhhhHHHHHHHHHHHHHhcCCCCCCCCcccCCccccccCCceeEEEEeCCceeeEeeeeccccccC
Q 001555 17 VEELLKEVHFARAPAITKLVDDTVSAVRKSISKIPDAFPVTADLAPGFVRDIGADKVEFKFNKPKTFKIGGSYSINCVVK 96 (1055)
Q Consensus 17 idELL~ev~~~~~~~~~~~le~~L~~lk~~i~~ip~~~~~~~~~~~~~~~~~~~~~~~f~f~~P~~v~vvGS~~l~t~~k 96 (1055)
++|.|+.|+|+... .+.+.+..+.|.+.|.+.=...+. + ..|.++|||+=+|..+
T Consensus 3 ~~evl~~i~Ps~eE--~~~l~~~~~~l~~~L~~~~~~~~~----------------------~-~~V~l~GS~ArgT~L~ 57 (447)
T PRK13300 3 LEEVLERIKPTEEE--REKLKKVAEELIERLEEAIKELGL----------------------D-AEVELVGSTARGTWLS 57 (447)
T ss_pred HHHHHHhcCCCHHH--HHHHHHHHHHHHHHHHHHHHhcCC----------------------c-eEEEEEeeecCCcccC
Confidence 57899999999655 456666666666665543211000 0 2577999999999999
Q ss_pred CCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhhccC-CCCccEEEeccCCCcceeeEEEEeCCCCCCCCCeE
Q 001555 97 PAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSS-PSFDKVEWSAMQNEARKPVLVVYPAVKSVEAPGFF 175 (1055)
Q Consensus 97 ~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~~-~~~~~v~~~~~~~d~~kPil~l~p~~~~~~~~~~~ 175 (1055)
++..|||.|-.|.+.=.+ .+.+...++ +..+.+. .....++| +-.|-+.+.-. ++.
T Consensus 58 GdsDIDIFv~fp~~~~~e-------~L~~~gl~i---~~~~~~~~~~~~~~~y------aeHpyv~~~~~-------G~~ 114 (447)
T PRK13300 58 GDRDIDIFVLFPKDTSRE-------ELEEKGLEI---GKEVAKELLGDYEERY------AEHPYVTGEID-------GFE 114 (447)
T ss_pred CCCceeEEEEeCCCCCHH-------HHHHHHHHH---HHHHHHhhCCcceeee------ccCceEEEEEC-------CEE
Confidence 999999999998765322 334444444 3333222 22234554 23466655543 599
Q ss_pred EEEeecCC---CcccccccCcccCCccCCCCCCCCCCCCccchhhhhccChHHHHHHHHHHhhChHHHHHHHHHHHHHHH
Q 001555 176 VRIIPTAA---SLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKELGEALILLKVWAR 252 (1055)
Q Consensus 176 IRii~~~~---~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssIl~D~~~~~~l~~l~~~~~~~~~f~dA~~LlkvWl~ 252 (1055)
|-|-||.. +. -+++ + -=.|| -|.+++.+-.+. .++|=++|+|-|++
T Consensus 115 VDiVPcy~v~~~~-----------~~~s----a-VDRtp-------------~H~~fv~~rl~~--~~~d~VRLlK~f~k 163 (447)
T PRK13300 115 VDIVPCYKVESGE-----------EIIS----A-VDRTP-------------FHTKYVKERLKG--KLEDEVRLLKQFLK 163 (447)
T ss_pred EEEEeeEEccCcC-----------cccc----c-ccCch-------------HHHHHHHHhhhh--hHHHHHHHHHHHHH
Confidence 99999841 11 0111 0 01377 567777666554 49999999999999
Q ss_pred hcCC---CcCCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCCChhHHHhhhhc
Q 001555 253 QRSS---IYVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGVSKEEKLQYKEA 329 (1055)
Q Consensus 253 QRg~---~~~~ggf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~~~~~~~~f~~~ 329 (1055)
.-|. ....+||+||+.=+|++| |.-|.++++-.+++.. +......+.... ..| .
T Consensus 164 ~~gvYGsE~k~~GFSGYl~ELLv~~-------------yG~F~~~l~~a~~w~~---~~~I~~~~~~~~-----~~f--~ 220 (447)
T PRK13300 164 GIGVYGSELKTRGFSGYLCELLIIH-------------YGSFENVLKAASKWKP---PVKIDLEKHGKE-----YKF--D 220 (447)
T ss_pred hCCccchhhccCCccHHHHHHHHHH-------------hCCHHHHHHHHHhCCC---CceEeccccCcc-----ccC--C
Confidence 9885 445789999999999988 6788999998887643 333322211100 012 3
Q ss_pred CCEEEeCCCC-ceeeccCCCHHHHHHHHHHHHHHHHhhhhcCCCcccccccccccc----cccccEEEEeecCCcccccc
Q 001555 330 FPVVICDPSA-QVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGFEETFLTKIDF----PAKYDYCVRLNLRGHTEVHA 404 (1055)
Q Consensus 330 f~vvf~D~sg-~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~~~~d~F~~lFl~~~~~----~~~fD~~~~i~~~~~~~~~~ 404 (1055)
-|+|++||.- .-|+++.+|...+.++.+.|+.= |.+++.+-|.+-=+.+... ..|-..++.+..+..
T Consensus 221 ~PlvViDPvDp~RNVAaa~S~~~~~~fv~aar~f---L~~Ps~~fF~~~~~~~~~~~~~l~~R~t~~~~v~f~~p----- 292 (447)
T PRK13300 221 DPLVVIDPVDPNRNVAAALSLENLATFILAAREF---LKNPSLEFFFPSDLSPEEILEELERRGTTVLALEFPRP----- 292 (447)
T ss_pred CCEEEeCCCCCcchHHHHcCHHHHHHHHHHHHHH---HhCCCHHhcCCCCCChHHHHHHHhhcCceEEEEEeCCC-----
Confidence 4888899954 88999999999999999998764 5566655553322222222 122234444432211
Q ss_pred cccCCchhhHHHHHHHHHHHHHHhhccccceEEEEecCCCCcccccCCCCcCCCCceEEEEEecCccccccccccCCCCC
Q 001555 405 LGFCLDDECWRLYEQKVHSLLNQGLVDRAKSIRVTWRNSPSEWNIENGLAVLDREPLLVGISVSSLEKLFRIVDIGPNAE 484 (1055)
Q Consensus 405 ~~~~~~~~~~~~~~~~i~~lL~~aLgdR~~~i~~~~~~~~~~w~i~~~~~~~~~~~l~vGl~l~~~~~~~r~vd~GP~ad 484 (1055)
. .-++..|-++ .++.+-|.+.|..+ -..+... ..|. +.....+-+.|...+--.=.+-.||+..
T Consensus 293 -~-~v~Dil~pQl-~r~~~~i~~~L~~~--gF~v~~~---~~~~--------d~~~~~l~~el~~~~lp~~~~h~GPpv~ 356 (447)
T PRK13300 293 -D-IVEDILYPQL-ERSLRSIVKLLERE--GFEVLRS---GAWA--------DEDRAYLLLELEVAELPNVKLHIGPPVW 356 (447)
T ss_pred -C-CCccchhHHH-HHHHHHHHHHHHHC--CCEEEEe---eeec--------CCCeEEEEEEeecccCCCeeeeeCCCcC
Confidence 0 1122445444 33333444444322 1222211 2232 1223455555542222223456899998
Q ss_pred CHHHHHHHHhhhcCc
Q 001555 485 NKEEALRFRKFWGEK 499 (1055)
Q Consensus 485 ~~~ea~~FR~FWG~K 499 (1055)
+.+.|.+|.+=|.++
T Consensus 357 ~~~~a~~F~~k~~~~ 371 (447)
T PRK13300 357 VREHAENFIEKYEDS 371 (447)
T ss_pred chhhHHHHHHHhccC
Confidence 776799999888554
No 9
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=98.21 E-value=0.00087 Score=77.08 Aligned_cols=258 Identities=18% Similarity=0.301 Sum_probs=168.7
Q ss_pred cHHHhhcccccCCCchhhhHHHHHHHHHHHHHhcCCCCCCCCcccCCccccccCCceeEEEEeCCceeeEeeeecccccc
Q 001555 16 KVEELLKEVHFARAPAITKLVDDTVSAVRKSISKIPDAFPVTADLAPGFVRDIGADKVEFKFNKPKTFKIGGSYSINCVV 95 (1055)
Q Consensus 16 QidELL~ev~~~~~~~~~~~le~~L~~lk~~i~~ip~~~~~~~~~~~~~~~~~~~~~~~f~f~~P~~v~vvGS~~l~t~~ 95 (1055)
-++|.|+.|+|++.. .+.++.+...|+..+.++=+... . +| .+.+|||++=+|-.
T Consensus 6 ~l~evl~~i~P~~eE--~~~~~~~~e~l~~~~~~~~~e~~--~-~a--------------------ev~lVGS~AkgTwL 60 (443)
T COG1746 6 VLEEVLKRIKPTEEE--RKKLKEVAEELRERINEIIEELG--I-DA--------------------EVVLVGSYAKGTWL 60 (443)
T ss_pred HHHHHHHHcCCCHHH--HHHHHHHHHHHHHHHHHHHHhcC--C-cc--------------------eEEEEeecccCccc
Confidence 367999999999877 67899999999888877744311 1 11 36699999999999
Q ss_pred CCCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhhccCCCCccEEEeccCCCcceeeEEEEeCCCCCCCCCeE
Q 001555 96 KPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLVVYPAVKSVEAPGFF 175 (1055)
Q Consensus 96 k~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~~~~~~~v~~~~~~~d~~kPil~l~p~~~~~~~~~~~ 175 (1055)
+.+..|||.|-.|++. ++|.|.-+ .+ .|+..+-+. ......|.- -|-+...- .++.
T Consensus 61 ~gd~DIDvFi~Fp~d~--~~eel~~~-----GL---~ig~~~l~~-~~~~~~YAe------HPYV~g~v-------~G~e 116 (443)
T COG1746 61 RGDHDIDVFIAFPKDT--SEEELEEK-----GL---EIGREVLKR-GNYEERYAE------HPYVTGEV-------DGYE 116 (443)
T ss_pred CCCcceeEEEECCCCC--CHHHHHHH-----HH---HHHHHHhcC-Cchhhhhcc------CCeeEEEE-------ccEE
Confidence 9999999999999885 45555322 22 333333332 233344432 35444433 2599
Q ss_pred EEEeecCCCcccccccCcccCCccCCCCCCCCCCCCccchhhhhccChHHHHHHHHHHhhChHHHHHHHHHHHHHHHhcC
Q 001555 176 VRIIPTAASLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKELGEALILLKVWARQRS 255 (1055)
Q Consensus 176 IRii~~~~~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssIl~D~~~~~~l~~l~~~~~~~~~f~dA~~LlkvWl~QRg 255 (1055)
|-|-||..--+. .++++. --.|| -|.+++.+.++.-.. |=++|||..++-=|
T Consensus 117 VDvVPCy~v~~~--------~~~~sA-----VDRTp-------------lHt~yv~e~L~~~~~--deVrLLK~FlK~iG 168 (443)
T COG1746 117 VDVVPCYKVEDG--------EKIISA-----VDRTP-------------LHTRYVEEHLKGRQK--DEVRLLKQFLKGIG 168 (443)
T ss_pred EEEEecccccCc--------cccccc-----ccCcc-------------hhHHHHHHHhcccch--hHHHHHHHHHhccC
Confidence 999998531111 123321 12577 466777776665443 88999999998877
Q ss_pred CC---cCCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCCChhHHHhhhhcCCE
Q 001555 256 SI---YVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGVSKEEKLQYKEAFPV 332 (1055)
Q Consensus 256 ~~---~~~ggf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~~~~~~~~f~~~f~v 332 (1055)
.. -..+||+|++-=+|+.|- .=|.+++.--+. | ..|......+. ..+-|.+ -|.
T Consensus 169 vYGaE~rt~GFSGYL~ELLII~y-------------GsFe~vl~~a~~--w-rp~~~ID~~~~------~~e~f~d-~Pl 225 (443)
T COG1746 169 VYGAELRTQGFSGYLCELLIIHY-------------GSFENVLKAASR--W-RPGKIIDLEGH------KRERFED-EPL 225 (443)
T ss_pred ccceeeeeccchHHHHHHHHhhh-------------ccHHHHHHHHhc--c-CCCeEEeccch------hhhccCC-CCe
Confidence 43 347899999877776653 336777766654 4 34644432210 0111222 277
Q ss_pred EEeCCC-CceeeccCCCHHHHHHHHHHHHHHHHhhhhcCCCcccc
Q 001555 333 VICDPS-AQVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGFEE 376 (1055)
Q Consensus 333 vf~D~s-g~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~~~~d~F~~ 376 (1055)
|++||. -.-|++|.+|.-.+.++++.|+. .|.+++.+-|.+
T Consensus 226 iVvDPVDP~RNVAAalSl~~la~f~~aar~---FL~~PS~efF~p 267 (443)
T COG1746 226 IVVDPVDPKRNVAAALSLENLARFVHAARE---FLKNPSPEFFFP 267 (443)
T ss_pred EecCCCCCccchhhhcCHHHHHHHHHHHHH---HhcCCChhhcCC
Confidence 778884 47899999999999999999875 566676666655
No 10
>PF03813 Nrap: Nrap protein; InterPro: IPR005554 Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus []. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [].
Probab=98.07 E-value=0.00073 Score=87.81 Aligned_cols=342 Identities=14% Similarity=0.185 Sum_probs=200.9
Q ss_pred ccccHHHhhc----ccccCCCchhhhHHHHHHHHHHHHHhcCCCCCCCCcccCC---ccccccCCceeEEEEeCCceeeE
Q 001555 13 MDYKVEELLK----EVHFARAPAITKLVDDTVSAVRKSISKIPDAFPVTADLAP---GFVRDIGADKVEFKFNKPKTFKI 85 (1055)
Q Consensus 13 f~LQidELL~----ev~~~~~~~~~~~le~~L~~lk~~i~~ip~~~~~~~~~~~---~~~~~~~~~~~~f~f~~P~~v~v 85 (1055)
.--|.|++|. +........ ...+-+...+|.+.|.++.+- |..+..+. ..++ |. ...+|...
T Consensus 478 ~~~~~~~~l~~~~~~~~~~~~~~-~~~~~~af~~L~k~lr~L~~L-PL~I~~v~p~sp~lR------yt-s~~pp~p~-- 546 (972)
T PF03813_consen 478 IGDQFDSLLPLPGSGSSPTDEES-FQSVMRAFDELEKDLRSLEDL-PLSITSVQPASPALR------YT-SVFPPVPH-- 546 (972)
T ss_pred ehhhhhhhhcCccccCCCCchHH-HHHHHHHHHHHHHHHhcCccC-CcceeeeccCCHhhh------cC-CCCCCCCc--
Confidence 3457788885 233332332 236777777888888887643 44332221 1111 11 11122221
Q ss_pred eeeeccccccCCCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhhcc-CCCC--ccEEEeccC-CCcceeeE-
Q 001555 86 GGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKS-SPSF--DKVEWSAMQ-NEARKPVL- 160 (1055)
Q Consensus 86 vGS~~l~t~~k~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~-~~~~--~~v~~~~~~-~d~~kPil- 160 (1055)
.+......+|+.++|=.|-==+.|-- -==--|-|+|| .||+.|++ .+.. ..|.++... .....--|
T Consensus 547 -------~~~~~~~p~~vvl~fE~S~kWPddl~-AI~~~K~Af~l-kiae~L~~~~~~~~~~~v~~~~~~~~~~~~~~ld 617 (972)
T PF03813_consen 547 -------AVPRYIPPIEVVLQFESSGKWPDDLE-AIQKTKTAFLL-KIAEELEKQYGDGIKARVGLDNSLSPIANQAFLD 617 (972)
T ss_pred -------cccCCCCCEEEEEEEecCCCCCCCHH-HHHHHHHHHHH-HHHHHHHHhhCCcceeeecccccccceeccceEE
Confidence 23334468999999977654443322 11234666665 99999984 3322 223222210 00111111
Q ss_pred EEEeCCCCCCCCCeEEEEeecC-CCcccccccC-cccCCccCCCCCCCCCCCCccchhhhhccChHHHHHHHHHHhhChH
Q 001555 161 VVYPAVKSVEAPGFFVRIIPTA-ASLFNIAKLN-LKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWK 238 (1055)
Q Consensus 161 ~l~p~~~~~~~~~~~IRii~~~-~~~F~~~rl~-P~rnnvR~~~~~~~~~pTP~YNssIl~D~~~~~~l~~l~~~~~~~~ 238 (1055)
++.| .+|..|+...- .+..=+.|.. ....-+|. ..++-+-+-...=...-.|...++.....+|
T Consensus 618 V~~~-------~G~~FRl~I~~~rE~~Ll~~~~~~~~~~~k~-------~~~~~~~~~~~~~~~~p~h~~~i~~l~~~~p 683 (972)
T PF03813_consen 618 VLYP-------EGYVFRLRIYHDREETLLKRQLKTEDGQLKQ-------EATEALASLERRFIHLPKHTSAIHGLHTRFP 683 (972)
T ss_pred EEec-------CccEEEEEEecchhHHHHHHhhcccCcccch-------hhhHHHHHHHHHHHhhHHHHHHHHHHHhhCC
Confidence 3333 25666776653 2322222222 11111221 1122221111111224568999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCcCCCCchhHHHHHHHHHHhhcc-ccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCC
Q 001555 239 ELGEALILLKVWARQRSSIYVHDCLNGYLISILLSYLVSLD-KINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIG 317 (1055)
Q Consensus 239 ~f~dA~~LlkvWl~QRg~~~~~ggf~gf~~s~lla~Ll~~~-~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~ 317 (1055)
+|.-||+|.|=|+.-.=+ .+.|..-.+=+|+|+++-.. ....-.|..--|=-+|++||++||..+|+.+..++ .
T Consensus 684 ~fs~tvRL~KrW~~shlL---s~~i~~E~vELlva~vfl~~~p~~~P~S~~~GFlRfL~lLs~~dW~~~PLiVd~~~--~ 758 (972)
T PF03813_consen 684 SFSPTVRLAKRWLSSHLL---SGHISEEAVELLVASVFLSPAPWSPPSSPQTGFLRFLHLLSTWDWREEPLIVDFNN--E 758 (972)
T ss_pred chhHHHHHHHHHHHhccC---cccCCHHHHHHHHHHHhcCCCCCCCCCCHhHHHHHHHHHHHhCCCCcCCEEEECCC--C
Confidence 999999999999998854 35677777888999988533 55666788889999999999999999999887653 2
Q ss_pred CChhHHH----hh---hh-----cCCEEEe----CCCCceeeccCCCHHHHHHHHHHHHHHHHhhhhcC--CCccccccc
Q 001555 318 VSKEEKL----QY---KE-----AFPVVIC----DPSAQVNLAFRMTSVGFCELQDEAASTLQCMDKCG--DGGFEETFL 379 (1055)
Q Consensus 318 ~~~~~~~----~f---~~-----~f~vvf~----D~sg~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~~~--~d~F~~lFl 379 (1055)
++.+... .| ++ ..|+.|+ |+.|.+==-.+-+.-..+.|+.-|+.|+++|...+ ...+..+|.
T Consensus 759 l~~~~~~~i~~~f~~~R~~dp~~~~p~~~IaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~sl~~l~~~~~~~~~~~~lF~ 838 (972)
T PF03813_consen 759 LTEEDRAEIETNFDAWRKIDPAMNLPAMFIATPYDPEGSLWTRNGPSKVVAKRLTALAKASLKLLEEQGLSDLDWKSLFR 838 (972)
T ss_pred CCHHHHHHHHHHHHHhhccCccccCCcEEEEeCCCCCCCEeECCCCCHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHhcC
Confidence 4443332 22 22 3455444 77774221234778999999999999999998543 467888885
Q ss_pred ccccccccccEEEEeec
Q 001555 380 TKIDFPAKYDYCVRLNL 396 (1055)
Q Consensus 380 ~~~~~~~~fD~~~~i~~ 396 (1055)
+-...||.+|++.-
T Consensus 839 ---~~l~~YD~vI~L~~ 852 (972)
T PF03813_consen 839 ---PPLSDYDFVIHLNP 852 (972)
T ss_pred ---CCccCCCEEEEecC
Confidence 33367999999974
No 11
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=96.26 E-value=0.16 Score=55.57 Aligned_cols=221 Identities=14% Similarity=0.197 Sum_probs=135.3
Q ss_pred eeeEeeeeccccccCCCcceeEEEec---CccccCcccccccchhhhHHhHHHHHHHhhccC-CCCccEEEeccCCCcce
Q 001555 82 TFKIGGSYSINCVVKPAVNVDLFVGL---PKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSS-PSFDKVEWSAMQNEARK 157 (1055)
Q Consensus 82 ~v~vvGS~~l~t~~k~~~~VDl~v~m---P~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~~-~~~~~v~~~~~~~d~~k 157 (1055)
.|.-|||++-||+.+.+..+|++|.. |..- -+..|+..|.+. +.. ..+ -
T Consensus 4 gV~rVG~~aKG~ll~Gd~~~~lVv~c~~~PT~~-----------------ll~~v~~~l~e~l~~~--------~~~--e 56 (246)
T smart00572 4 GVMRVGSFAKGTLLKGDNVAELVLLCKEKPTSE-----------------LVARLARKLPEQLKAV--------TED--E 56 (246)
T ss_pred ceEEeeeeccCceecCCCceeEEEEecCCCcHH-----------------HHHHHHHHHHHHHhhc--------Ccc--c
Confidence 57789999999999999999999964 4321 234565555332 000 000 0
Q ss_pred eeEEEEeCCCCCCCCCeEEEEeecCCCcccccccCc-ccCCccCCCCCCCCCCCCccchhhhhccChHHHHHHHHHHhhC
Q 001555 158 PVLVVYPAVKSVEAPGFFVRIIPTAASLFNIAKLNL-KRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISR 236 (1055)
Q Consensus 158 Pil~l~p~~~~~~~~~~~IRii~~~~~~F~~~rl~P-~rnnvR~~~~~~~~~pTP~YNssIl~D~~~~~~l~~l~~~~~~ 236 (1055)
..+++.... ....+++|.-+.+. +...-+.. ..-|.|. ..|+-+.=-...+.-+.-..|.+...+....
T Consensus 57 ~~~~~~~~~----~~~~~~~i~ltSp~-~r~~~~~~~~~~~~~~-----~~p~~~ld~~~cl~aLAalRhakWFq~~a~~ 126 (246)
T smart00572 57 ALIIVTSTK----EPTMEVGILITSPL-ARVELLITTVPENLRK-----LDPEDHLDRKKCLSALASLRHAKWFQARASG 126 (246)
T ss_pred ceeeeeccC----CCceeEEEEEeccc-ccccccccccCccccc-----CCccccCCHHHHHHHHHHHHHhHHHHHhccC
Confidence 112222111 12345566554221 00000000 0112221 1111111122233333456777887777777
Q ss_pred hHHHHHHHHHHHHHHHhcCCCcCCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCC
Q 001555 237 WKELGEALILLKVWARQRSSIYVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQI 316 (1055)
Q Consensus 237 ~~~f~dA~~LlkvWl~QRg~~~~~ggf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~ 316 (1055)
..+++--++++|=|.++-. ....+++|.+-++++|++.. -+..++.=+.||.++++||+..| |..+
T Consensus 127 l~s~~iviRilKd~~~R~~---~~~pL~~w~iELl~~~~i~~--~~~~l~~~~a~RR~fe~lAsG~l------~p~~--- 192 (246)
T smart00572 127 LQSCVIVIRVLRDLCNRVP---TWQPLSGWPLELLVEKAIGS--ARQPLGLGDAFRRVFECLASGIL------LPGS--- 192 (246)
T ss_pred CcchhhHHHHHHHHHHhcc---cccccccccHHHHHHHHhcc--CCCCCCHHHHHHHHHHHHHhccC------cCCC---
Confidence 6789999999997765542 12348999999999999873 35668889999999999996655 3211
Q ss_pred CCChhHHHhhhhcCCEEEeCCC--CceeeccCCCHHHHHHHHHHHHHHHHhhhh
Q 001555 317 GVSKEEKLQYKEAFPVVICDPS--AQVNLAFRMTSVGFCELQDEAASTLQCMDK 368 (1055)
Q Consensus 317 ~~~~~~~~~f~~~f~vvf~D~s--g~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~ 368 (1055)
+. +.||. +..|+...||....+.+-..|+.+++++.-
T Consensus 193 --------------~g-I~DPce~~~~nv~~~lT~qqrd~It~sAQ~alRl~Af 231 (246)
T smart00572 193 --------------PG-LTDPCEKDNTDALTALTLQQREDVTASAQTALRLLAF 231 (246)
T ss_pred --------------CC-CcCCCCCCcccHHHhcCHHHHHHHHHHHHHHHHHHHh
Confidence 11 36774 479999999999999999999999999954
No 12
>COG5260 TRF4 DNA polymerase sigma [DNA replication, recombination, and repair]
Probab=95.98 E-value=0.089 Score=61.95 Aligned_cols=130 Identities=21% Similarity=0.241 Sum_probs=85.4
Q ss_pred eeeEeeeeccccccCCCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhhccCCCCccEEEeccCCCcceeeEE
Q 001555 82 TFKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLV 161 (1055)
Q Consensus 82 ~v~vvGS~~l~t~~k~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~~~~~~~v~~~~~~~d~~kPil~ 161 (1055)
+..+.||+.-+...+ ...||+.|.||...-++ .|+.- .++.++.+..+..++.+..- .+-||+.
T Consensus 97 ~l~vFGS~~t~L~l~-~SDiDl~I~s~~~~~~e----------t~~~~--~l~~~l~~~~~~~~~~~v~t---arVPIIK 160 (482)
T COG5260 97 DLKVFGSTETGLALP-KSDIDLCIISDPRGYKE----------TRNAG--SLASHLFKKNLAKEVVVVST---ARVPIIK 160 (482)
T ss_pred ceeEecccccccccC-cccccEEEecCCccccc----------cccHH--HHHHHHHHhccCeeeEEEEe---cccceEE
Confidence 566999999886654 56799999998764333 44432 67777776666655554332 4689998
Q ss_pred EEeCCCCCCCCCeEEEEeecCCCcccccccCcccCCccCCCCCCCCCCCCccchhhhhccChHHHHHHHHHHhhChHHHH
Q 001555 162 VYPAVKSVEAPGFFVRIIPTAASLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKELG 241 (1055)
Q Consensus 162 l~p~~~~~~~~~~~IRii~~~~~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssIl~D~~~~~~l~~l~~~~~~~~~f~ 241 (1055)
+.-.. +++.+-|-. |- ..- ....+++....+..|.++
T Consensus 161 l~d~~-----s~l~~Disf----------------n~-----------------~~~-----~~~akl~~~~~~~~P~lr 197 (482)
T COG5260 161 LVDPQ-----SGLHCDISF----------------NN-----------------TNG-----IVNAKLIRSYLKEDPRLR 197 (482)
T ss_pred EecCc-----cceEEEeec----------------Cc-----------------hhH-----HHHHHHHHHHHhcCcccc
Confidence 87431 234444432 10 000 244677777788899999
Q ss_pred HHHHHHHHHHHhcCCCcC-CCCchhHHHHH
Q 001555 242 EALILLKVWARQRSSIYV-HDCLNGYLISI 270 (1055)
Q Consensus 242 dA~~LlkvWl~QRg~~~~-~ggf~gf~~s~ 270 (1055)
-=++++|=||.+|.+... .||.++|..+.
T Consensus 198 pLvliIKhwl~~R~ln~~~~GtL~sy~i~c 227 (482)
T COG5260 198 PLVLIIKHWLKRRALNDVATGTLSSYTISC 227 (482)
T ss_pred hHHHHHHHHHHHHhhcccccCcchhhhhHH
Confidence 999999999999997543 56655554333
No 13
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=95.79 E-value=0.043 Score=59.86 Aligned_cols=98 Identities=17% Similarity=0.027 Sum_probs=83.7
Q ss_pred hhHHHHHHHHHhcCCChhHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCCC-
Q 001555 729 GQHASMINGLQGRYPVFGPVVRVAKRWAASHLFSACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDWT- 807 (1055)
Q Consensus 729 p~h~~~i~~l~~r~pafs~tvRLaKrWl~shlLs~hi~eE~vELLva~vFl~p~p~~~P~S~~~GFlRfL~lLs~~DW~- 807 (1055)
-+|+..-+.-++..-+|-..||++|.|.+.+-.-..++.=.+|||++|+-- +...|.++..+|-|||.+||+=-.-
T Consensus 114 lRhakWFq~~a~~l~s~~iviRilKd~~~R~~~~~pL~~w~iELl~~~~i~---~~~~~l~~~~a~RR~fe~lAsG~l~p 190 (246)
T smart00572 114 LRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQPLSGWPLELLVEKAIG---SARQPLGLGDAFRRVFECLASGILLP 190 (246)
T ss_pred HHHhHHHHHhccCCcchhhHHHHHHHHHHhcccccccccccHHHHHHHHhc---cCCCCCCHHHHHHHHHHHHHhccCcC
Confidence 489999998888888999999999999999988778999999999999975 4568999999999999999987763
Q ss_pred CCeEEEeCCC--------CCCHhhHHHHHH
Q 001555 808 FSALVVDINN--------DFGPEDFKVIND 829 (1055)
Q Consensus 808 ~~PLiVd~~~--------~lt~~~~~~i~~ 829 (1055)
..|=|+|+-+ .||.+++++|..
T Consensus 191 ~~~gI~DPce~~~~nv~~~lT~qqrd~It~ 220 (246)
T smart00572 191 GSPGLTDPCEKDNTDALTALTLQQREDVTA 220 (246)
T ss_pred CCCCCcCCCCCCcccHHHhcCHHHHHHHHH
Confidence 3567777754 388998888764
No 14
>PF04928 PAP_central: Poly(A) polymerase central domain; InterPro: IPR007012 In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolutio has been determined []. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta-sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.; GO: 0004652 polynucleotide adenylyltransferase activity, 0006351 transcription, DNA-dependent; PDB: 1Q79_A 1Q78_A 1F5A_A 2O1P_A 2HHP_A 3C66_B 1FA0_A 2Q66_A.
Probab=95.64 E-value=0.03 Score=61.91 Aligned_cols=154 Identities=19% Similarity=0.234 Sum_probs=90.5
Q ss_pred HHHHHHHHhcCCChhHHHHHHHHHHHhcCCC----CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCCC
Q 001555 732 ASMINGLQGRYPVFGPVVRVAKRWAASHLFS----ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDWT 807 (1055)
Q Consensus 732 ~~~i~~l~~r~pafs~tvRLaKrWl~shlLs----~hi~eE~vELLva~vFl~p~p~~~P~S~~~GFlRfL~lLs~~DW~ 807 (1055)
+..|..+--....|-.+.|.+|.|..+..+. |++.--.+.+|||+|.-- +| -.++.+=+.||.+..|+|||.
T Consensus 96 ~~~il~~Vp~~~~Fr~~lR~IK~WAk~RGIYsn~~GylGGI~waILvArvcql-~P---n~~~~~ll~~FF~~ys~W~W~ 171 (254)
T PF04928_consen 96 TDYILRLVPNQETFRTALRFIKLWAKRRGIYSNVFGYLGGIHWAILVARVCQL-YP---NASPSTLLSRFFQIYSQWDWP 171 (254)
T ss_dssp HHHHHCTSS-HHHHHHHHHHHHHHHHHTT-B-CCCTSB-HHHHHHHHHHHHHH-ST---T--HHHHHHHHHHHHHCS-TT
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHccccchhhccchHHHHHHHHHHHHHH-Cc---cccccchHHHHHHHhcCCCCC
Confidence 3333333333367889999999999999885 578999999999999754 33 346666788999999999998
Q ss_pred CCeEEEeCCCCCCHhhHHHHHHHHHHhhhhccccccCCCCeEEEEecCCCCCCcccCCCCCHHHHHHHHHHHHHHHHHHH
Q 001555 808 FSALVVDINNDFGPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRLVAYARSSANLLT 887 (1055)
Q Consensus 808 ~~PLiVd~~~~lt~~~~~~i~~~F~~~R~~~~~dp~~~~p~mfIaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~s~~~l~ 887 (1055)
+ |++++.-.+-. -.+..|... ..+....-.|-|.||.=|.-.. ...=+..-+++|+.--+.+.++++
T Consensus 172 ~-PV~l~~~~~~~--------~~~~~w~p~--~~~~~~~~~MpIiTP~yP~~Ns--t~nVt~st~~~i~~Ef~ra~~i~~ 238 (254)
T PF04928_consen 172 N-PVVLDPIEDGP--------LGFKVWNPR--LYPRDRRHLMPIITPAYPSMNS--TYNVTRSTLRIIREEFQRAHEILS 238 (254)
T ss_dssp S--EESS-----S--------SSCGS--TT--T-HHHHC-SS-EE-SSSS--BT--TTT--HHHHHHHHHHHHHHHHHHH
T ss_pred C-ceeecccccCc--------ccccCCCCC--CCCCCcccceeEccCCCCcccc--ccccCHHHHHHHHHHHHHHHHHHH
Confidence 5 88775422111 000111110 0011134578899999887532 334567888888888888889887
Q ss_pred HHHhhcCCCcccccccccc
Q 001555 888 KLILEDQTDSCRWECLFRT 906 (1055)
Q Consensus 888 ~~~~~~~~~~~~~~~lF~p 906 (1055)
+... ...+|..||.|
T Consensus 239 ~~~~----~~~~W~~L~e~ 253 (254)
T PF04928_consen 239 EILK----GGASWSDLFEP 253 (254)
T ss_dssp HHHT----TSS-HHHCT--
T ss_pred HHHc----CCCCHHHHcCC
Confidence 7542 24689999976
No 15
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=94.96 E-value=1.6 Score=52.81 Aligned_cols=163 Identities=18% Similarity=0.262 Sum_probs=103.1
Q ss_pred CCceeeEeeeeccccccCCCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhhccCCCCccEEEeccCCCccee
Q 001555 79 KPKTFKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKP 158 (1055)
Q Consensus 79 ~P~~v~vvGS~~l~t~~k~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~~~~~~~v~~~~~~~d~~kP 158 (1055)
+=.+|.++|||.+||.. |...|||.|.=+ .++++= .|+.++ .++.++++......|. ...-.+-|
T Consensus 100 ~~a~v~~FGS~~tglyL-P~sDIDl~v~~~--------~~~~~e--~~~~~~-~l~~~~e~~~~~~~v~---~v~karvp 164 (514)
T KOG1906|consen 100 PDASVYVFGSVPTGLYL-PDSDIDLVVLSK--------FLNDKE--DRAVKL-ELALELEEDNSAFHVK---VVQKARVP 164 (514)
T ss_pred ccceeEEeeeeeccccc-cccceEEEEecc--------cccCch--hhHHHH-HHHHhhhhccccceEE---Eeeeeeee
Confidence 34579999999999855 677899998765 233332 333333 4455554332222222 22335677
Q ss_pred eEEEEeCCCCCCCCCeEEEEeecCCCcccccccCcccCCccCCCCCCCCCCCCccchhhhhccChHHHHHHHHHHhhChH
Q 001555 159 VLVVYPAVKSVEAPGFFVRIIPTAASLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWK 238 (1055)
Q Consensus 159 il~l~p~~~~~~~~~~~IRii~~~~~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssIl~D~~~~~~l~~l~~~~~~~~ 238 (1055)
|+.++-. .+++.|-|=+. .. .+ ..-.++.+...+++|
T Consensus 165 iik~~d~-----~s~i~vDISFn---------------~~-----~G------------------~~aa~~i~~~~~~~p 201 (514)
T KOG1906|consen 165 IIKFKDP-----VSNIHVDISFN---------------QT-----NG------------------VKAAKFIKDFLRDHP 201 (514)
T ss_pred eEEeecC-----ccceEEEeeec---------------cc-----Cc------------------hhHHHHHHHHHhcCc
Confidence 7766532 12344443321 00 01 233677788888999
Q ss_pred HHHHHHHHHHHHHHhcCCCcC-CCCchhHHHHHHHHHHhh-ccccCcCCcHHH-----HHHHHHHHHh
Q 001555 239 ELGEALILLKVWARQRSSIYV-HDCLNGYLISILLSYLVS-LDKINNSMKALQ-----ILRVVLDFIA 299 (1055)
Q Consensus 239 ~f~dA~~LlkvWl~QRg~~~~-~ggf~gf~~s~lla~Ll~-~~~l~~~~SsyQ-----ifr~~l~fLa 299 (1055)
.++--|+++|-|+.+|+++.. .||.++|.+..|+.+.++ ...+..+-.+.+ ++..++++..
T Consensus 202 ~~~~lvlvlk~fl~~r~ln~v~tGgisSyal~~Lv~~fl~l~~~~~s~~~~~~~~~~vll~~f~e~yG 269 (514)
T KOG1906|consen 202 FLRSLVLVLKQFLYERRLNGVHTGGISSYALELLVLSFLQLHPRSKSGRLAVLKNLGVLLIKFFELYG 269 (514)
T ss_pred cchhHHHHHHHHHHhhcccccccccchHHHHHHHHHHHHhhcccccCCccchhcccchHHHHHHHHhc
Confidence 999999999999999997654 689999988777777666 444434444433 7788888887
No 16
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=94.81 E-value=2.9 Score=49.97 Aligned_cols=229 Identities=14% Similarity=0.179 Sum_probs=138.4
Q ss_pred HHHHHHHHHHHHHHHhcc-CCCCeeeeecccCCcccccccCCCCCCCCCccccccccccCCCCCCccCceEEEEEeccCC
Q 001555 568 SASLLEAFEVLSKRLHLI-EDIPLKISSVQPLDSAFRFTSVFPPEPHPLANERHTVSRLHKLTPSCIQPLEVMIQLEGSG 646 (1055)
Q Consensus 568 ~~~~~~af~~L~k~Lr~L-~~LPL~I~~V~p~sp~lRyTsv~pP~p~~~~~~~~~~~~~~~~~p~~~~pi~vvlqfE~Sg 646 (1055)
...+.+..+++...|+.. .+.|.. ..|..+.++-|+|-+-. . .=|||.|-| ..
T Consensus 17 ~~~l~~~~~~l~~~L~~~~~~~~~~-~~V~l~GS~ArgT~L~G---------------------d--sDIDIFv~f--p~ 70 (447)
T PRK13300 17 REKLKKVAEELIERLEEAIKELGLD-AEVELVGSTARGTWLSG---------------------D--RDIDIFVLF--PK 70 (447)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCc-eEEEEEeeecCCcccCC---------------------C--CceeEEEEe--CC
Confidence 346777888888887774 456766 78888888889986631 0 136899999 44
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhcc--CCe-eeecCCceeeeccceeEEEEEeccchhhHHhhhccccccccccchh
Q 001555 647 NWPMDHVAIEKTKSAFLIKIGESLQNRW--GMT-CSATEDDADIFMSGYAFRLKILHERGLSLVKSENGNKAKRVYSTDK 723 (1055)
Q Consensus 647 kWPddl~AIq~~K~AF~lkia~~L~~~~--~~~-~~v~~d~lDV~~~G~~FRl~I~~~rE~~Ll~~~~~~k~~~~~~~~~ 723 (1055)
..|. +-+++. .+.|++.+.+.+ +.. -.+..-|+-+.++||-==+.-++..+- + .+.. .+.++
T Consensus 71 ~~~~--e~L~~~----gl~i~~~~~~~~~~~~~~~yaeHpyv~~~~~G~~VDiVPcy~v~~------~-~~~~--saVDR 135 (447)
T PRK13300 71 DTSR--EELEEK----GLEIGKEVAKELLGDYEERYAEHPYVTGEIDGFEVDIVPCYKVES------G-EEII--SAVDR 135 (447)
T ss_pred CCCH--HHHHHH----HHHHHHHHHHhhCCcceeeeccCceEEEEECCEEEEEEeeEEccC------c-Cccc--ccccC
Confidence 5553 233332 344555544331 111 123344566666777666666664211 1 1111 11111
Q ss_pred hhhhhhhHHHHHHHHHhcCCChhHHHHHHHHHHHhcCCCC------CCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHH
Q 001555 724 ILFIRGQHASMINGLQGRYPVFGPVVRVAKRWAASHLFSA------CLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRF 797 (1055)
Q Consensus 724 ~~~~~p~h~~~i~~l~~r~pafs~tvRLaKrWl~shlLs~------hi~eE~vELLva~vFl~p~p~~~P~S~~~GFlRf 797 (1055)
.|.|+..|..=-.. -+.--|||+|+|+.+..+.| .|+-=++|||+++ | .||.-.
T Consensus 136 ----tp~H~~fv~~rl~~--~~~d~VRLlK~f~k~~gvYGsE~k~~GFSGYl~ELLv~~-y-------------G~F~~~ 195 (447)
T PRK13300 136 ----TPFHTKYVKERLKG--KLEDEVRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIH-Y-------------GSFENV 195 (447)
T ss_pred ----chHHHHHHHHhhhh--hHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHH-h-------------CCHHHH
Confidence 27888887542211 27889999999999998753 5899999999999 2 489999
Q ss_pred HHHHhcCCCCCCeEEEeCCCCCCHhhHHHHHHHHHHhhhhccccccCCCCeEEEEecCCCCCCcccCCCCCHHHHHHHHH
Q 001555 798 LRLLAEYDWTFSALVVDINNDFGPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRLVA 877 (1055)
Q Consensus 798 L~lLs~~DW~~~PLiVd~~~~lt~~~~~~i~~~F~~~R~~~~~dp~~~~p~mfIaT~~D~~g~~wT~~~Ps~~v~~Rl~~ 877 (1055)
|.-.++| + -|.+||+.+..+.. .| ..+++|.=|-||.-. --.++-..++..
T Consensus 196 l~~a~~w--~-~~~~I~~~~~~~~~-------~f--------------~~PlvViDPvDp~RN-----VAaa~S~~~~~~ 246 (447)
T PRK13300 196 LKAASKW--K-PPVKIDLEKHGKEY-------KF--------------DDPLVVIDPVDPNRN-----VAAALSLENLAT 246 (447)
T ss_pred HHHHHhC--C-CCceEeccccCccc-------cC--------------CCCEEEeCCCCCcch-----HHHHcCHHHHHH
Confidence 9999985 4 36889987543221 11 246888888887642 222333344444
Q ss_pred HHHHHHHHH
Q 001555 878 YARSSANLL 886 (1055)
Q Consensus 878 LAk~s~~~l 886 (1055)
+--+|-..|
T Consensus 247 fv~aar~fL 255 (447)
T PRK13300 247 FILAAREFL 255 (447)
T ss_pred HHHHHHHHH
Confidence 444444554
No 17
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=92.85 E-value=0.93 Score=57.60 Aligned_cols=169 Identities=14% Similarity=0.107 Sum_probs=109.8
Q ss_pred hHHHHHHHHHHhhChHHHHHHHHHHHHHHHhcCCCcCCCCchhHHHHHHHHHHhh-ccccCcCCcHHHHHHHHHHHHhcC
Q 001555 223 LEDNAEYVEKTISRWKELGEALILLKVWARQRSSIYVHDCLNGYLISILLSYLVS-LDKINNSMKALQILRVVLDFIATS 301 (1055)
Q Consensus 223 ~~~~l~~l~~~~~~~~~f~dA~~LlkvWl~QRg~~~~~ggf~gf~~s~lla~Ll~-~~~l~~~~SsyQifr~~l~fLa~~ 301 (1055)
.-.|...|+...+.+|+|.-+++|.|=|+.-.=+ .||+-.-.+=.|+|++.. .+....--|..--|=-+|+|||++
T Consensus 804 ~p~ht~aL~~l~qsh~~ys~vvrLaKrWl~shLL---~~h~~De~iELLva~lf~~p~p~~~psS~~~gFlRfL~llS~~ 880 (1121)
T KOG2054|consen 804 LPLHTLALQSLSQSHPFYSSVVRLAKRWLGSHLL---SGHHLDEAIELLVAALFLKPGPLVPPSSPENGFLRFLSLLSTW 880 (1121)
T ss_pred hHHHHHHHHHHhhcccchhHHHHHHHHHHHHHhh---ccchHHHHHHHHHHHHhcCccCCCCCCCcchhHHHHHHHHhcC
Confidence 3467788999999999999999999999987744 245556667778888876 444455567777899999999999
Q ss_pred CCCCCceeecCCCCCCCChhHHHh----h---hhcCCE--EEeCCCCceeeccCCCHHHHHHHHHH--HHHHHHhhhhcC
Q 001555 302 KLWNRGLYFPPKGQIGVSKEEKLQ----Y---KEAFPV--VICDPSAQVNLAFRMTSVGFCELQDE--AASTLQCMDKCG 370 (1055)
Q Consensus 302 d~~~~~i~~~~~~~~~~~~~~~~~----f---~~~f~v--vf~D~sg~lNl~~~~t~~s~~~L~~e--A~~tl~~Ld~~~ 370 (1055)
||.-.|+.+.... +.+.....+ | ++..|. |..+-++.-|-..+.++...-+.+-. |+.++++++...
T Consensus 881 dW~~~PLIvd~nn--~~~ed~~~e~~e~f~s~R~~lp~m~vit~yD~~~~~~t~~~P~~~v~~r~~alar~sl~ll~k~~ 958 (1121)
T KOG2054|consen 881 DWKFDPLIVDFNN--GFPEDERSELEEKFISARKQLPPMVVITPYDHLGSKFTRTSPNQIVLNRLVALARESLKLLEKQA 958 (1121)
T ss_pred cccCCceEEEcCC--CCcHHHHHHHHHHHhhhcccCCceEEeeccccccccccccCchHHHHHHHHHhhhhhHHhhcccc
Confidence 9998998886642 233322222 2 223443 33455554455555556655544444 477888887643
Q ss_pred CCccccccccccccc---ccccEEEEeec
Q 001555 371 DGGFEETFLTKIDFP---AKYDYCVRLNL 396 (1055)
Q Consensus 371 ~d~F~~lFl~~~~~~---~~fD~~~~i~~ 396 (1055)
...=-.+++-..-|. ..||.++.+..
T Consensus 959 p~~~~t~~~~~~lf~~~L~~yd~vi~~~~ 987 (1121)
T KOG2054|consen 959 PGEIKTIVRPTSLFRENLSPYDAVIQLEP 987 (1121)
T ss_pred cccchhhhhhhhhhhcccccccchhcccc
Confidence 222122332233332 58998888763
No 18
>PF09249 tRNA_NucTransf2: tRNA nucleotidyltransferase, second domain; InterPro: IPR015329 This domain adopts a structure consisting of a five helical bundle core. It is predominantly found in Archaeal tRNA nucleotidyltransferases, following the catalytic nucleotidyltransferase domain []. ; GO: 0004810 tRNA adenylyltransferase activity, 0016437 tRNA cytidylyltransferase activity; PDB: 3OUY_B 2ZHB_A 2ZH1_A 2ZH2_A 1UET_A 2ZH7_A 1R8B_A 2DR5_A 1TFW_C 3OVA_A ....
Probab=92.52 E-value=1.1 Score=43.29 Aligned_cols=108 Identities=19% Similarity=0.218 Sum_probs=69.5
Q ss_pred HHHHHHHHHHHhcC---CCcCCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCC
Q 001555 242 EALILLKVWARQRS---SIYVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGV 318 (1055)
Q Consensus 242 dA~~LlkvWl~QRg---~~~~~ggf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~ 318 (1055)
|-++|||..++--| +....+||+|++-=+|+.+ |.=|+.+++..|+ | ..|..+...+...
T Consensus 1 ddVrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~-------------yGsF~~~l~~a~~--W-~~~~~Id~~~~~~- 63 (114)
T PF09249_consen 1 DDVRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIH-------------YGSFENVLEAAAK--W-KPPVVIDLEDHGE- 63 (114)
T ss_dssp HHHHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHH-------------HSSHHHHHHHHTT-----TTEEEETT-TTE-
T ss_pred ChhHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHH-------------HCCHHHHHHHHHh--c-CCCeEEccCccch-
Confidence 45789999999887 4455799999987666655 4458999999884 4 3466665442110
Q ss_pred ChhHHHhhhhcCCEEEeCCCC-ceeeccCCCHHHHHHHHHHHHHHHHhhhhcCCCcc
Q 001555 319 SKEEKLQYKEAFPVVICDPSA-QVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGF 374 (1055)
Q Consensus 319 ~~~~~~~f~~~f~vvf~D~sg-~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~~~~d~F 374 (1055)
....| .-|+|++||.- .-|++|.+|...+.+.++.|+.= |.+++.+-|
T Consensus 64 ---~~~~f--~~PlvviDPvDp~RNVAAalS~~~~~~fv~~ar~f---l~~Ps~~fF 112 (114)
T PF09249_consen 64 ---PSKKF--DDPLVVIDPVDPNRNVAAALSLENLAEFVHAAREF---LKNPSIEFF 112 (114)
T ss_dssp -----EEE---SS-EEEETTEEEEETTTTS-HHHHHHHHHHHHHH---HHS--GGGG
T ss_pred ---hhhhc--CCCeEEcCCCCCCchHhHhcCHHHHHHHHHHHHHH---HHCcCHHhc
Confidence 11122 34888899965 89999999999999999998764 444444444
No 19
>PF07528 DZF: DZF domain; InterPro: IPR006561 This domain is found in proteins containing the double-stranded RNA-binding motif, DSRM (IPR001159 from INTERPRO), or the zinc finger domain C2H2 (IPR007087 from INTERPRO). This domain is found exclusively in the metazoa.
Probab=92.27 E-value=4 Score=45.21 Aligned_cols=131 Identities=18% Similarity=0.273 Sum_probs=87.0
Q ss_pred hhccChHHHHHHHHHHhhChHHHHHHHHHHHHHHHhcCCCcCCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHH
Q 001555 218 LEDMFLEDNAEYVEKTISRWKELGEALILLKVWARQRSSIYVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDF 297 (1055)
Q Consensus 218 l~D~~~~~~l~~l~~~~~~~~~f~dA~~LlkvWl~QRg~~~~~ggf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~f 297 (1055)
+..+....|.+...+.+...++.+--|+++|= ++||- .+...++++.+=.|+-|-+..+.-+..+|....||-+++.
T Consensus 108 l~aLaalRhakWFq~~a~~l~s~~~viRIlrD-l~~R~--p~w~~L~~W~leLL~~~~i~~~~~~~~l~~g~a~RRvle~ 184 (248)
T PF07528_consen 108 LSALAALRHAKWFQARANGLQSCVIVIRILRD-LRQRV--PTWQPLSSWALELLVEKAISNNSSRQPLSPGDAFRRVLEC 184 (248)
T ss_pred HHHHHHHHHhHHHHHHhccCCCcceehhhHHH-HHHhC--CCCCCCChhHHHHHHHHHeeeCCCCCCCChHHHHHHHHHH
Confidence 33344567777777766655555444444442 44552 2234456665555555555555556679999999999999
Q ss_pred HhcCCCCCCceeecCCCCCCCChhHHHhhhhcCCEEEeCCC--CceeeccCCCHHHHHHHHHHHHHHHHhhhhcCCCccc
Q 001555 298 IATSKLWNRGLYFPPKGQIGVSKEEKLQYKEAFPVVICDPS--AQVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGFE 375 (1055)
Q Consensus 298 La~~d~~~~~i~~~~~~~~~~~~~~~~~f~~~f~vvf~D~s--g~lNl~~~~t~~s~~~L~~eA~~tl~~Ld~~~~d~F~ 375 (1055)
|| .|+++... +. +.||. +..+++..||.-..+.+-.-|+..|.++-- +++.
T Consensus 185 la------sGillp~~-----------------~g-l~DPcE~~~~~~~~~lt~qq~e~it~sAQ~~LRllaf---gq~~ 237 (248)
T PF07528_consen 185 LA------SGILLPGS-----------------PG-LRDPCEKDPVDVLDTLTLQQREDITSSAQTALRLLAF---GQIH 237 (248)
T ss_pred Hh------CceecCCC-----------------CC-CcCCCCCCCceeeccCCHHHHHHHHHHHHHHHHHHHh---cCcc
Confidence 98 47776432 11 25664 478999999999999999999999999953 3444
Q ss_pred ccc
Q 001555 376 ETF 378 (1055)
Q Consensus 376 ~lF 378 (1055)
.++
T Consensus 238 kvL 240 (248)
T PF07528_consen 238 KVL 240 (248)
T ss_pred eec
Confidence 443
No 20
>PTZ00418 Poly(A) polymerase; Provisional
Probab=90.75 E-value=3.1 Score=51.17 Aligned_cols=173 Identities=13% Similarity=0.182 Sum_probs=113.5
Q ss_pred hHHHHHHHHHhcCCChhHHHHHHHHHHHhcCCC----CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCC
Q 001555 730 QHASMINGLQGRYPVFGPVVRVAKRWAASHLFS----ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYD 805 (1055)
Q Consensus 730 ~h~~~i~~l~~r~pafs~tvRLaKrWl~shlLs----~hi~eE~vELLva~vFl~p~p~~~P~S~~~GFlRfL~lLs~~D 805 (1055)
+-+..|..+--....|-.+.|-+|.|...+.+. |++.--.+-+|||.|-- -+| ..++.+=..||.+..++|+
T Consensus 238 Rvtd~Il~lVPn~~~Fr~aLR~IKlWAkrRGIYsNv~GflGGV~wAILvARVCQ-LyP---na~~s~Lv~~FF~iys~W~ 313 (593)
T PTZ00418 238 RVADLILASVPNKDYFRTTLRFIKLWAKRRGIYSNVLGYLGGVSWAILTARICQ-LYP---NFAPSQLIHKFFRVYSIWN 313 (593)
T ss_pred HHHHHHHHHCCChHHHHHHHHHHHHHHHHhccccccccccchHHHHHHHHHHHH-hCC---CCCHHHHHHHHHHHhhcCC
Confidence 455555566566778999999999999999875 57888899999999963 233 5778888899999999999
Q ss_pred CCCCeEEEeCCCCCC-HhhHHHHHHHHHHhhhhccccccCCCCeEEEEecCCCCCCcccCCCCCHHHHHHHHHHHHHHHH
Q 001555 806 WTFSALVVDINNDFG-PEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRLVAYARSSAN 884 (1055)
Q Consensus 806 W~~~PLiVd~~~~lt-~~~~~~i~~~F~~~R~~~~~dp~~~~p~mfIaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~s~~ 884 (1055)
|.+ |+++.--.+-. .+. ...|.-|... .+|+.....|-|.||.=|.-.. ...-+..-++.|+.-=+.+.+
T Consensus 314 Wp~-PV~L~~i~~~~~~~g----~~~~~VWdPr--~~~~dr~h~MPIITPayP~mNs--t~nVt~sT~~vI~~Ef~Ra~~ 384 (593)
T PTZ00418 314 WKN-PVLLCKIKEVPNIPG----LMNFKVWDPR--VNPQDRAHLMPIITPAFPSMNS--THNVTYTTKRVITEEFKRAHE 384 (593)
T ss_pred CCC-CeEcccccccccCCc----ccCCcccCCC--CCcccccccCCeecCCCCCccc--cccccHHHHHHHHHHHHHHHH
Confidence 985 76553111000 000 0012222211 2344456789999998765432 233456667777777677888
Q ss_pred HHHHHHhhcCCCccccccccccc--CCCCcEEEEec
Q 001555 885 LLTKLILEDQTDSCRWECLFRTP--LNNYDAVVLLH 918 (1055)
Q Consensus 885 ~l~~~~~~~~~~~~~~~~lF~p~--l~~YD~vI~L~ 918 (1055)
++++...+ ....|..||.|. +..|-.-|.+.
T Consensus 385 i~~~i~~~---~~~~W~~Lfep~~Ff~~Yk~yl~V~ 417 (593)
T PTZ00418 385 IIKYIEKN---SENTWTNVLEPLDFFTSYKHFLVIQ 417 (593)
T ss_pred HHHHHHhc---CCCCHHHHcCCcchhhhcceEEEEE
Confidence 87654221 246899999874 56666655554
No 21
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=90.75 E-value=2.1 Score=50.55 Aligned_cols=205 Identities=17% Similarity=0.193 Sum_probs=122.2
Q ss_pred HHHHHHHHHHHHHHHhcc-CCCCeeeeecccCCcccccccCCCCCCCCCccccccccccCCCCCCccCceEEEEEeccCC
Q 001555 568 SASLLEAFEVLSKRLHLI-EDIPLKISSVQPLDSAFRFTSVFPPEPHPLANERHTVSRLHKLTPSCIQPLEVMIQLEGSG 646 (1055)
Q Consensus 568 ~~~~~~af~~L~k~Lr~L-~~LPL~I~~V~p~sp~lRyTsv~pP~p~~~~~~~~~~~~~~~~~p~~~~pi~vvlqfE~Sg 646 (1055)
...+....++|...|+.. .+.+.. ..|.-..+.-|+|-+-- -.=|||.|-|. .
T Consensus 16 ~~~~~~~~~~l~~~l~~~~~e~~~~-~~v~~~GS~ArgT~L~G-----------------------~sDIDIfi~f~--~ 69 (408)
T TIGR03671 16 REKLKKVADELIARLEEIIEELGVD-AEVVLVGSYARGTWLKG-----------------------DRDIDIFILFP--K 69 (408)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCc-ceEEEEeeEecCCccCC-----------------------CCceeEEEEeC--C
Confidence 345667777777777664 233322 46666777778775420 01368999994 3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhccCC---eeeecCCceeeeccceeEEEEEeccchhhHHhhhccccccccccchh
Q 001555 647 NWPMDHVAIEKTKSAFLIKIGESLQNRWGM---TCSATEDDADIFMSGYAFRLKILHERGLSLVKSENGNKAKRVYSTDK 723 (1055)
Q Consensus 647 kWPddl~AIq~~K~AF~lkia~~L~~~~~~---~~~v~~d~lDV~~~G~~FRl~I~~~rE~~Ll~~~~~~k~~~~~~~~~ 723 (1055)
..| +..--...+.|++.+.+. |. ...+..-|+-+.++||-==+.-++..+ .+.. .. .+.++
T Consensus 70 ~~~------~e~l~~~gl~i~~~~~~~-~~~~~~~yaeHpYv~~~~~G~~VDiVPcy~v~------~g~~-~~--taVDR 133 (408)
T TIGR03671 70 DTS------REELEEYGLEIGHEVLKR-GGNYEERYAEHPYVSGEIEGFEVDVVPCYKVE------SGEE-II--SAVDR 133 (408)
T ss_pred CCC------HHHHHHHHHHHHHHHHhh-CCCHhheeccCceEEEEEccEEEEEEeeEEcc------CcCe-ee--ccccC
Confidence 333 223334556666666533 21 122233356666666655555565521 1111 11 01111
Q ss_pred hhhhhhhHHHHHHHHHhcCCChhHHHHHHHHHHHhcCCCC------CCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHH
Q 001555 724 ILFIRGQHASMINGLQGRYPVFGPVVRVAKRWAASHLFSA------CLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRF 797 (1055)
Q Consensus 724 ~~~~~p~h~~~i~~l~~r~pafs~tvRLaKrWl~shlLs~------hi~eE~vELLva~vFl~p~p~~~P~S~~~GFlRf 797 (1055)
.|.|+..+..=-... +.--|||+|+|+.+..+.| .|+-=++|||+++ | .||.-.
T Consensus 134 ----tp~H~~fv~~rl~~~--~~d~VRLlK~f~k~igvYGsE~~~~GFSGYl~ELLv~~-y-------------G~F~~~ 193 (408)
T TIGR03671 134 ----TPFHTRYVLERLDGK--LRDDVRLLKQFLKGIGVYGSELKTRGFSGYLCELLVIH-Y-------------GSFENV 193 (408)
T ss_pred ----chHHHHHHHHhhhhh--HHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHH-h-------------CCHHHH
Confidence 278888775422221 7789999999999998743 5899999999999 2 489999
Q ss_pred HHHHhcCCCCCCeEEEeCCCCCCHhhHHHHHHHHHHhhhhccccccCCCCeEEEEecCCCCC
Q 001555 798 LRLLAEYDWTFSALVVDINNDFGPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKAS 859 (1055)
Q Consensus 798 L~lLs~~DW~~~PLiVd~~~~lt~~~~~~i~~~F~~~R~~~~~dp~~~~p~mfIaT~~D~~g 859 (1055)
|.-.++ |+ .+.++|+.+..+. .| ..+++|.=|-||.-
T Consensus 194 l~~a~~--wk-~~~~id~~~~~~~--------~f--------------~~PlvViDPvDp~R 230 (408)
T TIGR03671 194 LKAASK--WK-PGVVIDIEEHGTK--------KF--------------DDPLVVIDPVDPKR 230 (408)
T ss_pred HHHHHh--cC-CCeEEecCccccc--------cC--------------CCCEEEeCCCCCcc
Confidence 999987 55 5778887532211 11 24688888888774
No 22
>cd05400 NT_2-5OAS_ClassI-CCAase Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme. In vertebrates, 2-5OASs are induced by interferon during the innate immune response to protect against RNA virus infections. In the presence of an RNA activator, 2-5OASs catalyze the oligomerization of ATP into 2-5A. 2-5A activates endoribonuclease L, which leads to degradation of the viral RNA. 2-5OASs are also implicated in cell growth control, differentiation, and apoptosis. This family includes human OAS1, -2, -3, and OASL. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This class I group includes the archaeal Sulfolobus shibatae and Archeoglobus fulgidus CCA-adding enzymes. It belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more dis
Probab=89.34 E-value=1.6 Score=43.76 Aligned_cols=83 Identities=20% Similarity=0.238 Sum_probs=58.4
Q ss_pred ceeeEeeeeccccccCCCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhhccCCCCccEEEeccCCCcceeeE
Q 001555 81 KTFKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVL 160 (1055)
Q Consensus 81 ~~v~vvGS~~l~t~~k~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~~~~~~~v~~~~~~~d~~kPil 160 (1055)
..|-+.|||+-+|.+++...||++|.|+..... .-....-++..|...|.+.... ...-...+|.+
T Consensus 28 ~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~--------~~~~~~~~~~~l~~~L~~~~~~------~~~~~~~~~~v 93 (143)
T cd05400 28 AEVFLQGSYARGTALRGDSDIDLVVVLPDDTSF--------AEYGPAELLDELGEALKEYYGA------NEEVKAQHRSV 93 (143)
T ss_pred cEEEEEcceeCCCCCCCCCceeEEEEEcCcccc--------cccCHHHHHHHHHHHHHHhcCc------ccccccCceEE
Confidence 367799999999999999999999999987553 1224456778888888764211 11223455677
Q ss_pred EEEeCCCCCCCCCeEEEEeecC
Q 001555 161 VVYPAVKSVEAPGFFVRIIPTA 182 (1055)
Q Consensus 161 ~l~p~~~~~~~~~~~IRii~~~ 182 (1055)
.|.-.+ .++.|-|.||.
T Consensus 94 ~v~~~~-----~~~~vDvvP~~ 110 (143)
T cd05400 94 TVKFKG-----QGFHVDVVPAF 110 (143)
T ss_pred EEEEcC-----CCeEEEEEEEe
Confidence 666543 24889999983
No 23
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
Probab=89.01 E-value=2 Score=41.17 Aligned_cols=79 Identities=25% Similarity=0.220 Sum_probs=57.2
Q ss_pred ceeeEeeeeccccccCCCcceeEEEecCccccCcccccccchhhhHHhHHHHHHHhhccCCCCccEEEeccCCCcceeeE
Q 001555 81 KTFKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVL 160 (1055)
Q Consensus 81 ~~v~vvGS~~l~t~~k~~~~VDl~v~mP~~~fq~KDylN~RYf~KRA~YLa~iA~~L~~~~~~~~v~~~~~~~d~~kPil 160 (1055)
..+.+.||++.|+..+ +..||++|..|.. .......+..+++.|++.+.+.++. .--+++.|++
T Consensus 20 ~~v~~fGS~~~g~~~~-~SDiDl~i~~~~~------------~~~~~~~l~~l~~~l~~~~~~~~~~---~i~~ArVPii 83 (114)
T cd05402 20 AKLYPFGSYVTGLGLP-GSDIDLCLLGPNH------------RVDREDFLRKLAKLLKKSGEVVEVE---PIINARVPII 83 (114)
T ss_pred CEEEEecccccCCCCC-CCCeeEEEEeCCC------------CccHHHHHHHHHHHHHhCCCceeeE---EeccCCCCEE
Confidence 3578999999987665 6799999999976 2345577788999998876544443 2356899999
Q ss_pred EEEeCCCCCCCCCeEEEEee
Q 001555 161 VVYPAVKSVEAPGFFVRIIP 180 (1055)
Q Consensus 161 ~l~p~~~~~~~~~~~IRii~ 180 (1055)
.+.-.. ++..+.|-.
T Consensus 84 k~~~~~-----~~i~~Dis~ 98 (114)
T cd05402 84 KFVDKP-----TGIEVDISF 98 (114)
T ss_pred EEEEcC-----CCeEEEEEc
Confidence 887653 346666654
No 24
>PF07528 DZF: DZF domain; InterPro: IPR006561 This domain is found in proteins containing the double-stranded RNA-binding motif, DSRM (IPR001159 from INTERPRO), or the zinc finger domain C2H2 (IPR007087 from INTERPRO). This domain is found exclusively in the metazoa.
Probab=88.38 E-value=2.2 Score=47.16 Aligned_cols=101 Identities=20% Similarity=0.059 Sum_probs=82.5
Q ss_pred hhHHHHHHHHHhcCCChhHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCC-C
Q 001555 729 GQHASMINGLQGRYPVFGPVVRVAKRWAASHLFSACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDW-T 807 (1055)
Q Consensus 729 p~h~~~i~~l~~r~pafs~tvRLaKrWl~shlLs~hi~eE~vELLva~vFl~p~p~~~P~S~~~GFlRfL~lLs~~DW-~ 807 (1055)
-+|+.+-+.-++..++.-..+|++|---+..--...++.=.+||||-++..+ .|-..|-++..+|-|+|++||+==. .
T Consensus 114 lRhakWFq~~a~~l~s~~~viRIlrDl~~R~p~w~~L~~W~leLL~~~~i~~-~~~~~~l~~g~a~RRvle~lasGillp 192 (248)
T PF07528_consen 114 LRHAKWFQARANGLQSCVIVIRILRDLRQRVPTWQPLSSWALELLVEKAISN-NSSRQPLSPGDAFRRVLECLASGILLP 192 (248)
T ss_pred HHHhHHHHHHhccCCCcceehhhHHHHHHhCCCCCCCChhHHHHHHHHHeee-CCCCCCCChHHHHHHHHHHHhCceecC
Confidence 4899999999999999999999999988887767789999999999999774 3446788999999999999997332 2
Q ss_pred CCeEEEeCC--------CCCCHhhHHHHHHH
Q 001555 808 FSALVVDIN--------NDFGPEDFKVINDN 830 (1055)
Q Consensus 808 ~~PLiVd~~--------~~lt~~~~~~i~~~ 830 (1055)
..|=|.|+- +.||.+++++|...
T Consensus 193 ~~~gl~DPcE~~~~~~~~~lt~qq~e~it~s 223 (248)
T PF07528_consen 193 GSPGLRDPCEKDPVDVLDTLTLQQREDITSS 223 (248)
T ss_pred CCCCCcCCCCCCCceeeccCCHHHHHHHHHH
Confidence 456666665 47999999887643
No 25
>PF10421 OAS1_C: 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus ; InterPro: IPR018952 This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between residues 320 and 344 at the extreme C-terminal end []. Oligoadenylate synthetases are antiviral enzymes that counteract viral attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesise 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication []. This domain is often associated with IPR002934 from INTERPRO. ; PDB: 1PX5_B.
Probab=86.37 E-value=4.5 Score=42.78 Aligned_cols=125 Identities=22% Similarity=0.202 Sum_probs=76.0
Q ss_pred hHHHHHHHHHHHHHHHhcCCC--cCCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCC
Q 001555 237 WKELGEALILLKVWARQRSSI--YVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKG 314 (1055)
Q Consensus 237 ~~~f~dA~~LlkvWl~QRg~~--~~~ggf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~ 314 (1055)
..-+++=++|.|-|.+|=--. .+.+--..|.+..|+.|..++|.=...++--|-||.||+.|.+..- =-|+-...
T Consensus 41 P~klK~LIrLVKhWy~~~~~~~~~~~~lPpsYaLELLtIyAWE~g~~~~~F~~a~gfrtVLeLi~~y~~--LcIyWt~~- 117 (190)
T PF10421_consen 41 PTKLKNLIRLVKHWYQQCKKKKCGGGSLPPSYALELLTIYAWEQGCGAEDFSTAEGFRTVLELIQKYEQ--LCIYWTVY- 117 (190)
T ss_dssp -HHHHHHHHHHHHHHHHHHCC--HTT-S--HHHHHHHHHHHHHHHT-SSS--HHHHHHHHHHHHHCGGG---EE---SS-
T ss_pred CHHHHHHHHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHhcCCCcCcchhhhHhHHHHHHhCcce--eEEEeccc-
Confidence 467899999999999884321 1222346799999999999988777888999999999999975421 12222111
Q ss_pred CCCCChhH-----HHhhhhcCCEEEeCCCC-ceeeccCCCHHHHHHHHHHHHHHHHhhh
Q 001555 315 QIGVSKEE-----KLQYKEAFPVVICDPSA-QVNLAFRMTSVGFCELQDEAASTLQCMD 367 (1055)
Q Consensus 315 ~~~~~~~~-----~~~f~~~f~vvf~D~sg-~lNl~~~~t~~s~~~L~~eA~~tl~~Ld 367 (1055)
-+...+. ..+....-||+ +||.- +-|+..+ ..+.+++|.+||+..++..-
T Consensus 118 -Y~f~~~~v~~~l~~qL~~~RPvI-LDPAdPtnNV~~~-~~~~W~~la~eA~~wl~~~c 173 (190)
T PF10421_consen 118 -YDFEDETVRNYLQSQLKKPRPVI-LDPADPTNNVAGG-NRWCWDLLAQEAAEWLSSPC 173 (190)
T ss_dssp ---SSSHHHHHHHHHHHTSSS-EE-B-TT-TT-BTT-S--HHHHHHHHHHHHHHTTSGG
T ss_pred -CCCcCHHHHHHHHHhhccCCCce-eCCCCCCCccccC-CccchHHHHHHHHHHhcCcc
Confidence 0111222 23445566876 89866 4455554 67899999999999887763
No 26
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=84.42 E-value=8.5 Score=46.02 Aligned_cols=142 Identities=16% Similarity=0.204 Sum_probs=92.8
Q ss_pred ChhHHHHHHHHHHHhcCCC----CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCCCCCeEEEeCCCCC
Q 001555 744 VFGPVVRVAKRWAASHLFS----ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDWTFSALVVDINNDF 819 (1055)
Q Consensus 744 afs~tvRLaKrWl~shlLs----~hi~eE~vELLva~vFl~p~p~~~P~S~~~GFlRfL~lLs~~DW~~~PLiVd~~~~l 819 (1055)
-|..|-|-.|-|.-.|... |++---.-=+|||.+ .+=+| =.+|.+=.-||....++|.|- .|.+++.-++-
T Consensus 214 ~F~~tLRaiKlWAKrrgVYsN~~GF~GGV~wA~LVARi-CQLYP---NA~~s~Lv~kfF~ifs~W~WP-~PVlL~~ie~~ 288 (562)
T KOG2245|consen 214 NFRITLRAIKLWAKRRGVYSNVMGFLGGVAWAMLVARI-CQLYP---NASPSTLVAKFFRVFSQWNWP-NPVLLKPIEEG 288 (562)
T ss_pred HHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHH-HccCC---CcchHHHHHHHHHHHhhccCC-CceEecccccc
Confidence 4677889999999999864 577778889999998 33233 345666677888899999997 89988875432
Q ss_pred CHhhHHHHHHHHHHhhhhccccccCCCCeEEEEecCCCC-CCcccCCCCCHHHHHHHHHHHHHHHHHHHHHHhhcCCCcc
Q 001555 820 GPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKA-SEAWTTCSPNFTELKRLVAYARSSANLLTKLILEDQTDSC 898 (1055)
Q Consensus 820 t~~~~~~i~~~F~~~R~~~~~dp~~~~p~mfIaT~~D~~-g~~wT~~~Ps~~v~~Rl~~LAk~s~~~l~~~~~~~~~~~~ 898 (1055)
+-. +.-|-. ..+|...-..|=|.||-=|+ ++..+ -|.--..-|+.-=+.+++...+.. .+ ..
T Consensus 289 ~L~--------~~VWdP--r~n~~DryHlMPIITPAyP~~nsthN---VS~ST~~Vi~~Ef~~g~~I~~~i~-~~---k~ 351 (562)
T KOG2245|consen 289 NLN--------LPVWDP--RVNPSDRYHLMPIITPAYPQMNSTHN---VSRSTLKVITEEFKRGLEICDDIE-LN---KL 351 (562)
T ss_pred ccC--------ccccCC--CCCCCCcceecccccCCccccccccc---ccHHHHHHHHHHHHHHHHHHHHHH-hc---cc
Confidence 211 111211 13455666689899996554 33332 234444445555556666655543 22 56
Q ss_pred ccccccccc
Q 001555 899 RWECLFRTP 907 (1055)
Q Consensus 899 ~~~~lF~p~ 907 (1055)
+|..||.+.
T Consensus 352 ~W~~LFE~~ 360 (562)
T KOG2245|consen 352 DWSDLFELY 360 (562)
T ss_pred cHHHHhhhh
Confidence 899999763
No 27
>PF10421 OAS1_C: 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus ; InterPro: IPR018952 This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between residues 320 and 344 at the extreme C-terminal end []. Oligoadenylate synthetases are antiviral enzymes that counteract viral attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesise 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication []. This domain is often associated with IPR002934 from INTERPRO. ; PDB: 1PX5_B.
Probab=66.31 E-value=7 Score=41.40 Aligned_cols=59 Identities=24% Similarity=0.329 Sum_probs=41.5
Q ss_pred hHHHHHHHHHHHhcCCC-----CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCC
Q 001555 746 GPVVRVAKRWAASHLFS-----ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYD 805 (1055)
Q Consensus 746 s~tvRLaKrWl~shlLs-----~hi~eE~vELLva~vFl~p~p~~~P~S~~~GFlRfL~lLs~~D 805 (1055)
---+||+|+|-....-- .--+.=++|||++|++-+- .-..-.+-.-||--+|.||..+.
T Consensus 45 K~LIrLVKhWy~~~~~~~~~~~~lPpsYaLELLtIyAWE~g-~~~~~F~~a~gfrtVLeLi~~y~ 108 (190)
T PF10421_consen 45 KNLIRLVKHWYQQCKKKKCGGGSLPPSYALELLTIYAWEQG-CGAEDFSTAEGFRTVLELIQKYE 108 (190)
T ss_dssp HHHHHHHHHHHHHHHCC--HTT-S--HHHHHHHHHHHHHHH-T-SSS--HHHHHHHHHHHHHCGG
T ss_pred HHHHHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHhc-CCCcCcchhhhHhHHHHHHhCcc
Confidence 34589999999887643 2345789999999999764 22233467889988899998865
No 28
>PF09249 tRNA_NucTransf2: tRNA nucleotidyltransferase, second domain; InterPro: IPR015329 This domain adopts a structure consisting of a five helical bundle core. It is predominantly found in Archaeal tRNA nucleotidyltransferases, following the catalytic nucleotidyltransferase domain []. ; GO: 0004810 tRNA adenylyltransferase activity, 0016437 tRNA cytidylyltransferase activity; PDB: 3OUY_B 2ZHB_A 2ZH1_A 2ZH2_A 1UET_A 2ZH7_A 1R8B_A 2DR5_A 1TFW_C 3OVA_A ....
Probab=66.01 E-value=9.4 Score=37.05 Aligned_cols=96 Identities=21% Similarity=0.329 Sum_probs=60.1
Q ss_pred HHHHHHHHHhcCCCC------CCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCCCCCeEEEeCCCCCCHh
Q 001555 749 VRVAKRWAASHLFSA------CLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDWTFSALVVDINNDFGPE 822 (1055)
Q Consensus 749 vRLaKrWl~shlLs~------hi~eE~vELLva~vFl~p~p~~~P~S~~~GFlRfL~lLs~~DW~~~PLiVd~~~~lt~~ 822 (1055)
|||+|+.+-+....| -||-=+.|||+++- -||.-+|+-.+ +|+ -|.+||+.+.-+.
T Consensus 3 VrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~y--------------GsF~~~l~~a~--~W~-~~~~Id~~~~~~~- 64 (114)
T PF09249_consen 3 VRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHY--------------GSFENVLEAAA--KWK-PPVVIDLEDHGEP- 64 (114)
T ss_dssp HHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHHH--------------SSHHHHHHHHT--T---TTEEEETT-TTE--
T ss_pred hHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHHH--------------CCHHHHHHHHH--hcC-CCeEEccCccchh-
Confidence 899999999988743 68999999999875 47899999998 587 5999998732110
Q ss_pred hHHHHHHHHHHhhhhccccccCCCCeEEEEecCCCCCCcccCCCCCHHHHHHHHHHHHHHHHHH
Q 001555 823 DFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRLVAYARSSANLL 886 (1055)
Q Consensus 823 ~~~~i~~~F~~~R~~~~~dp~~~~p~mfIaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~s~~~l 886 (1055)
.++ -.-+++|.-|.||.- +--..+-++++..+.-+|-..+
T Consensus 65 -----------~~~--------f~~PlvviDPvDp~R-----NVAAalS~~~~~~fv~~ar~fl 104 (114)
T PF09249_consen 65 -----------SKK--------FDDPLVVIDPVDPNR-----NVAAALSLENLAEFVHAAREFL 104 (114)
T ss_dssp ------------EE--------E-SS-EEEETTEEEE-----ETTTTS-HHHHHHHHHHHHHHH
T ss_pred -----------hhh--------cCCCeEEcCCCCCCc-----hHhHhcCHHHHHHHHHHHHHHH
Confidence 011 124688888999874 2233444555555545454554
No 29
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=50.68 E-value=44 Score=38.61 Aligned_cols=151 Identities=18% Similarity=0.188 Sum_probs=86.3
Q ss_pred HHHHHHHHhcCCChhHHHHHHHHHHHhcCCC----CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCCC
Q 001555 732 ASMINGLQGRYPVFGPVVRVAKRWAASHLFS----ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDWT 807 (1055)
Q Consensus 732 ~~~i~~l~~r~pafs~tvRLaKrWl~shlLs----~hi~eE~vELLva~vFl~p~p~~~P~S~~~GFlRfL~lLs~~DW~ 807 (1055)
+.-|-.|--.-..|..+.|-.|-|....... ++.-.-+--++||.+- +-+ |-.+..+-..||..+|++|+|-
T Consensus 194 TDeiL~LVP~~~vF~~ALRaIK~WAqRRavYaN~~GfpGGVAwam~VARiC-QLY---PNA~S~vIv~kFF~ils~WnWP 269 (552)
T COG5186 194 TDEILNLVPSVKVFHSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVARIC-QLY---PNASSFVIVCKFFEILSSWNWP 269 (552)
T ss_pred hHHHHHhCCchHHHHHHHHHHHHHHHhhhhhccccCCcchHHHHHHHHHHH-hhc---cCcchHhHHHHHHHHHHhcCCC
Confidence 3333344334445677889999999888764 4556677888888872 223 2356677789999999999997
Q ss_pred CCeEEEeCCCCCCHhhHHHHHHHHHHhhhhccccccCCCCeEEEEecCCCCCCcccC---CCCCHHHHHHHHHHHHHHHH
Q 001555 808 FSALVVDINNDFGPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTT---CSPNFTELKRLVAYARSSAN 884 (1055)
Q Consensus 808 ~~PLiVd~~~~lt~~~~~~i~~~F~~~R~~~~~dp~~~~p~mfIaT~~D~~g~~wT~---~~Ps~~v~~Rl~~LAk~s~~ 884 (1055)
+|+|+-+-.+.+-+-+ -|-. ..=|+.+..-|=|.||-=|+-.+ |. .....+|+.-++.-- +
T Consensus 270 -qPviLkPieDgplqvr--------vWnP--KvYpsDk~HRMPvITPAYPSMCA-THNit~STq~vIl~EfvRa~----~ 333 (552)
T COG5186 270 -QPVILKPIEDGPLQVR--------VWNP--KVYPSDKYHRMPVITPAYPSMCA-THNITNSTQHVILMEFVRAH----K 333 (552)
T ss_pred -CCeEeeeccCCCeeEE--------eeCC--ccCcccccccCccccCCchhhhh-hccccchhhhhHHHHHHHHH----H
Confidence 8988866544332210 1110 01133344456677776554322 32 234566666665432 2
Q ss_pred HHHHHHhhcCCCcccccccccc
Q 001555 885 LLTKLILEDQTDSCRWECLFRT 906 (1055)
Q Consensus 885 ~l~~~~~~~~~~~~~~~~lF~p 906 (1055)
.+.+ +.. ...+|..||.-
T Consensus 334 I~~d-i~~---n~~~w~~lFek 351 (552)
T COG5186 334 ILSD-IER---NALDWRRLFEK 351 (552)
T ss_pred hhhh-Hhh---ccccHHHHHHh
Confidence 2222 111 14577777753
No 30
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=44.68 E-value=20 Score=34.02 Aligned_cols=29 Identities=28% Similarity=0.463 Sum_probs=24.2
Q ss_pred ceeeEeeeeccccccCCCcceeEEEecCcc
Q 001555 81 KTFKIGGSYSINCVVKPAVNVDLFVGLPKE 110 (1055)
Q Consensus 81 ~~v~vvGS~~l~t~~k~~~~VDl~v~mP~~ 110 (1055)
+.+.|.|||+ +.-.+|+..||+.|+.=..
T Consensus 25 ~~~~vFGS~a-RgE~~~~SDIDILVef~~~ 53 (97)
T COG1669 25 KRVAVFGSYA-RGEQKPDSDIDILVEFEPG 53 (97)
T ss_pred ceEEEeeeee-cCCCCCCCCceeEEeecCC
Confidence 3688999999 6678889999999997554
No 31
>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]
Probab=39.11 E-value=1.7e+02 Score=35.57 Aligned_cols=91 Identities=18% Similarity=0.273 Sum_probs=61.8
Q ss_pred HHHHHHhhhcCcccccccCCCCeEEEEecCCCcccccchHHHHHHHHHHHcCCCCCCcEEEecccchhhhccCCCCccch
Q 001555 488 EALRFRKFWGEKAELRRFKDGTIAESTVWESEQWTRHLILKGIIEYVLLRHLSLSKENVVQIVDQLDFSLLHGAKDLVSF 567 (1055)
Q Consensus 488 ea~~FR~FWG~KsELRRFkDGsI~E~VvW~~~~~~~~~I~~~Iv~yiL~~H~~~~~~~i~~~~~~~d~~l~~~~~~~~~~ 567 (1055)
.|.+|++|||+-- |=--+.---.|-+.|+... +.-.+.+++-+|+.|..-.+.+|-.+- ++
T Consensus 202 ~a~Kfq~yf~n~P-ll~vpg~~PvEi~Yt~e~e---rDylEaairtV~qih~~ee~GDilvFL---------------tg 262 (699)
T KOG0925|consen 202 DAEKFQRYFGNAP-LLAVPGTHPVEIFYTPEPE---RDYLEAAIRTVLQIHMCEEPGDILVFL---------------TG 262 (699)
T ss_pred chHHHHHHhCCCC-eeecCCCCceEEEecCCCC---hhHHHHHHHHHHHHHhccCCCCEEEEe---------------cC
Confidence 4789999999742 2222334457778887654 356789999999999975444444321 13
Q ss_pred HHHHHHHHHHHHHHHhcc--CCCCeeeeeccc
Q 001555 568 SASLLEAFEVLSKRLHLI--EDIPLKISSVQP 597 (1055)
Q Consensus 568 ~~~~~~af~~L~k~Lr~L--~~LPL~I~~V~p 597 (1055)
.+.+-+|...+.+...+| +..||+|.-+.|
T Consensus 263 eeeIe~aC~~i~re~~~L~~~~g~l~v~PLyP 294 (699)
T KOG0925|consen 263 EEEIEDACRKISREVDNLGPQVGPLKVVPLYP 294 (699)
T ss_pred HHHHHHHHHHHHHHHHhhccccCCceEEecCc
Confidence 345777888888888887 478888877665
No 32
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=36.64 E-value=40 Score=27.60 Aligned_cols=27 Identities=19% Similarity=0.140 Sum_probs=21.4
Q ss_pred CCceeeEeeeeccccccCCCcceeEEEe
Q 001555 79 KPKTFKIGGSYSINCVVKPAVNVDLFVG 106 (1055)
Q Consensus 79 ~P~~v~vvGS~~l~t~~k~~~~VDl~v~ 106 (1055)
.+..+-+.|||+-++ .++...||++|.
T Consensus 16 ~~~~v~lfGS~arg~-~~~~SDIDi~v~ 42 (49)
T cd05397 16 PGYEIVVYGSLVRGL-LKKSSDIDLACV 42 (49)
T ss_pred CCcEEEEECCcCCCC-CCCCCCEEEEEE
Confidence 356788999999765 456678999987
No 33
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=30.58 E-value=2.3e+02 Score=33.95 Aligned_cols=228 Identities=18% Similarity=0.229 Sum_probs=129.8
Q ss_pred hHHHHHHHHHHHHHHHhcc-CCCCeeeeecccCCcccccccCCCCCCCCCccccccccccCCCCCCccCceEEEEEeccC
Q 001555 567 FSASLLEAFEVLSKRLHLI-EDIPLKISSVQPLDSAFRFTSVFPPEPHPLANERHTVSRLHKLTPSCIQPLEVMIQLEGS 645 (1055)
Q Consensus 567 ~~~~~~~af~~L~k~Lr~L-~~LPL~I~~V~p~sp~lRyTsv~pP~p~~~~~~~~~~~~~~~~~p~~~~pi~vvlqfE~S 645 (1055)
....+...-++|...+.++ +++++ ...|-=+.++-|.|=+- .. .=|||-|-|-
T Consensus 20 E~~~~~~~~e~l~~~~~~~~~e~~~-~aev~lVGS~AkgTwL~--------gd---------------~DIDvFi~Fp-- 73 (443)
T COG1746 20 ERKKLKEVAEELRERINEIIEELGI-DAEVVLVGSYAKGTWLR--------GD---------------HDIDVFIAFP-- 73 (443)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCC-cceEEEEeecccCcccC--------CC---------------cceeEEEECC--
Confidence 3456777888888888776 35555 33344444555666331 00 1357777663
Q ss_pred CCCCCC--HHHHHHHHHHHHHHHHHHHhhccCC-eeeecCCceeeeccceeEEEEEeccchhhHHhhhccccccccccch
Q 001555 646 GNWPMD--HVAIEKTKSAFLIKIGESLQNRWGM-TCSATEDDADIFMSGYAFRLKILHERGLSLVKSENGNKAKRVYSTD 722 (1055)
Q Consensus 646 gkWPdd--l~AIq~~K~AF~lkia~~L~~~~~~-~~~v~~d~lDV~~~G~~FRl~I~~~rE~~Ll~~~~~~k~~~~~~~~ 722 (1055)
.| .+-+++. -+.|+...-+..++ ...+.--|+-...+||-==+.-+|.-|-. . +. +...+
T Consensus 74 ----~d~~~eel~~~----GL~ig~~~l~~~~~~~~YAeHPYV~g~v~G~eVDvVPCy~v~~~------~-~~--~sAVD 136 (443)
T COG1746 74 ----KDTSEEELEEK----GLEIGREVLKRGNYEERYAEHPYVTGEVDGYEVDVVPCYKVEDG------E-KI--ISAVD 136 (443)
T ss_pred ----CCCCHHHHHHH----HHHHHHHHhcCCchhhhhccCCeeEEEEccEEEEEEecccccCc------c-cc--ccccc
Confidence 33 3333322 12333333221111 11122234555666765555555542211 1 01 11112
Q ss_pred hhhhhhhhHHHHHHHH-HhcCCChhHHHHHHHHHHHhcCCCC------CCcHHHHHHHHHHhhcCCCCCCCCCchhhHHH
Q 001555 723 KILFIRGQHASMINGL-QGRYPVFGPVVRVAKRWAASHLFSA------CLVEEAVELLVAYLFLKPLPFNVPCSRVTGFL 795 (1055)
Q Consensus 723 ~~~~~~p~h~~~i~~l-~~r~pafs~tvRLaKrWl~shlLs~------hi~eE~vELLva~vFl~p~p~~~P~S~~~GFl 795 (1055)
+ .|.||..+.+= -.+-- -=|||+|+.+-+-...| -||-=+.|||+.|- .+|.
T Consensus 137 R----TplHt~yv~e~L~~~~~---deVrLLK~FlK~iGvYGaE~rt~GFSGYL~ELLII~y--------------GsFe 195 (443)
T COG1746 137 R----TPLHTRYVEEHLKGRQK---DEVRLLKQFLKGIGVYGAELRTQGFSGYLCELLIIHY--------------GSFE 195 (443)
T ss_pred C----cchhHHHHHHHhcccch---hHHHHHHHHHhccCccceeeeeccchHHHHHHHHhhh--------------ccHH
Confidence 2 26788776652 22211 47999999999887754 68888999999874 3678
Q ss_pred HHHHHHhcCCCCCCeEEEeCCCCCCHhhHHHHHHHHHHhhhhccccccCCCCeEEEEecCCCCCCcccCCCCCHHHHHHH
Q 001555 796 RFLRLLAEYDWTFSALVVDINNDFGPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRL 875 (1055)
Q Consensus 796 RfL~lLs~~DW~~~PLiVd~~~~lt~~~~~~i~~~F~~~R~~~~~dp~~~~p~mfIaT~~D~~g~~wT~~~Ps~~v~~Rl 875 (1055)
-+|+--++ |+ -|.+||+.+- .|... .--+|+|.-|.||.- +--.++-++||
T Consensus 196 ~vl~~a~~--wr-p~~~ID~~~~---------------~~e~f------~d~PliVvDPVDP~R-----NVAAalSl~~l 246 (443)
T COG1746 196 NVLKAASR--WR-PGKIIDLEGH---------------KRERF------EDEPLIVVDPVDPKR-----NVAAALSLENL 246 (443)
T ss_pred HHHHHHhc--cC-CCeEEeccch---------------hhhcc------CCCCeEecCCCCCcc-----chhhhcCHHHH
Confidence 78887777 87 4599998654 11110 112799999999984 33456777777
Q ss_pred HHHHHHHHHHHH
Q 001555 876 VAYARSSANLLT 887 (1055)
Q Consensus 876 ~~LAk~s~~~l~ 887 (1055)
..+--+|-..|+
T Consensus 247 a~f~~aar~FL~ 258 (443)
T COG1746 247 ARFVHAAREFLK 258 (443)
T ss_pred HHHHHHHHHHhc
Confidence 777777767663
No 34
>cd05403 NT_KNTase_like Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is
Probab=30.08 E-value=58 Score=29.22 Aligned_cols=32 Identities=22% Similarity=0.268 Sum_probs=25.7
Q ss_pred CCceeeEeeeeccccccCCCcceeEEEecCccc
Q 001555 79 KPKTFKIGGSYSINCVVKPAVNVDLFVGLPKEC 111 (1055)
Q Consensus 79 ~P~~v~vvGS~~l~t~~k~~~~VDl~v~mP~~~ 111 (1055)
....|-+.||++-|... +...||++|.++...
T Consensus 17 ~i~~i~LfGS~arg~~~-~~SDiDl~vi~~~~~ 48 (93)
T cd05403 17 GVEKVYLFGSYARGDAR-PDSDIDLLVIFDDPL 48 (93)
T ss_pred CccEEEEEeeeecCCCC-CCCCeeEEEEeCCCC
Confidence 35578899999998655 677899999998764
No 35
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=29.58 E-value=24 Score=36.16 Aligned_cols=27 Identities=44% Similarity=0.833 Sum_probs=18.8
Q ss_pred HHHHHHHHHHhcCCCCCCcHHHHHHHHHHhhcCCCCC
Q 001555 748 VVRVAKRWAASHLFSACLVEEAVELLVAYLFLKPLPF 784 (1055)
Q Consensus 748 tvRLaKrWl~shlLs~hi~eE~vELLva~vFl~p~p~ 784 (1055)
+||| |||+.++-...+| | |+.-+|.||
T Consensus 100 aVRL-KRWM~aMHVDAFF-----e----Yllg~~~~Y 126 (175)
T PF09441_consen 100 AVRL-KRWMRAMHVDAFF-----E----YLLGKPHPY 126 (175)
T ss_pred HHHH-HHHHHHhhHHHHH-----H----HHhCCCCcc
Confidence 6888 9999998765433 2 455667776
No 36
>PF01909 NTP_transf_2: Nucleotidyltransferase domain A subset of this Pfam family; InterPro: IPR002934 A small region that overlaps with a nuclear localization signal and binds to the RNA primer contains three aspartates that are essential for catalysis. Sequence and secondary structure comparisons of regions surrounding these aspartates with sequences of other polymerases revealed a significant homology to the palm structure of DNA polymerase beta, terminal deoxynucleotidyltransferase and DNA polymerase IV of Saccharomyces cerevisiae, all members of the family X of polymerases. This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor [, ]. Proteins containing this domain include kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase inactivates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. In experiments, Mn2+ strongly stimulated this reaction due to a 50-fold lower Ki for 8-azido-ATP in the presence of Mn2+. Mutations of the highly conserved Asp residues 113, 115, and 167, critical for metal binding in the catalytic domain of bovine poly(A) polymerase, led to a strong reduction of cross-linking efficiency, and Mn2+ no longer stimulated the reaction. Mutations in the region of the "helical turn motif" (a domain binding the triphosphate moiety of the nucleotide) and in the suspected nucleotide-binding helix of bovine poly(A) polymerase impaired ATP binding and catalysis. The results indicate that ATP is bound in part by the helical turn motif and in part by a region that may be a structural analogue of the fingers domain found in many polymerases.; GO: 0016779 nucleotidyltransferase activity; PDB: 4EBK_B 4EBJ_A 1KNY_A 2B4V_A 2B56_A 2B51_A 1NO5_B 1Q79_A 1Q78_A 1F5A_A ....
Probab=25.95 E-value=48 Score=30.03 Aligned_cols=32 Identities=22% Similarity=0.244 Sum_probs=26.2
Q ss_pred CceeeEeeeeccccccCCCcceeEEEecCcccc
Q 001555 80 PKTFKIGGSYSINCVVKPAVNVDLFVGLPKECF 112 (1055)
Q Consensus 80 P~~v~vvGS~~l~t~~k~~~~VDl~v~mP~~~f 112 (1055)
...|-+.||++-|+.. +...||++|..+...-
T Consensus 14 ~~~v~lfGS~a~g~~~-~~SDIDl~i~~~~~~~ 45 (93)
T PF01909_consen 14 VAEVYLFGSYARGDAT-PDSDIDLLIILDEPED 45 (93)
T ss_dssp TEEEEEEHHHHHTSSC-TTSCEEEEEEESSTSC
T ss_pred CCEEEEECCcccCcCC-CCCCEEEEEEeCCccc
Confidence 5678899999998754 4589999999998753
No 37
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=23.81 E-value=4.8e+02 Score=32.52 Aligned_cols=132 Identities=15% Similarity=0.166 Sum_probs=85.8
Q ss_pred hhChHHHHHHHHHHHHHHHhcCC-CcCCCCch-hHHHHHHHHHHhhccc--c----------------------------
Q 001555 234 ISRWKELGEALILLKVWARQRSS-IYVHDCLN-GYLISILLSYLVSLDK--I---------------------------- 281 (1055)
Q Consensus 234 ~~~~~~f~dA~~LlkvWl~QRg~-~~~~ggf~-gf~~s~lla~Ll~~~~--l---------------------------- 281 (1055)
+..-+.|+-.|.++|.|+..++. +...|+++ .+.+++++.|-+++.. +
T Consensus 256 ~~~d~r~~~L~~~vk~wa~~~~~~d~~~g~~~s~ysl~lmvi~fLq~~~~~ilp~l~~l~~~~~~~~~~~~~~~~~~~~~ 335 (596)
T KOG2277|consen 256 SEIDPRVRPLVLLVKHWAKEKGLNDAKPGGLNSSYSLTLMVIHFLQTLSPPILPPLSKLLPESDSNDKPVVKKKVLCSFL 335 (596)
T ss_pred HhcCCCcchHhHHHHHHHHhccCCCCCCCceeccccHHHHHHHHHHhcCCcCCCchhhhchhcccccccchhhhhhhccc
Confidence 33345999999999999999986 44567888 5888888888776210 1
Q ss_pred ---------CcCCcHH-HHHHHHHHHHh-cCCCCCCceeecCCCCCCCChhHHHhhhhcCCEEEeCCCC-ceeeccCCCH
Q 001555 282 ---------NNSMKAL-QILRVVLDFIA-TSKLWNRGLYFPPKGQIGVSKEEKLQYKEAFPVVICDPSA-QVNLAFRMTS 349 (1055)
Q Consensus 282 ---------~~~~Ssy-Qifr~~l~fLa-~~d~~~~~i~~~~~~~~~~~~~~~~~f~~~f~vvf~D~sg-~lNl~~~~t~ 349 (1055)
....+++ .++-+++.|-+ .-|+.++.|.+..... .... ...+. ..+..+-|+-. ..|+-..++.
T Consensus 336 ~~~~~~~~~~~~~~~l~~l~~~f~~yy~~~Fdf~~~~I~~r~~~~--l~~~-~~~~~-~~~l~i~dp~~~~~n~~~~~~~ 411 (596)
T KOG2277|consen 336 RVFQRNPSNSQNTGSLGELLLGFFSYYASLFDFRKNAISIRRGRA--LKRA-KKIKS-KKFLCIEDPFEVSHNADAGVTL 411 (596)
T ss_pred cccccccccccccchHHHHHHHHHHHHhhhcccccceeeeeeccc--cccc-chhhh-ccceeeccccccccCccccchH
Confidence 1122222 36667778878 6788777766654321 1100 00111 12333345544 4588899999
Q ss_pred HHHHHHHHHHHHHHHhhhhc
Q 001555 350 VGFCELQDEAASTLQCMDKC 369 (1055)
Q Consensus 350 ~s~~~L~~eA~~tl~~Ld~~ 369 (1055)
-....++.+.+.+...+.+.
T Consensus 412 ~~~~~i~~~~~~~~~~~~~~ 431 (596)
T KOG2277|consen 412 KVLLLIQDEFQESRRVFKDV 431 (596)
T ss_pred HHHHHHHHHHHHHHHHhhhh
Confidence 99999999999999998764
Done!