Query 002406
Match_columns 927
No_of_seqs 141 out of 309
Neff 6.5
Searched_HMMs 46136
Date Thu Mar 28 23:18:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002406.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002406hhsearch_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 5E-206 1E-210 1895.0 78.8 805 88-920 1-853 (972)
2 KOG2054 Nucleolar RNA-associat 100.0 1E-189 3E-194 1640.9 64.5 880 10-914 81-982 (1121)
3 PTZ00418 Poly(A) polymerase; P 99.7 1.9E-15 4.1E-20 176.3 26.1 369 81-509 127-515 (593)
4 COG5186 PAP1 Poly(A) polymeras 99.6 2.5E-15 5.4E-20 161.9 15.8 272 83-396 84-366 (552)
5 KOG2245 Poly(A) polymerase and 99.6 2.6E-14 5.5E-19 160.5 20.6 308 83-441 92-411 (562)
6 PF04928 PAP_central: Poly(A) 99.2 8.4E-11 1.8E-15 126.7 13.7 147 227-378 96-251 (254)
7 TIGR03671 cca_archaeal CCA-add 98.9 1E-06 2.2E-11 100.5 30.5 255 17-374 2-260 (408)
8 PRK13300 tRNA CCA-pyrophosphor 98.9 1.3E-06 2.8E-11 101.0 30.8 360 17-499 3-371 (447)
9 COG1746 CCA1 tRNA nucleotidylt 98.5 6.6E-05 1.4E-09 84.9 27.5 258 16-376 6-267 (443)
10 PF03813 Nrap: Nrap protein; 98.2 0.00027 5.9E-09 90.3 26.5 342 13-396 478-852 (972)
11 smart00572 DZF domain in DSRM 96.6 0.14 3.1E-06 55.2 18.1 220 82-368 4-231 (246)
12 COG5260 TRF4 DNA polymerase si 96.2 0.043 9.4E-07 63.6 12.6 137 82-277 97-234 (482)
13 PF04928 PAP_central: Poly(A) 96.2 0.014 3E-07 63.6 7.9 143 743-906 107-253 (254)
14 smart00572 DZF domain in DSRM 95.7 0.053 1.2E-06 58.3 9.5 98 729-829 114-220 (246)
15 KOG1906 DNA polymerase sigma [ 95.4 1.3 2.8E-05 52.9 20.2 229 80-368 101-341 (514)
16 PRK13300 tRNA CCA-pyrophosphor 94.7 2.8 6.1E-05 49.4 20.4 228 568-886 17-255 (447)
17 PF07528 DZF: DZF domain; Int 94.0 1.7 3.7E-05 47.4 15.7 132 217-378 107-240 (248)
18 PF09249 tRNA_NucTransf2: tRNA 93.7 0.6 1.3E-05 44.5 9.9 108 242-374 1-112 (114)
19 KOG2054 Nucleolar RNA-associat 93.6 0.63 1.4E-05 58.3 12.6 168 224-396 805-987 (1121)
20 PTZ00418 Poly(A) polymerase; P 92.3 1.4 2.9E-05 53.4 12.7 169 730-917 238-411 (593)
21 TIGR03671 cca_archaeal CCA-add 91.9 12 0.00026 43.7 19.3 184 568-816 16-209 (408)
22 cd05400 NT_2-5OAS_ClassI-CCAas 91.4 0.85 1.9E-05 44.9 8.4 83 81-182 28-110 (143)
23 cd05402 NT_PAP_TUTase Nucleoti 91.0 1.1 2.5E-05 42.2 8.5 79 81-180 20-98 (114)
24 PF07528 DZF: DZF domain; Int 88.4 2.4 5.2E-05 46.2 9.5 101 729-830 114-223 (248)
25 KOG2245 Poly(A) polymerase and 87.7 3.2 7E-05 48.7 10.3 150 744-918 214-368 (562)
26 PF10421 OAS1_C: 2'-5'-oligoad 85.6 5.7 0.00012 41.5 9.8 124 237-366 41-172 (190)
27 PF10421 OAS1_C: 2'-5'-oligoad 66.8 7 0.00015 40.8 4.2 120 746-887 45-170 (190)
28 COG5186 PAP1 Poly(A) polymeras 57.8 32 0.0007 39.2 7.5 161 731-918 193-360 (552)
29 PF09249 tRNA_NucTransf2: tRNA 57.2 19 0.00041 34.6 4.8 97 749-887 3-105 (114)
30 COG1669 Predicted nucleotidylt 52.6 13 0.00029 34.7 3.0 29 81-110 25-53 (97)
31 cd05397 NT_Pol-beta-like Nucle 43.3 27 0.00059 28.2 3.1 27 79-106 16-42 (49)
32 cd05403 NT_KNTase_like Nucleot 41.5 32 0.00069 30.4 3.7 32 79-111 17-48 (93)
33 KOG0925 mRNA splicing factor A 35.1 2.2E+02 0.0047 34.2 9.7 91 488-597 202-294 (699)
34 PF01909 NTP_transf_2: Nucleot 32.2 30 0.00066 30.8 2.0 31 80-111 14-44 (93)
35 KOG2277 S-M checkpoint control 29.8 3.5E+02 0.0077 33.1 11.3 134 232-369 254-431 (596)
36 PF06755 DUF1219: Protein of u 27.9 42 0.00092 31.9 2.1 75 525-607 20-94 (114)
37 PF09441 Abp2: ARS binding pro 24.9 31 0.00067 34.9 0.7 27 748-784 100-126 (175)
38 COG1746 CCA1 tRNA nucleotidylt 24.4 5.1E+02 0.011 30.7 10.3 226 568-886 21-257 (443)
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=5.1e-206 Score=1895.01 Aligned_cols=805 Identities=41% Similarity=0.642 Sum_probs=723.6
Q ss_pred eeecccccC--CCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhh--ccCCCCCceEeecCCCCCcceeEEEE
Q 002406 88 SYSINCVVK--PAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHL--KSSPSFDKVEWSAMQNEARKPVLVVY 163 (927)
Q Consensus 88 S~~l~t~~k--~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L--~~~~~~~~v~~~~~~~d~~kPil~l~ 163 (927)
||+++|++| ++.+|||+||||++|||+|||||||||+|||+|||+||++| ++.+...+++|+++|||++||||+|+
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 45578899999999999999999999
Q ss_pred eCCCCCC----CCCeEEEEEecCC-CCCcccccccccCCccCCCCC----CCCCCCCCcchhhhhccChHHHHHHHHHHh
Q 002406 164 PAVKSVE----APGFFVRIIPTAA-SLFNIAKLNLKRNNVRAFNQD----GIPRATPKYNSSILEDMFLEDNAEYVEKTI 234 (927)
Q Consensus 164 p~~~~~~----~~~~~iRi~~~~~-~~F~~~rl~P~rnnvR~~~~~----~~~~pTP~YNssil~D~~~~~~l~~l~~~~ 234 (927)
|.++... +.+|+||||||++ ++||++||+|+|||||+.... ..++|||+||++||+||++.+|+++|+++.
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 9876432 4579999999975 999999999999999986432 256999999999999999999999999999
Q ss_pred hChHHHHHHHHHHHHHHHhcCCCccC--CCchhHHHHHHHHHHhhc------cccCcCCcHHHHHHHHHHHHhcCCCCCC
Q 002406 235 SRWKELGEALILLKVWARQRSSIYVH--DCLNGYLISILLSYLVSL------DKINNSMKALQILRVVLDFIATSKLWNR 306 (927)
Q Consensus 235 ~~~~~f~dA~~LlkvWl~QRg~~~~~--~gf~gf~~s~lla~Ll~~------~~l~~~~SsyQifr~~l~fLa~~d~~~~ 306 (927)
++||+|+|||+||||||+|||++.+. ||||||+|+|||+||+++ ++++++||||||||++|+|||++||+++
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 99999999999999999999999988 999999999999999999 9999999999999999999999999999
Q ss_pred ceeecCCCCCCCChhHHHhhhhcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHHhhccCCCccccccccc-cccc
Q 002406 307 GLYFPPKGQIGVSKEEKLQYKEAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGFEETFLTK-IDFP 385 (927)
Q Consensus 307 ~i~~~~~~~~~~~~~~~~~~~~~f~vvf~D~sg~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~~~~d~F~~lFl~~-~~~~ 385 (927)
|++|+..++ +.+...++++.|++||+|++|++|||++||+|+|++||+||+.|+++||+...|+|+++||++ .++.
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 445678899999999999999999999999999999999999999999999999999999999 5778
Q ss_pred ccCcEEEEeecCCcccccccccCCchhhHH-HHHHHHHHHHHHhhccccceEEEEecCCCCcccccCCCccCCCCceEEE
Q 002406 386 AKYDYCVRLNLRGHTEVHALGFCLDDECWR-LYEQKVHSLLNQGLVDRAKSIRVTWRNSPSEWNIENGLAVLDREPLLVG 464 (927)
Q Consensus 386 ~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~lL~raLgdR~~~I~~~~~~~~~~w~i~~~~~~~~~~~l~vG 464 (927)
.+||++++|...............+...+. .+..+|+++|+||||||+++|++. .++.++|++.+.++.....+++||
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 999999999322111111111111222222 467899999999999999999997 777899999988776555589999
Q ss_pred EEecCccccchhcccCCCCCCHHHHHHHHhhhcCcccccccCCCCeEEEEeccCCcccccchHHHHHHHHHHHcCCCCCC
Q 002406 465 ISVSSLEKLFRIVDIGPNAENKEEALRFRKFWGEKAELRRFKDGTIAESTVWESEQWTRHLILKGIIEYVLLRHLSLSKE 544 (927)
Q Consensus 465 l~l~~~~~a~r~vd~GP~ad~~~eA~~FR~FWG~KsELRRFkDGsI~EsVvW~~~~~~r~~I~~~Iv~yiL~~H~~i~~~ 544 (927)
++| ||+||+|+||+||+|||++||++||+|||+||||||||||||+|||||+. .+|+.||+|||+|||++|++++.+
T Consensus 397 l~l-n~~~~~r~vd~GP~a~d~~ea~~FR~FWG~KsELRRFkDGsI~EsVvWs~--~~~~~I~~~Iv~yiL~~H~~~~~~ 473 (972)
T PF03813_consen 397 LIL-NPENAFRLVDRGPSAEDKEEAAAFREFWGEKSELRRFKDGSICESVVWSS--AERRLIPEQIVRYILQRHLKIPSD 473 (972)
T ss_pred EEE-chhhceeeeeeCcCCcCcHHHHHHHHHhCchhhhcccCCCCEEEEEecCC--CCCCchHHHHHHHHHHHhcCCccc
Confidence 999 59999999999999998899999999999999999999999999999955 688999999999999999999999
Q ss_pred cEEEecccchhhhccC----CCCccchHHHHHHHHHHHHHHHhccCCCCeeeeecccCCcccccccCCCCCCCCCccccc
Q 002406 545 NVVQIVDQLDFSLLHG----AKDLVSFSASLLEAFEVLSKRLHLIEDIPLKISSVQPLDSAFRFTSVFPPEPHPLANERH 620 (927)
Q Consensus 545 ~i~~~~~~~d~~l~~~----~~~~~~~~~~v~~af~~L~k~Lr~L~~LPL~I~~V~p~sp~lRytsv~pp~p~~~~~~~~ 620 (927)
+|.+.++++|..+... ......++.++++||++|+|.||+|+||||+|++|+|+||+|||||||||.|+
T Consensus 474 ~i~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~af~~L~k~lr~L~~LPL~I~~v~p~sp~lRyts~~pp~p~------- 546 (972)
T PF03813_consen 474 SISFIGDQFDSLLPLPGSGSSPTDEESFQSVMRAFDELEKDLRSLEDLPLSITSVQPASPALRYTSVFPPVPH------- 546 (972)
T ss_pred eEEeehhhhhhhhcCccccCCCCchHHHHHHHHHHHHHHHHHhcCccCCcceeeeccCCHhhhcCCCCCCCCc-------
Confidence 9999999999876421 22234578899999999999999999999999999999999999999999988
Q ss_pred cccccCCCCCCccCcEEEEEEeccCCCCCCCHHHHHHHHHHHHHHHHHHHhhccC------------CeeeecCCceeee
Q 002406 621 TVSRLHKLTPSCIQPLEVMIQLEGSGNWPMDHVAIEKTKSAFLIKIGESLQNRWG------------MTCSATEDDADIF 688 (927)
Q Consensus 621 ~~~~~~~~~p~~~~pi~vvlqfE~SgkWPddl~AIq~~K~AF~lkIae~L~~~~~------------~~~~v~~d~lDV~ 688 (927)
.++.|++|++||||||+|||||||++|||++|+||+++|+|.|+++++ +.+.++.+++||+
T Consensus 547 -------~~~~~~~p~~vvl~fE~S~kWPddl~AI~~~K~Af~lkiae~L~~~~~~~~~~~v~~~~~~~~~~~~~~ldV~ 619 (972)
T PF03813_consen 547 -------AVPRYIPPIEVVLQFESSGKWPDDLEAIQKTKTAFLLKIAEELEKQYGDGIKARVGLDNSLSPIANQAFLDVL 619 (972)
T ss_pred -------cccCCCCCEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHhhCCcceeeecccccccceeccceEEEE
Confidence 256899999999999999999999999999999999999999997776 4455566679999
Q ss_pred c-cceeEEEEEeccchhHHHhhhc--cc---cccc--c-cchhhhHHHhhhHHHHHHHHHhcCCChhHHHHHHHHHHHhc
Q 002406 689 M-SGYAFRLKILHERGLSLVKSEN--GN---KAKR--V-YSTDKILFIRGQHASMINGLQGRYPVFGPVVRVAKRWAASH 759 (927)
Q Consensus 689 ~-~G~~FRl~I~~~rE~~Ll~~~~--~~---~~~~--~-~~~~~~~~~~p~h~~~i~~l~~r~paf~~tvRLaKRWl~sh 759 (927)
+ +||+||+||+|+||++||+++. .+ +... . ...+++.++.|+||++|++||+|||+|||||||+|||++||
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 9999999999999999999885 22 1111 1 12244556679999999999999999999999999999999
Q ss_pred CCCCCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCCCCCeEEEeCCCCCCHHhHHHHHHHHHHhhhccc
Q 002406 760 LFSACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDWTFSALVVDINNDFGPEDFKVINDNFMSSRKASE 839 (927)
Q Consensus 760 lLs~hi~eE~vELLva~vfl~p~p~~~P~S~~~GFlRfL~lLa~~DW~~~PLiVd~~~~lt~~~~~~i~~~F~~~R~~~~ 839 (927)
||++||+||+||||||++|++|+||.+|+|+++||+|||+|||+|||+++|||||+|++|+++++++|+++|.++|+
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 ccccCCCCeEEEEeCCCCCCCccccCCCCHHHHHHHHHHHHHHHHHHHHHhhccCCCcccccccccccCCCCCccccccc
Q 002406 840 ENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRLVAYARSSANLLTKLILEDQTDSCRWEGQVTLPTSPSFPVRSKQR 919 (927)
Q Consensus 840 ~dp~~~~p~~fIaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~s~~~l~~~~~~~~~~~~~~~~lF~~pl~~~~~~~~~~~ 919 (927)
+||++++|+|||||++|++|..||+.+|+++|++||++|||+|+++|+... ....+|+++|+||+++|+++-+-..
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 2367999999999999987655444
Q ss_pred c
Q 002406 920 E 920 (927)
Q Consensus 920 ~ 920 (927)
.
T Consensus 853 ~ 853 (972)
T PF03813_consen 853 K 853 (972)
T ss_pred c
Confidence 3
No 2
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=100.00 E-value=1.2e-189 Score=1640.88 Aligned_cols=880 Identities=37% Similarity=0.568 Sum_probs=773.6
Q ss_pred cCcccccHHHHhccccCCCCccchhHHHHHHHHHHHHHhcCCCCCCCCcccCCccccccCCceeEEEEeCCceee-Eeee
Q 002406 10 TDPMDYKVEELLKEVHFARAPAITKLVDDTVSAVRKSISKIPDAFPVTADLAPGFVRDIGADKVEFKFNKPKTFK-IGGS 88 (927)
Q Consensus 10 ~~~f~LQidELL~ev~~~~~~~~~~~~e~~L~~lk~~i~~ip~~~~~~~~~~~~~~~~~~~~~~~f~f~~P~~v~-vvGS 88 (927)
++.||||++|+++|++++.++ ...+|.||+...+.+.+..+.--.+.-+-..+ ++. .-.-+|.|.||.+|. ||||
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--KDRIEAFLESPNKRLVELKDQLNLPYAVKVPL-KDC-PYAVKFRFLPPAQVTKVVGS 156 (1121)
T ss_pred cchhhcchhhhhhhhcccccc--ccHHHHHHHHHHHHHHHhhhhhcccccccccc-ccc-cccccccccCccccceeeee
Confidence 468999999999999999888 55699999999999984333211111000111 111 112238899999999 8888
Q ss_pred eecccccCCCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhhccCCCCCceEeecCCCCCcceeEEEEeCCCC
Q 002406 89 YSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLVVYPAVKS 168 (927)
Q Consensus 89 ~~l~t~~k~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~~~~~~v~~~~~~~d~~kPil~l~p~~~~ 168 (927)
+..+++.+|+..||++|+||++.|+.|||||.|||+|||.||+|+++||.....+.+++|.|.|||++||||.|+|.+++
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 88999999999999999999999999999999999999999999999999888889999999999999999999999876
Q ss_pred CCC--CCeEEEEEecCCCCCcccccccccCCccCCCCCCCCCCCCCcchhhhhccChHHHHHHHHHHhhChHHHHHHHHH
Q 002406 169 VEA--PGFFVRIIPTAASLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKELGEALIL 246 (927)
Q Consensus 169 ~~~--~~~~iRi~~~~~~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssil~D~~~~~~l~~l~~~~~~~~~f~dA~~L 246 (927)
... .++..-+|||.--.|+.+||+|.+||+|+.++.+++||||.||+++|+|++.++|+++|.++.+..++|+|||.|
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 542 235556777766789999999999999999887889999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCccCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCCChhHHHhh
Q 002406 247 LKVWARQRSSIYVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGVSKEEKLQY 326 (927)
Q Consensus 247 lkvWl~QRg~~~~~~gf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~~~~~~~~~ 326 (927)
||+|+|||.++.+.||||||+|+|+|+||+.+++|+.+||+||+||.+|+|||++||+.+||.++.+. .+.+...+|
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 99999999988889999999999999999999999999999999999999999999999999887653 345677889
Q ss_pred hhcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHHhhccCCCcccccccccccccccCcEEEEeecCCcc---ccc
Q 002406 327 KEAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGFEETFLTKIDFPAKYDYCVRLNLRGHT---EVH 403 (927)
Q Consensus 327 ~~~f~vvf~D~sg~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~~~~d~F~~lFl~~~~~~~~fD~~~~i~~~~~~---~~~ 403 (927)
++++.++|+|.+|.+|||++||.++|+++|+||+.|+.|||+...|+|+.+||+++|.+..||+++++...... ...
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 99999999999999999999999999999999999999999999999999999999999999999999643211 122
Q ss_pred ccccCCc---hhhHHHHHHHHHHHHHHhhccccceEEEEecCCCCcccccCCCccCCCCceEEEEEecCccccchhcccC
Q 002406 404 ALGFCLD---DECWRLYEQKVHSLLNQGLVDRAKSIRVTWRNSPSEWNIENGLAVLDREPLLVGISVSSLEKLFRIVDIG 480 (927)
Q Consensus 404 ~~~~~~~---~~~~~~~~~~i~~lL~raLgdR~~~I~~~~~~~~~~w~i~~~~~~~~~~~l~vGl~l~~~~~a~r~vd~G 480 (927)
...+|.. ...|..+...+..+|++|||||++.|.+. ....++|++++.+++..++.+.+|+++ +|+.+.|+||+|
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-RPIVPEWSISEDPPKHGDKTITLGLLL-SPEGLYRVLTIG 551 (1121)
T ss_pred cccchhhhhcccHHHHHHHHHHHHHHHHHHHHHhhhhhc-cCCccccccccCcccccCceEEEEEEe-chHHhcchhhcC
Confidence 2233432 22456777888899999999999999986 667899999998887666899999999 599999999999
Q ss_pred CCCCCHHHHHHHHhhhcCcccccccCCCCeEEEEeccCCc-ccccchHHHHHHHHHHHcCCCCCCcEEEecccchhhhcc
Q 002406 481 PNAENKEEALRFRKFWGEKAELRRFKDGTIAESTVWESEQ-WTRHLILKGIIEYVLLRHLSLSKENVVQIVDQLDFSLLH 559 (927)
Q Consensus 481 P~ad~~~eA~~FR~FWG~KsELRRFkDGsI~EsVvW~~~~-~~r~~I~~~Iv~yiL~~H~~i~~~~i~~~~~~~d~~l~~ 559 (927)
|+|||.+||++||+|||+||||||||||+|+|||||++.+ .+||.|++|||+|||++|++++..++.++++++|..+..
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 568999999999999999999999999999999976543
Q ss_pred CCCCc----cchHHHHHHHHHHHHHHHhccCCCCeeeeecccCCcccccccCCCCCCCCCccccccccccCCCCCCccCc
Q 002406 560 GAKDL----VSFSASLLEAFEVLSKRLHLIEDIPLKISSVQPLDSAFRFTSVFPPEPHPLANERHTVSRLHKLTPSCIQP 635 (927)
Q Consensus 560 ~~~~~----~~~~~~v~~af~~L~k~Lr~L~~LPL~I~~V~p~sp~lRytsv~pp~p~~~~~~~~~~~~~~~~~p~~~~p 635 (927)
....+ ..-+ +|++|||+|+|.|++|+||||+|++|+|+||+|||||||||.| ..+....... .+-+++
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 22111 1123 8999999999999999999999999999999999999999976 2221111000 111222
Q ss_pred EEEEEEeccCCCCCCCHHHHHHHHHHHHHHHHHH-HhhccCCeeeecCCceeeeccceeEEEEEeccchhHHHhhh----
Q 002406 636 LEVMIQLEGSGNWPMDHVAIEKTKSAFLIKIGES-LQNRWGMTCSATEDDADIFMSGYAFRLKILHERGLSLVKSE---- 710 (927)
Q Consensus 636 i~vvlqfE~SgkWPddl~AIq~~K~AF~lkIae~-L~~~~~~~~~v~~d~lDV~~~G~~FRl~I~~~rE~~Ll~~~---- 710 (927)
|+||||||+|||||||++||||+|+||++||||+ |++++|+.|+++.|++||+.+||+||+||.|+||..++++.
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 99999999999999999999999999999999999999876
Q ss_pred cccccc---cccchhhhHHHhhhHHHHHHHHHhcCCChhHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHhhcCCCCCCCC
Q 002406 711 NGNKAK---RVYSTDKILFIRGQHASMINGLQGRYPVFGPVVRVAKRWAASHLFSACLVEEAVELLVAYLFLKPLPFNVP 787 (927)
Q Consensus 711 ~~~~~~---~~~~~~~~~~~~p~h~~~i~~l~~r~paf~~tvRLaKRWl~shlLs~hi~eE~vELLva~vfl~p~p~~~P 787 (927)
+..+.. .....++..++.|+|+++||++||+||+||+||||||||+++|+|++|+.||++|||||++|++|.||.+|
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 222322 23345667778899999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhhHHHHHHHHHhcCCCCCCeEEEeCCCCCCHHhHHHHHHHHHHhhhcccccccCCCCeEEEEeCCCCCCCccccCCC
Q 002406 788 CSRVTGFLRFLRLLAEYDWTFSALVVDINNDFGPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSP 867 (927)
Q Consensus 788 ~S~~~GFlRfL~lLa~~DW~~~PLiVd~~~~lt~~~~~~i~~~F~~~R~~~~~dp~~~~p~~fIaT~~D~~g~~wT~~~P 867 (927)
+|+++||+|||+|||+|||+.+|||||+|++++++|+.+++++|.+.|+. .|+|+|+|+||+.|..||+.+|
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 SSPENGFLRFLSLLSTWDWKFDPLIVDFNNGFPEDERSELEEKFISARKQ--------LPPMVVITPYDHLGSKFTRTSP 935 (1121)
T ss_pred CCcchhHHHHHHHHhcCcccCCceEEEcCCCCcHHHHHHHHHHHhhhccc--------CCceEEeeccccccccccccCc
Confidence 99999999999999999999999999999999999999999999999994 5899999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhccCCCcccccccccccCCCCCcc
Q 002406 868 NFTELKRLVAYARSSANLLTKLILEDQTDSCRWEGQVTLPTSPSFPV 914 (927)
Q Consensus 868 s~~v~~Rl~~LAk~s~~~l~~~~~~~~~~~~~~~~lF~~pl~~~~~~ 914 (927)
+..|+.|++++|++|+++++..+.++-...+.+.++|+.+|+.|+.+
T Consensus 936 ~~~v~~r~~alar~sl~ll~k~~p~~~~t~~~~~~lf~~~L~~yd~v 982 (1121)
T KOG2054|consen 936 NQIVLNRLVALARESLKLLEKQAPGEIKTIVRPTSLFRENLSPYDAV 982 (1121)
T ss_pred hHHHHHHHHHhhhhhHHhhcccccccchhhhhhhhhhhcccccccch
Confidence 99999999999999999999887655445677899999999988765
No 3
>PTZ00418 Poly(A) polymerase; Provisional
Probab=99.70 E-value=1.9e-15 Score=176.32 Aligned_cols=369 Identities=12% Similarity=0.196 Sum_probs=239.5
Q ss_pred ceeeEeeeeecccccCCCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhhccCCCCCceEeecCCCCCcceeE
Q 002406 81 KTFKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVL 160 (927)
Q Consensus 81 ~~v~vvGS~~l~t~~k~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~~~~~~v~~~~~~~d~~kPil 160 (927)
..|-.+|||.||. ..|+..||.++..|+.+ .|.-|...+...|++.+.+.++. --.|+..|+|
T Consensus 127 g~I~tfGSYrLGV-~~pgSDID~L~V~P~~v-------------tredFF~~f~~~L~~~~~V~eL~---~V~~A~VPiI 189 (593)
T PTZ00418 127 GKLFTFGSYRLGV-VAPGSDIDTLCLAPRHI-------------TRESFFSDFYAKLQQDPNITKLQ---PVPDAYTPVI 189 (593)
T ss_pred eEEEEeccccccC-CCCCCcccEEEECCCCC-------------CHHHHHHHHHHHHhcCCCcceee---ccCccccCeE
Confidence 3466899999996 66789999999999876 45556678888888765444444 4578999999
Q ss_pred EEEeCCCCCCCCCeEEEEEec--CCCCCcccccccccC-CccCCCCCCCCCCCCCcchhhhhccChHHHHHHHHHHhhCh
Q 002406 161 VVYPAVKSVEAPGFFVRIIPT--AASLFNIAKLNLKRN-NVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRW 237 (927)
Q Consensus 161 ~l~p~~~~~~~~~~~iRi~~~--~~~~F~~~rl~P~rn-nvR~~~~~~~~~pTP~YNssil~D~~~~~~l~~l~~~~~~~ 237 (927)
.+... ++.|.|..| +...-|.+-=.++.+ -+|...+ ..----|.. .-..++-+...+.
T Consensus 190 k~~~~-------GI~iDL~fa~l~~~~vp~~~~~l~d~~lL~nlde----~s~rSLNG~--------Rvtd~Il~lVPn~ 250 (593)
T PTZ00418 190 KFVYD-------GIDIDLLFANLPLPTIPDCLNSLDDDYILRNVDE----KTVRSLNGC--------RVADLILASVPNK 250 (593)
T ss_pred EEEEC-------CEEEeeeecccCCCCCCccccccCchhhhhcCCH----HHhhhhccH--------HHHHHHHHHCCCh
Confidence 99875 488888887 223333221112221 2332111 000011111 2245556667778
Q ss_pred HHHHHHHHHHHHHHHhcCCCccC-CCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCC-
Q 002406 238 KELGEALILLKVWARQRSSIYVH-DCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQ- 315 (927)
Q Consensus 238 ~~f~dA~~LlkvWl~QRg~~~~~-~gf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~- 315 (927)
.+|+-|++.+|.||++||++++. |.+||..||||+|++|| +.+.+++-+|+..++...++++|- +||.++...+
T Consensus 251 ~~Fr~aLR~IKlWAkrRGIYsNv~GflGGV~wAILvARVCQ---LyPna~~s~Lv~~FF~iys~W~Wp-~PV~L~~i~~~ 326 (593)
T PTZ00418 251 DYFRTTLRFIKLWAKRRGIYSNVLGYLGGVSWAILTARICQ---LYPNFAPSQLIHKFFRVYSIWNWK-NPVLLCKIKEV 326 (593)
T ss_pred HHHHHHHHHHHHHHHHhccccccccccchHHHHHHHHHHHH---hCCCCCHHHHHHHHHHHhhcCCCC-CCeEccccccc
Confidence 99999999999999999988774 55799999999999998 999999999999999999999995 6988875432
Q ss_pred ----CCCC----hh--HHHhhhhcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHHhhc--c-CCCcccccccccc
Q 002406 316 ----IGVS----KE--EKLQYKEAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDK--C-GDGGFEETFLTKI 382 (927)
Q Consensus 316 ----~~~~----~~--~~~~~~~~f~vvf~D~sg~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~--~-~~d~F~~lFl~~~ 382 (927)
+... +| +..+-.+.+||+ .-..-.+|-++++|.++.+.|+.|-+++.+++++ . +...+..|| .+.
T Consensus 327 ~~~~g~~~~~VWdPr~~~~dr~h~MPII-TPayP~mNst~nVt~sT~~vI~~Ef~Ra~~i~~~i~~~~~~~W~~Lf-ep~ 404 (593)
T PTZ00418 327 PNIPGLMNFKVWDPRVNPQDRAHLMPII-TPAFPSMNSTHNVTYTTKRVITEEFKRAHEIIKYIEKNSENTWTNVL-EPL 404 (593)
T ss_pred ccCCcccCCcccCCCCCcccccccCCee-cCCCCCccccccccHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHc-CCc
Confidence 1110 01 122334556664 6777899999999999999999999999999986 2 456899999 688
Q ss_pred cccccCcEEEEeecCCcccccccccCCchhhHHHH-HHHHHHHHHHhhccccceEEEEecCCCCcccccCCCcc-CCCCc
Q 002406 383 DFPAKYDYCVRLNLRGHTEVHALGFCLDDECWRLY-EQKVHSLLNQGLVDRAKSIRVTWRNSPSEWNIENGLAV-LDREP 460 (927)
Q Consensus 383 ~~~~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~i~~lL~raLgdR~~~I~~~~~~~~~~w~i~~~~~~-~~~~~ 460 (927)
+|..+|-+++.|.+.+... .+...|..+ +.++.. |...|- |...|.+. +-+ ... ...... .-.+.
T Consensus 405 ~Ff~~Yk~yl~V~v~a~~~-------~~~~~w~G~VESRlR~-Lv~~LE-~~~~i~~~-p~P-~~f--~~~~~~~~~~~~ 471 (593)
T PTZ00418 405 DFFTSYKHFLVIQVYATNE-------HVHNKWEGWIESKIRF-LIKKLE-TLNNLKIR-PYP-KFF--KYQDDGWDYASS 471 (593)
T ss_pred chhhhcceEEEEEEEECCH-------HHhhhhhhHHHHHHHH-HHHHhh-ccCCceEe-ecC-ccc--ccCCCCceeEEE
Confidence 8999999999998643211 112335443 455554 666664 45555442 111 111 110000 11245
Q ss_pred eEEEEEecCccccchhcccCCCCCCHHHHHHHHhhhcCcccccccCCCC
Q 002406 461 LLVGISVSSLEKLFRIVDIGPNAENKEEALRFRKFWGEKAELRRFKDGT 509 (927)
Q Consensus 461 l~vGl~l~~~~~a~r~vd~GP~ad~~~eA~~FR~FWG~KsELRRFkDGs 509 (927)
+.|||.+. ..+.. .+-.-|=.....+|.+.=..-.+-..++|+.
T Consensus 472 ffIGL~~~-~~~~~----~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~ 515 (593)
T PTZ00418 472 FFIGLVFF-SKNVY----NNSTFDLRYAIRDFVDIINNWPEMEKYPDQI 515 (593)
T ss_pred EEEeEeec-cCCCC----CCceEecHHHHHHHHHHHHhhhhcccCCCCc
Confidence 99999994 32211 1112232334567775432222222455654
No 4
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=99.64 E-value=2.5e-15 Score=161.89 Aligned_cols=272 Identities=14% Similarity=0.203 Sum_probs=210.4
Q ss_pred eeEeeeeecccccCCCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhhccCCCCCceEeecCCCCCcceeEEE
Q 002406 83 FKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLVV 162 (927)
Q Consensus 83 v~vvGS~~l~t~~k~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~~~~~~v~~~~~~~d~~kPil~l 162 (927)
|-..|||.||. .+|+..||-.|.+|++. -|.-|..++...|+..+...++. --.|+..|||.+
T Consensus 84 IFTyGSYRLGV-hgpGsDIDtLvvVPkHV-------------sR~dFFt~f~~~Lrer~ei~eva---~vpDAfVPIIK~ 146 (552)
T COG5186 84 IFTYGSYRLGV-HGPGSDIDTLVVVPKHV-------------SRSDFFTHFYEELRERPEIEEVA---KVPDAFVPIIKL 146 (552)
T ss_pred eeeecceeeec-cCCCCCcceEEEecccc-------------cHHHHHHHHHHHhccCcchhhhc---cCCcccceeEEE
Confidence 44679999985 67788999999999976 67777889999998875444433 558999999999
Q ss_pred EeCCCCCCCCCeEEEEEec-CC-CCCcccccccccCCccCCCCCCCCCCCCCcchhhhhccChHHHHHHHHHHhhChHHH
Q 002406 163 YPAVKSVEAPGFFVRIIPT-AA-SLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKEL 240 (927)
Q Consensus 163 ~p~~~~~~~~~~~iRi~~~-~~-~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssil~D~~~~~~l~~l~~~~~~~~~f 240 (927)
+..| ..|.++.+ .. ..-|..--+-++|-+|.-.+.. -=--|.+-..| +.+++ ..+...|
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 77888876 22 3444444455666666533211 11235555554 44444 4566799
Q ss_pred HHHHHHHHHHHHhcCCCccCCCc-hhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCCC
Q 002406 241 GEALILLKVWARQRSSIYVHDCL-NGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGVS 319 (927)
Q Consensus 241 ~dA~~LlkvWl~QRg~~~~~~gf-~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~~ 319 (927)
+-|++-+|.|+++|..+.+.-|| ||..|+|++|.+|| |.+..+|.-|+-.++..|++++| .+|+.+.+.+|+++.
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 99999999999999988776665 99999999999999 99999999999999999999998 579999887765543
Q ss_pred h------hHHHhhhhcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHHhhccCCC--cccccccccccccccCcEE
Q 002406 320 K------EEKLQYKEAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDKCGDG--GFEETFLTKIDFPAKYDYC 391 (927)
Q Consensus 320 ~------~~~~~~~~~f~vvf~D~sg~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~~~~d--~F~~lFl~~~~~~~~fD~~ 391 (927)
. -+.++-.+..||+ ..+...+.-..++|.++-..+-+|--++.++++|.-.+ .|..+| .+.+|..||-++
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 2444444557774 66677778888899999999999999999999997655 899999 889999999999
Q ss_pred EEeec
Q 002406 392 VRLNL 396 (927)
Q Consensus 392 ~~i~~ 396 (927)
+.|..
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=99.61 E-value=2.6e-14 Score=160.52 Aligned_cols=308 Identities=14% Similarity=0.206 Sum_probs=219.3
Q ss_pred eeEeeeeecccccCCCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhhccCCCCCceEeecCCCCCcceeEEE
Q 002406 83 FKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLVV 162 (927)
Q Consensus 83 v~vvGS~~l~t~~k~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~~~~~~v~~~~~~~d~~kPil~l 162 (927)
|-..|||.||. ..++..||-.+.-|+.. -|+-|...+-..|++.+.+.++. --.|+..||+.+
T Consensus 92 IftfGSYRLGV-hg~GADIDtLcV~Prhv-------------~R~DFF~sf~~mL~~~~eVteL~---~V~dAfVPiikf 154 (562)
T KOG2245|consen 92 IFTFGSYRLGV-HGPGADIDTLCVGPRHV-------------SRSDFFTSFYDMLKERPEVTELH---AVEDAFVPIIKF 154 (562)
T ss_pred EEeccceeecc-cCCCCCcceeeeccccc-------------cHHHHHHHHHHHHhcCccccccc---cccccccceEEE
Confidence 44679999985 66788999999999865 67777789999999876555444 558999999999
Q ss_pred EeCCCCCCCCCeEEEEEec-CC-CCCcccccccccCCccCCCCCCCCCCCCCcchhhhhccChHHHHHHHHHHhhChHHH
Q 002406 163 YPAVKSVEAPGFFVRIIPT-AA-SLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKEL 240 (927)
Q Consensus 163 ~p~~~~~~~~~~~iRi~~~-~~-~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssil~D~~~~~~l~~l~~~~~~~~~f 240 (927)
+-. |+.|.|+.+ -+ -..|.+-=.-+.|-+|..++ ..----|..-..| +.|++ .-+-.+|
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 875 478888876 12 22222111112222222111 0001123333333 33333 4566799
Q ss_pred HHHHHHHHHHHHhcCCCccCCCc-hhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCCC
Q 002406 241 GEALILLKVWARQRSSIYVHDCL-NGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGVS 319 (927)
Q Consensus 241 ~dA~~LlkvWl~QRg~~~~~~gf-~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~~ 319 (927)
+-+++-+|.||+.||.+++.-|| ||..||||+|..|| |.+..++--|+..++--++++.| .+||.++..+++++.
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 99999999999999998887665 99999999999999 99999999999999999999998 579999877655443
Q ss_pred hh------HHHhhhhcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHHhhccCC--CcccccccccccccccCcEE
Q 002406 320 KE------EKLQYKEAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDKCGD--GGFEETFLTKIDFPAKYDYC 391 (927)
Q Consensus 320 ~~------~~~~~~~~f~vvf~D~sg~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~~~~--d~F~~lFl~~~~~~~~fD~~ 391 (927)
.+ +..+--+..|++ .-+-...|-.+++|.++..-++.|-+.++++.++... -.|..|| .+.+|..+|-++
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 32 112222346775 6777799999999999999999999999999998644 4889999 888999999999
Q ss_pred EEeecCCcccccccccCCchhhHHHHH-HHHHHHHHHhhccccceEEEEec
Q 002406 392 VRLNLRGHTEVHALGFCLDDECWRLYE-QKVHSLLNQGLVDRAKSIRVTWR 441 (927)
Q Consensus 392 ~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~i~~lL~raLgdR~~~I~~~~~ 441 (927)
+.|.+...... +...|..+. +++. +|..-|. |...|.+..+
T Consensus 370 l~i~~~A~~~e-------d~l~w~G~vESriR-~Lv~klE-~~~~i~~ahp 411 (562)
T KOG2245|consen 370 LQITASAATEE-------DLLKWVGWVESRIR-QLVLKLE-RNQVILIAHP 411 (562)
T ss_pred heeeeeccChH-------HHhhhhhHHHHHHH-HHHHHHH-hhcceEEecC
Confidence 99986543111 224465444 4444 3333343 4666666534
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=99.23 E-value=8.4e-11 Score=126.69 Aligned_cols=147 Identities=13% Similarity=0.261 Sum_probs=103.3
Q ss_pred HHHHHHHhhChHHHHHHHHHHHHHHHhcCCCccC-CCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCC
Q 002406 227 AEYVEKTISRWKELGEALILLKVWARQRSSIYVH-DCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWN 305 (927)
Q Consensus 227 l~~l~~~~~~~~~f~dA~~LlkvWl~QRg~~~~~-~gf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~ 305 (927)
..++.+...+...|+.|++.+|.|+++||++++. |-+||..|++|+|+.|| +.+..++-+|+..++.+.|++||.
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 4556666777799999999999999999988764 55799999999999999 889999999999999999999995
Q ss_pred CceeecCCCCCCC------ChhHHHhhhhcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHHhhcc--CCCccccc
Q 002406 306 RGLYFPPKGQIGV------SKEEKLQYKEAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDKC--GDGGFEET 377 (927)
Q Consensus 306 ~~i~~~~~~~~~~------~~~~~~~~~~~f~vvf~D~sg~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~~--~~d~F~~l 377 (927)
+||.+....+... +..+..+-++.+||+ .-..-.+|.++++|.++++.|+.|-+++.+++++. +...++.|
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 6988865432221 111334556667774 45557999999999999999999999999999874 45667777
Q ss_pred c
Q 002406 378 F 378 (927)
Q Consensus 378 F 378 (927)
|
T Consensus 251 ~ 251 (254)
T PF04928_consen 251 F 251 (254)
T ss_dssp T
T ss_pred c
Confidence 7
No 7
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=98.93 E-value=1e-06 Score=100.50 Aligned_cols=255 Identities=17% Similarity=0.232 Sum_probs=168.4
Q ss_pred HHHHhccccCCCCccchhHHHHHHHHHHHHHhcCCCCCCCCcccCCccccccCCceeEEEEeCCceeeEeeeeecccccC
Q 002406 17 VEELLKEVHFARAPAITKLVDDTVSAVRKSISKIPDAFPVTADLAPGFVRDIGADKVEFKFNKPKTFKIGGSYSINCVVK 96 (927)
Q Consensus 17 idELL~ev~~~~~~~~~~~~e~~L~~lk~~i~~ip~~~~~~~~~~~~~~~~~~~~~~~f~f~~P~~v~vvGS~~l~t~~k 96 (927)
++|.|+.|+|+... .+.+.+..+.|.+.|.+.-.. . -....|.++||++=||..+
T Consensus 2 ~~~vl~~i~Ps~eE--~~~~~~~~~~l~~~l~~~~~e-------------------~----~~~~~v~~~GS~ArgT~L~ 56 (408)
T TIGR03671 2 LEEVLERIKPTEEE--REKLKKVADELIARLEEIIEE-------------------L----GVDAEVVLVGSYARGTWLK 56 (408)
T ss_pred hHHHhhhcCCCHHH--HHHHHHHHHHHHHHHHHHHHh-------------------c----CCcceEEEEeeEecCCccC
Confidence 47899999999766 556777777766665533111 0 1113688999999999999
Q ss_pred CCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhhccCCCCCceEeecCCCCCcceeEEEEeCCCCCCCCCeEE
Q 002406 97 PAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLVVYPAVKSVEAPGFFV 176 (927)
Q Consensus 97 ~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~~~~~~v~~~~~~~d~~kPil~l~p~~~~~~~~~~~i 176 (927)
++..|||.|-.|.+.=. ..+.+... .|+..+.+........|. -.|.+.+.-. ++.|
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 88999999999876532 22333333 344444332222233332 4566666543 5999
Q ss_pred EEEecCCCCCcccccccccCCccCCCCCCCCCCCCCcchhhhhccChHHHHHHHHHHhhChHHHHHHHHHHHHHHHhcCC
Q 002406 177 RIIPTAASLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKELGEALILLKVWARQRSS 256 (927)
Q Consensus 177 Ri~~~~~~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssil~D~~~~~~l~~l~~~~~~~~~f~dA~~LlkvWl~QRg~ 256 (927)
.|.||.. .- +-.-+++ +. =.|| -|.+++.+-.+. .++|=++|+|-|++.-|.
T Consensus 114 DiVPcy~-v~-------~g~~~~t----aV-DRtp-------------~H~~fv~~rl~~--~~~d~VRLlK~f~k~igv 165 (408)
T TIGR03671 114 DVVPCYK-VE-------SGEEIIS----AV-DRTP-------------FHTRYVLERLDG--KLRDDVRLLKQFLKGIGV 165 (408)
T ss_pred EEEeeEE-cc-------CcCeeec----cc-cCch-------------HHHHHHHHhhhh--hHHHHHHHHHHHHHhCCc
Confidence 9999843 00 0000111 00 1266 577777766654 499999999999999986
Q ss_pred C---ccCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCCChhHHHhhhhcCCEE
Q 002406 257 I---YVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGVSKEEKLQYKEAFPVV 333 (927)
Q Consensus 257 ~---~~~~gf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~~~~~~~~~~~~f~vv 333 (927)
+ ....||+||+.=+|++| |.-|..++.-.+++ +.++.+...+... ..| .-|+|
T Consensus 166 YGsE~~~~GFSGYl~ELLv~~-------------yG~F~~~l~~a~~w---k~~~~id~~~~~~------~~f--~~Plv 221 (408)
T TIGR03671 166 YGSELKTRGFSGYLCELLVIH-------------YGSFENVLKAASKW---KPGVVIDIEEHGT------KKF--DDPLV 221 (408)
T ss_pred cchhhccCCccHHHHHHHHHH-------------hCCHHHHHHHHHhc---CCCeEEecCcccc------ccC--CCCEE
Confidence 4 34789999999999998 56688888888754 3466653221100 122 34888
Q ss_pred EeCCCC-ceeeccCCCHHHHHHHHHHHHHHHHHhhccCCCcc
Q 002406 334 ICDPSA-QVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGF 374 (927)
Q Consensus 334 f~D~sg-~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~~~~d~F 374 (927)
++||.- .-|+++.+|...+.++.+.|+..+ .+++.+=|
T Consensus 222 ViDPvDp~RNVAaalS~~~~~~fv~aar~fl---~~Ps~~fF 260 (408)
T TIGR03671 222 VIDPVDPKRNVAAALSLENLARFILAARMFL---KNPSLEFF 260 (408)
T ss_pred EeCCCCCcchHHHHcCHHHHHHHHHHHHHHH---HCCCHHHc
Confidence 899954 899999999999999999998876 44444545
No 8
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=98.91 E-value=1.3e-06 Score=101.02 Aligned_cols=360 Identities=17% Similarity=0.224 Sum_probs=212.3
Q ss_pred HHHHhccccCCCCccchhHHHHHHHHHHHHHhcCCCCCCCCcccCCccccccCCceeEEEEeCCceeeEeeeeecccccC
Q 002406 17 VEELLKEVHFARAPAITKLVDDTVSAVRKSISKIPDAFPVTADLAPGFVRDIGADKVEFKFNKPKTFKIGGSYSINCVVK 96 (927)
Q Consensus 17 idELL~ev~~~~~~~~~~~~e~~L~~lk~~i~~ip~~~~~~~~~~~~~~~~~~~~~~~f~f~~P~~v~vvGS~~l~t~~k 96 (927)
++|.|+.|+|+... .+.+.+..+.|.+.|.+.=.. .+ . + ..|.++|||+=+|..+
T Consensus 3 ~~evl~~i~Ps~eE--~~~l~~~~~~l~~~L~~~~~~--------------~~---~-----~-~~V~l~GS~ArgT~L~ 57 (447)
T PRK13300 3 LEEVLERIKPTEEE--REKLKKVAEELIERLEEAIKE--------------LG---L-----D-AEVELVGSTARGTWLS 57 (447)
T ss_pred HHHHHHhcCCCHHH--HHHHHHHHHHHHHHHHHHHHh--------------cC---C-----c-eEEEEEeeecCCcccC
Confidence 57899999999665 456666666666665543111 00 0 1 4678999999999999
Q ss_pred CCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhhccC-CCCCceEeecCCCCCcceeEEEEeCCCCCCCCCeE
Q 002406 97 PAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSS-PSFDKVEWSAMQNEARKPVLVVYPAVKSVEAPGFF 175 (927)
Q Consensus 97 ~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~-~~~~~v~~~~~~~d~~kPil~l~p~~~~~~~~~~~ 175 (927)
++..|||.|-.|.+.=.+ .+.+...++ +..+.+. .....++| +-.|.+.+.-. ++.
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 999999999998765222 334444444 3333222 12234555 24576666553 599
Q ss_pred EEEEecCCCCCcccccccccCCccCCCCCCCCCCCCCcchhhhhccChHHHHHHHHHHhhChHHHHHHHHHHHHHHHhcC
Q 002406 176 VRIIPTAASLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKELGEALILLKVWARQRS 255 (927)
Q Consensus 176 iRi~~~~~~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssil~D~~~~~~l~~l~~~~~~~~~f~dA~~LlkvWl~QRg 255 (927)
|.|.||.. . . +-.-+++ +. =-|| -|.+++.+-.+. .++|=++|+|-|++.-|
T Consensus 115 VDiVPcy~-v------~-~~~~~~s----aV-DRtp-------------~H~~fv~~rl~~--~~~d~VRLlK~f~k~~g 166 (447)
T PRK13300 115 VDIVPCYK-V------E-SGEEIIS----AV-DRTP-------------FHTKYVKERLKG--KLEDEVRLLKQFLKGIG 166 (447)
T ss_pred EEEEeeEE-c------c-CcCcccc----cc-cCch-------------HHHHHHHHhhhh--hHHHHHHHHHHHHHhCC
Confidence 99999841 0 0 0001111 00 1276 577777766654 49999999999999998
Q ss_pred CC---ccCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCCChhHHHhhhhcCCE
Q 002406 256 SI---YVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGVSKEEKLQYKEAFPV 332 (927)
Q Consensus 256 ~~---~~~~gf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~~~~~~~~~~~~f~v 332 (927)
.+ ...+||+||+.=+|++| |.-|.++++-.+++.. +..+...+.... ..| .-|+
T Consensus 167 vYGsE~k~~GFSGYl~ELLv~~-------------yG~F~~~l~~a~~w~~---~~~I~~~~~~~~-----~~f--~~Pl 223 (447)
T PRK13300 167 VYGSELKTRGFSGYLCELLIIH-------------YGSFENVLKAASKWKP---PVKIDLEKHGKE-----YKF--DDPL 223 (447)
T ss_pred ccchhhccCCccHHHHHHHHHH-------------hCCHHHHHHHHHhCCC---CceEeccccCcc-----ccC--CCCE
Confidence 65 34789999999999998 6678999988887643 333222211100 011 3488
Q ss_pred EEeCCCC-ceeeccCCCHHHHHHHHHHHHHHHHHhhccCCCccccccccccccc----ccCcEEEEeecCCccccccccc
Q 002406 333 VICDPSA-QVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGFEETFLTKIDFP----AKYDYCVRLNLRGHTEVHALGF 407 (927)
Q Consensus 333 vf~D~sg-~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~~~~d~F~~lFl~~~~~~----~~fD~~~~i~~~~~~~~~~~~~ 407 (927)
|++||.- .-|+++.+|...+.++.+.|+.= |.+++.+=|.+-=+.+.... .|-..++.+..+.. .
T Consensus 224 vViDPvDp~RNVAaa~S~~~~~~fv~aar~f---L~~Ps~~fF~~~~~~~~~~~~~l~~R~t~~~~v~f~~p------~- 293 (447)
T PRK13300 224 VVIDPVDPNRNVAAALSLENLATFILAAREF---LKNPSLEFFFPSDLSPEEILEELERRGTTVLALEFPRP------D- 293 (447)
T ss_pred EEeCCCCCcchHHHHcCHHHHHHHHHHHHHH---HhCCCHHhcCCCCCChHHHHHHHhhcCceEEEEEeCCC------C-
Confidence 8899954 89999999999999999998764 66665555522222222221 22234444432210 0
Q ss_pred CCchhhHHHHHHHHHHHHHHhhccccceEEEEecCCCCcccccCCCccCCCCceEEEEEecCccccchhcccCCCCCCHH
Q 002406 408 CLDDECWRLYEQKVHSLLNQGLVDRAKSIRVTWRNSPSEWNIENGLAVLDREPLLVGISVSSLEKLFRIVDIGPNAENKE 487 (927)
Q Consensus 408 ~~~~~~~~~~~~~i~~lL~raLgdR~~~I~~~~~~~~~~w~i~~~~~~~~~~~l~vGl~l~~~~~a~r~vd~GP~ad~~~ 487 (927)
.-++..|.++. ++.+-|.+.|..+ -..+. +. ..|. +.....+-+.|...+--.=.+-.||+..+.+
T Consensus 294 ~v~Dil~pQl~-r~~~~i~~~L~~~--gF~v~-~~--~~~~--------d~~~~~l~~el~~~~lp~~~~h~GPpv~~~~ 359 (447)
T PRK13300 294 IVEDILYPQLE-RSLRSIVKLLERE--GFEVL-RS--GAWA--------DEDRAYLLLELEVAELPNVKLHIGPPVWVRE 359 (447)
T ss_pred CCccchhHHHH-HHHHHHHHHHHHC--CCEEE-Ee--eeec--------CCCeEEEEEEeecccCCCeeeeeCCCcCchh
Confidence 01224454443 3333344444322 22232 11 2232 1233555566532222222345699998776
Q ss_pred HHHHHHhhhcCc
Q 002406 488 EALRFRKFWGEK 499 (927)
Q Consensus 488 eA~~FR~FWG~K 499 (927)
.|.+|.+=|.++
T Consensus 360 ~a~~F~~k~~~~ 371 (447)
T PRK13300 360 HAENFIEKYEDS 371 (447)
T ss_pred hHHHHHHHhccC
Confidence 699999888554
No 9
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=98.50 E-value=6.6e-05 Score=84.93 Aligned_cols=258 Identities=17% Similarity=0.303 Sum_probs=171.7
Q ss_pred cHHHHhccccCCCCccchhHHHHHHHHHHHHHhcCCCCCCCCcccCCccccccCCceeEEEEeCCceeeEeeeeeccccc
Q 002406 16 KVEELLKEVHFARAPAITKLVDDTVSAVRKSISKIPDAFPVTADLAPGFVRDIGADKVEFKFNKPKTFKIGGSYSINCVV 95 (927)
Q Consensus 16 QidELL~ev~~~~~~~~~~~~e~~L~~lk~~i~~ip~~~~~~~~~~~~~~~~~~~~~~~f~f~~P~~v~vvGS~~l~t~~ 95 (927)
-++|.|+.|+|++.. .+.+......|+..+.++-+. ... + ..+.+|||++=||..
T Consensus 6 ~l~evl~~i~P~~eE--~~~~~~~~e~l~~~~~~~~~e--~~~-~--------------------aev~lVGS~AkgTwL 60 (443)
T COG1746 6 VLEEVLKRIKPTEEE--RKKLKEVAEELRERINEIIEE--LGI-D--------------------AEVVLVGSYAKGTWL 60 (443)
T ss_pred HHHHHHHHcCCCHHH--HHHHHHHHHHHHHHHHHHHHh--cCC-c--------------------ceEEEEeecccCccc
Confidence 367999999999877 678888888888888776433 111 1 246799999999999
Q ss_pred CCCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhhccCCCCCceEeecCCCCCcceeEEEEeCCCCCCCCCeE
Q 002406 96 KPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLVVYPAVKSVEAPGFF 175 (927)
Q Consensus 96 k~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~~~~~~v~~~~~~~d~~kPil~l~p~~~~~~~~~~~ 175 (927)
+.+..|||.|-.|++. ++|.|+ .+.+ .|+..+-+. ....++|+ --|.+...-. ++.
T Consensus 61 ~gd~DIDvFi~Fp~d~--~~eel~-----~~GL---~ig~~~l~~-~~~~~~YA------eHPYV~g~v~-------G~e 116 (443)
T COG1746 61 RGDHDIDVFIAFPKDT--SEEELE-----EKGL---EIGREVLKR-GNYEERYA------EHPYVTGEVD-------GYE 116 (443)
T ss_pred CCCcceeEEEECCCCC--CHHHHH-----HHHH---HHHHHHhcC-Cchhhhhc------cCCeeEEEEc-------cEE
Confidence 9999999999999986 455552 2222 233333222 33344443 3465554432 599
Q ss_pred EEEEecCCCCCcccccccccCCccCCCCCCCCCCCCCcchhhhhccChHHHHHHHHHHhhChHHHHHHHHHHHHHHHhcC
Q 002406 176 VRIIPTAASLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKELGEALILLKVWARQRS 255 (927)
Q Consensus 176 iRi~~~~~~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssil~D~~~~~~l~~l~~~~~~~~~f~dA~~LlkvWl~QRg 255 (927)
|.|.||..--+. .+++++ . -.|| -|.+++.+.++.-.. |=++|||..++-=|
T Consensus 117 VDvVPCy~v~~~--------~~~~sA----V-DRTp-------------lHt~yv~e~L~~~~~--deVrLLK~FlK~iG 168 (443)
T COG1746 117 VDVVPCYKVEDG--------EKIISA----V-DRTP-------------LHTRYVEEHLKGRQK--DEVRLLKQFLKGIG 168 (443)
T ss_pred EEEEecccccCc--------cccccc----c-cCcc-------------hhHHHHHHHhcccch--hHHHHHHHHHhccC
Confidence 999999531111 123321 1 1477 467777777776443 88999999999888
Q ss_pred CCc---cCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCCChhHHHhhhhcCCE
Q 002406 256 SIY---VHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGVSKEEKLQYKEAFPV 332 (927)
Q Consensus 256 ~~~---~~~gf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~~~~~~~~~~~~f~v 332 (927)
.++ ..+||+|++-=+|+.|- .=|.+++.--+. | ..|......+. ..+.|.. -|.
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 654 36899999877777663 337777776654 4 34644432210 0111222 278
Q ss_pred EEeCC-CCceeeccCCCHHHHHHHHHHHHHHHHHhhccCCCcccc
Q 002406 333 VICDP-SAQVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGFEE 376 (927)
Q Consensus 333 vf~D~-sg~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~~~~d~F~~ 376 (927)
|++|| +-.-|.+|.+|.-.+.++++.|+. .|.+++.+-|.+
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 88898 458999999999999999999875 667776666654
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=98.19 E-value=0.00027 Score=90.26 Aligned_cols=342 Identities=14% Similarity=0.202 Sum_probs=198.5
Q ss_pred ccccHHHHhcc----ccCCCCccchhHHHHHHHHHHHHHhcCCCCCCCCcccCCccccccCCceeEEEEe---CCceeeE
Q 002406 13 MDYKVEELLKE----VHFARAPAITKLVDDTVSAVRKSISKIPDAFPVTADLAPGFVRDIGADKVEFKFN---KPKTFKI 85 (927)
Q Consensus 13 f~LQidELL~e----v~~~~~~~~~~~~e~~L~~lk~~i~~ip~~~~~~~~~~~~~~~~~~~~~~~f~f~---~P~~v~v 85 (927)
..-|.|++|.. ........ ...+-+.+.+|.+.|.++.+- |..+..+.. .--.|+|. +|...
T Consensus 478 ~~~~~~~~l~~~~~~~~~~~~~~-~~~~~~af~~L~k~lr~L~~L-PL~I~~v~p-------~sp~lRyts~~pp~p~-- 546 (972)
T PF03813_consen 478 IGDQFDSLLPLPGSGSSPTDEES-FQSVMRAFDELEKDLRSLEDL-PLSITSVQP-------ASPALRYTSVFPPVPH-- 546 (972)
T ss_pred ehhhhhhhhcCccccCCCCchHH-HHHHHHHHHHHHHHHhcCccC-Ccceeeecc-------CCHhhhcCCCCCCCCc--
Confidence 34477888852 22332222 235667777777777777643 333222110 00111121 22222
Q ss_pred eeeeecccccCCCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhhccC-C--CCCceEeecC-CCCCcceeE-
Q 002406 86 GGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSS-P--SFDKVEWSAM-QNEARKPVL- 160 (927)
Q Consensus 86 vGS~~l~t~~k~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~-~--~~~~v~~~~~-~~d~~kPil- 160 (927)
.+......+|+.++|=.+-==+.| +.--=--|-|+|| .||+.|.+. + ....|.++.. ......-.|
T Consensus 547 -------~~~~~~~p~~vvl~fE~S~kWPdd-l~AI~~~K~Af~l-kiae~L~~~~~~~~~~~v~~~~~~~~~~~~~~ld 617 (972)
T PF03813_consen 547 -------AVPRYIPPIEVVLQFESSGKWPDD-LEAIQKTKTAFLL-KIAEELEKQYGDGIKARVGLDNSLSPIANQAFLD 617 (972)
T ss_pred -------cccCCCCCEEEEEEEecCCCCCCC-HHHHHHHHHHHHH-HHHHHHHHhhCCcceeeecccccccceeccceEE
Confidence 233334678999998666433322 2222234666555 899999843 3 1222322221 111111122
Q ss_pred EEEeCCCCCCCCCeEEEEEecCC-CCCcccccc-cccCCccCCCCCCCCCCCCCcchhhhhccChHHHHHHHHHHhhChH
Q 002406 161 VVYPAVKSVEAPGFFVRIIPTAA-SLFNIAKLN-LKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWK 238 (927)
Q Consensus 161 ~l~p~~~~~~~~~~~iRi~~~~~-~~F~~~rl~-P~rnnvR~~~~~~~~~pTP~YNssil~D~~~~~~l~~l~~~~~~~~ 238 (927)
++.| .|+..|+....+ +.-=+.|.. ....-+|. ..++-+-+-...=...-.|...|+.....+|
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 2233 256677776632 322222222 11111221 1122221111111224468899999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCccCCCchhHHHHHHHHHHhhcc-ccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCC
Q 002406 239 ELGEALILLKVWARQRSSIYVHDCLNGYLISILLSYLVSLD-KINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIG 317 (927)
Q Consensus 239 ~f~dA~~LlkvWl~QRg~~~~~~gf~gf~~s~lla~Ll~~~-~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~ 317 (927)
+|.-+|+|.|-|+.-.=+ .+.|..-.+=+|+|+++-.. ....-.|..--|=-+|++||++||..+|+.+..++ .
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 35577777888999988533 55566788889999999999999999999887653 2
Q ss_pred CChhHHHh-------hhh-----cCCEEEe----CCCCceeeccCCCHHHHHHHHHHHHHHHHHhhccC--CCccccccc
Q 002406 318 VSKEEKLQ-------YKE-----AFPVVIC----DPSAQVNLAFRMTSVGFCELQDEAASTLQCMDKCG--DGGFEETFL 379 (927)
Q Consensus 318 ~~~~~~~~-------~~~-----~f~vvf~----D~sg~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~~~--~d~F~~lFl 379 (927)
++.+...+ .++ ..|+.|+ |+.|.+==-.+-+...+++|+.-|+.|+++|...+ ...+..+|.
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 44333322 233 3455444 77774322234788999999999999999998543 467888995
Q ss_pred ccccccccCcEEEEeec
Q 002406 380 TKIDFPAKYDYCVRLNL 396 (927)
Q Consensus 380 ~~~~~~~~fD~~~~i~~ 396 (927)
+....||.++++.-
T Consensus 839 ---~~l~~YD~vI~L~~ 852 (972)
T PF03813_consen 839 ---PPLSDYDFVIHLNP 852 (972)
T ss_pred ---CCccCCCEEEEecC
Confidence 44468999999974
No 11
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=96.58 E-value=0.14 Score=55.15 Aligned_cols=220 Identities=14% Similarity=0.176 Sum_probs=136.8
Q ss_pred eeeEeeeeecccccCCCCceeEEEec---CccccCcccccccchhHHHHhHHHHHHHhhccC-CCCCceEeecCCCCCcc
Q 002406 82 TFKIGGSYSINCVVKPAVNVDLFVGL---PKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSS-PSFDKVEWSAMQNEARK 157 (927)
Q Consensus 82 ~v~vvGS~~l~t~~k~~~~VDl~V~m---P~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~-~~~~~v~~~~~~~d~~k 157 (927)
.|.-|||++-||+.+.+..+|++|.. |..- -+..|+..|.+. +.. ..+
T Consensus 4 gV~rVG~~aKG~ll~Gd~~~~lVv~c~~~PT~~-----------------ll~~v~~~l~e~l~~~--------~~~--- 55 (246)
T smart00572 4 GVMRVGSFAKGTLLKGDNVAELVLLCKEKPTSE-----------------LVARLARKLPEQLKAV--------TED--- 55 (246)
T ss_pred ceEEeeeeccCceecCCCceeEEEEecCCCcHH-----------------HHHHHHHHHHHHHhhc--------Ccc---
Confidence 57789999999999999999999964 4221 235566665432 100 000
Q ss_pred ee-EEEEeCCCCCCCCCeEEEEEecCCCCCccccccc-ccCCccCCCCCCCCCCCCCcchhhhhccChHHHHHHHHHHhh
Q 002406 158 PV-LVVYPAVKSVEAPGFFVRIIPTAASLFNIAKLNL-KRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTIS 235 (927)
Q Consensus 158 Pi-l~l~p~~~~~~~~~~~iRi~~~~~~~F~~~rl~P-~rnnvR~~~~~~~~~pTP~YNssil~D~~~~~~l~~l~~~~~ 235 (927)
+. +.+.... .....++|..+.|. +...-+.. ..-|.|.. .|+=+.=-...+.-+.-..|.+...+...
T Consensus 56 e~~~~~~~~~----~~~~~~~i~ltSp~-~r~~~~~~~~~~~~~~~-----~p~~~ld~~~cl~aLAalRhakWFq~~a~ 125 (246)
T smart00572 56 EALIIVTSTK----EPTMEVGILITSPL-ARVELLITTVPENLRKL-----DPEDHLDRKKCLSALASLRHAKWFQARAS 125 (246)
T ss_pred cceeeeeccC----CCceeEEEEEeccc-ccccccccccCcccccC-----CccccCCHHHHHHHHHHHHHhHHHHHhcc
Confidence 11 1121111 12345666655321 10000000 01222211 11111112233333445678888887777
Q ss_pred ChHHHHHHHHHHHHHHHhcCCCccCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCC
Q 002406 236 RWKELGEALILLKVWARQRSSIYVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQ 315 (927)
Q Consensus 236 ~~~~f~dA~~LlkvWl~QRg~~~~~~gf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~ 315 (927)
...+++--++++|=|.++-. ....+++|.+-++++|++.. -+..++.=+.||.++++||+..|...+
T Consensus 126 ~l~s~~iviRilKd~~~R~~---~~~pL~~w~iELl~~~~i~~--~~~~l~~~~a~RR~fe~lAsG~l~p~~-------- 192 (246)
T smart00572 126 GLQSCVIVIRVLRDLCNRVP---TWQPLSGWPLELLVEKAIGS--ARQPLGLGDAFRRVFECLASGILLPGS-------- 192 (246)
T ss_pred CCcchhhHHHHHHHHHHhcc---cccccccccHHHHHHHHhcc--CCCCCCHHHHHHHHHHHHHhccCcCCC--------
Confidence 77789999999996655442 12348899999999999873 356688889999999999976653211
Q ss_pred CCCChhHHHhhhhcCCEEEeCCC--CceeeccCCCHHHHHHHHHHHHHHHHHhhc
Q 002406 316 IGVSKEEKLQYKEAFPVVICDPS--AQVNLAFRMTSVGFCELQDEAASTLQCMDK 368 (927)
Q Consensus 316 ~~~~~~~~~~~~~~f~vvf~D~s--g~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~ 368 (927)
+. +.||+ +..|+...||....+.+-..|+.++.++.-
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 36775 489999999999999999999999999964
No 12
>COG5260 TRF4 DNA polymerase sigma [DNA replication, recombination, and repair]
Probab=96.24 E-value=0.043 Score=63.65 Aligned_cols=137 Identities=21% Similarity=0.276 Sum_probs=88.0
Q ss_pred eeeEeeeeecccccCCCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhhccCCCCCceEeecCCCCCcceeEE
Q 002406 82 TFKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVLV 161 (927)
Q Consensus 82 ~v~vvGS~~l~t~~k~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~~~~~~v~~~~~~~d~~kPil~ 161 (927)
+..+.||+.-+... +...||+.|.||..--++ .|+.- .++.++.+..+..++.+.. -++-||+.
T Consensus 97 ~l~vFGS~~t~L~l-~~SDiDl~I~s~~~~~~e----------t~~~~--~l~~~l~~~~~~~~~~~v~---tarVPIIK 160 (482)
T COG5260 97 DLKVFGSTETGLAL-PKSDIDLCIISDPRGYKE----------TRNAG--SLASHLFKKNLAKEVVVVS---TARVPIIK 160 (482)
T ss_pred ceeEeccccccccc-CcccccEEEecCCccccc----------cccHH--HHHHHHHHhccCeeeEEEE---ecccceEE
Confidence 56689999888755 456799999998765443 34422 5677776655555555333 24689988
Q ss_pred EEeCCCCCCCCCeEEEEEecCCCCCcccccccccCCccCCCCCCCCCCCCCcchhhhhccChHHHHHHHHHHhhChHHHH
Q 002406 162 VYPAVKSVEAPGFFVRIIPTAASLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKELG 241 (927)
Q Consensus 162 l~p~~~~~~~~~~~iRi~~~~~~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssil~D~~~~~~l~~l~~~~~~~~~f~ 241 (927)
++-.. .++.+.|-. || ..- ....+++....+..|.++
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 76431 234444432 11 000 245677778888999999
Q ss_pred HHHHHHHHHHHhcCCCcc-CCCchhHHHHHHHHHHhh
Q 002406 242 EALILLKVWARQRSSIYV-HDCLNGYLISILLSYLVS 277 (927)
Q Consensus 242 dA~~LlkvWl~QRg~~~~-~~gf~gf~~s~lla~Ll~ 277 (927)
-=++++|=||.+|.+... .||.+++..+.+|..-++
T Consensus 198 pLvliIKhwl~~R~ln~~~~GtL~sy~i~cmV~sfLq 234 (482)
T COG5260 198 PLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQ 234 (482)
T ss_pred hHHHHHHHHHHHHhhcccccCcchhhhhHHHHHHHHH
Confidence 999999999999997644 466655544444333333
No 13
>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=96.18 E-value=0.014 Score=63.62 Aligned_cols=143 Identities=17% Similarity=0.230 Sum_probs=86.3
Q ss_pred CChhHHHHHHHHHHHhcCCC----CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCCCCCeEEEeCCCC
Q 002406 743 PVFGPVVRVAKRWAASHLFS----ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDWTFSALVVDINND 818 (927)
Q Consensus 743 paf~~tvRLaKRWl~shlLs----~hi~eE~vELLva~vfl~p~p~~~P~S~~~GFlRfL~lLa~~DW~~~PLiVd~~~~ 818 (927)
..|-.+.|.+|.|..+..+. |++..-.+.+|||.|.-- .| -.++.+=+.||.+..++|||.+ |++++.-.+
T Consensus 107 ~~Fr~~lR~IK~WAk~RGIYsn~~GylGGI~waILvArvcql-~P---n~~~~~ll~~FF~~ys~W~W~~-PV~l~~~~~ 181 (254)
T PF04928_consen 107 ETFRTALRFIKLWAKRRGIYSNVFGYLGGIHWAILVARVCQL-YP---NASPSTLLSRFFQIYSQWDWPN-PVVLDPIED 181 (254)
T ss_dssp HHHHHHHHHHHHHHHHTT-B-CCCTSB-HHHHHHHHHHHHHH-ST---T--HHHHHHHHHHHHHCS-TTS--EESS----
T ss_pred HHHHHHHHHHHHHHHHccccchhhccchHHHHHHHHHHHHHH-Cc---cccccchHHHHHHHhcCCCCCC-ceeeccccc
Confidence 67889999999999999874 468999999999999754 33 3466678899999999999985 887754322
Q ss_pred CCHHhHHHHHHHHHHhhhcccccccCCCCeEEEEeCCCCCCCccccCCCCHHHHHHHHHHHHHHHHHHHHHhhccCCCcc
Q 002406 819 FGPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRLVAYARSSANLLTKLILEDQTDSC 898 (927)
Q Consensus 819 lt~~~~~~i~~~F~~~R~~~~~dp~~~~p~~fIaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~s~~~l~~~~~~~~~~~~ 898 (927)
-. -.|..|... ..+....-.|-|.||.=|.-.. ...=+..-+++|+.=-+.+.+++++.. . +..
T Consensus 182 ~~--------~~~~~w~p~--~~~~~~~~~MpIiTP~yP~~Ns--t~nVt~st~~~i~~Ef~ra~~i~~~~~-~---~~~ 245 (254)
T PF04928_consen 182 GP--------LGFKVWNPR--LYPRDRRHLMPIITPAYPSMNS--TYNVTRSTLRIIREEFQRAHEILSEIL-K---GGA 245 (254)
T ss_dssp -S--------SSCGS--TT--T-HHHHC-SS-EE-SSSS--BT--TTT--HHHHHHHHHHHHHHHHHHHHHH-T---TSS
T ss_pred Cc--------ccccCCCCC--CCCCCcccceeEccCCCCcccc--ccccCHHHHHHHHHHHHHHHHHHHHHH-c---CCC
Confidence 11 000111100 0011134579999998876532 345567788888888888888887754 2 247
Q ss_pred cccccccc
Q 002406 899 RWEGQVTL 906 (927)
Q Consensus 899 ~~~~lF~~ 906 (927)
+|..||.|
T Consensus 246 ~W~~L~e~ 253 (254)
T PF04928_consen 246 SWSDLFEP 253 (254)
T ss_dssp -HHHCT--
T ss_pred CHHHHcCC
Confidence 89999986
No 14
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=95.68 E-value=0.053 Score=58.34 Aligned_cols=98 Identities=17% Similarity=0.027 Sum_probs=81.8
Q ss_pred hhHHHHHHHHHhcCCChhHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCCC-
Q 002406 729 GQHASMINGLQGRYPVFGPVVRVAKRWAASHLFSACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDWT- 807 (927)
Q Consensus 729 p~h~~~i~~l~~r~paf~~tvRLaKRWl~shlLs~hi~eE~vELLva~vfl~p~p~~~P~S~~~GFlRfL~lLa~~DW~- 807 (927)
-+|+..-+.-++..-+|-..||++|.|...+-.-..++.=.+|||++|+-- +...|.++..+|-|||++||+=-.-
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 489998888888888999999999999999876667899999999999964 4468999999999999999987763
Q ss_pred CCeEEEeCCC--------CCCHHhHHHHHH
Q 002406 808 FSALVVDINN--------DFGPEDFKVIND 829 (927)
Q Consensus 808 ~~PLiVd~~~--------~lt~~~~~~i~~ 829 (927)
..|=|+|+-+ .||.+++.+|..
T Consensus 191 ~~~gI~DPce~~~~nv~~~lT~qqrd~It~ 220 (246)
T smart00572 191 GSPGLTDPCEKDNTDALTALTLQQREDVTA 220 (246)
T ss_pred CCCCCcCCCCCCcccHHHhcCHHHHHHHHH
Confidence 3567777753 389998887763
No 15
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=95.36 E-value=1.3 Score=52.87 Aligned_cols=229 Identities=17% Similarity=0.216 Sum_probs=128.0
Q ss_pred CceeeEeeeeecccccCCCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhhccCCCCCceEeecCCCCCccee
Q 002406 80 PKTFKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPV 159 (927)
Q Consensus 80 P~~v~vvGS~~l~t~~k~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~~~~~~v~~~~~~~d~~kPi 159 (927)
=.+|.++|||.+||.. |...|||.|.=+ .++++=...+.+ .++.++.+......+. ...-.+-||
T Consensus 101 ~a~v~~FGS~~tglyL-P~sDIDl~v~~~--------~~~~~e~~~~~~---~l~~~~e~~~~~~~v~---~v~karvpi 165 (514)
T KOG1906|consen 101 DASVYVFGSVPTGLYL-PDSDIDLVVLSK--------FLNDKEDRAVKL---ELALELEEDNSAFHVK---VVQKARVPI 165 (514)
T ss_pred cceeEEeeeeeccccc-cccceEEEEecc--------cccCchhhHHHH---HHHHhhhhccccceEE---Eeeeeeeee
Confidence 3578899999999844 788899999655 233333333333 3444443322222222 223356787
Q ss_pred EEEEeCCCCCCCCCeEEEEEecCCCCCcccccccccCCccCCCCCCCCCCCCCcchhhhhccChHHHHHHHHHHhhChHH
Q 002406 160 LVVYPAVKSVEAPGFFVRIIPTAASLFNIAKLNLKRNNVRAFNQDGIPRATPKYNSSILEDMFLEDNAEYVEKTISRWKE 239 (927)
Q Consensus 160 l~l~p~~~~~~~~~~~iRi~~~~~~~F~~~rl~P~rnnvR~~~~~~~~~pTP~YNssil~D~~~~~~l~~l~~~~~~~~~ 239 (927)
+.++-. .+++.|.|-.. .+ .+ ..-.++.+...+++|.
T Consensus 166 ik~~d~-----~s~i~vDISFn---------------~~-----~G------------------~~aa~~i~~~~~~~p~ 202 (514)
T KOG1906|consen 166 IKFKDP-----VSNIHVDISFN---------------QT-----NG------------------VKAAKFIKDFLRDHPF 202 (514)
T ss_pred EEeecC-----ccceEEEeeec---------------cc-----Cc------------------hhHHHHHHHHHhcCcc
Confidence 776532 12344444331 11 01 1336778888889999
Q ss_pred HHHHHHHHHHHHHhcCCCcc-CCCchhHHHHHHHHHHhh-ccccCcCCcHHH-----HHHHHHHHHhcCCCCC-Cceeec
Q 002406 240 LGEALILLKVWARQRSSIYV-HDCLNGYLISILLSYLVS-LDKINNSMKALQ-----ILRVVLDFIATSKLWN-RGLYFP 311 (927)
Q Consensus 240 f~dA~~LlkvWl~QRg~~~~-~~gf~gf~~s~lla~Ll~-~~~l~~~~SsyQ-----ifr~~l~fLa~~d~~~-~~i~~~ 311 (927)
++--|+++|-|+.+|++... .||.++|.+..|+.+.++ ...+..+-.+.+ ++..++++....-+.. -|+.+.
T Consensus 203 ~~~lvlvlk~fl~~r~ln~v~tGgisSyal~~Lv~~fl~l~~~~~s~~~~~~~~~~vll~~f~e~yG~~f~~~k~~i~~~ 282 (514)
T KOG1906|consen 203 LRSLVLVLKQFLYERRLNGVHTGGISSYALELLVLSFLQLHPRSKSGRLAVLKNLGVLLIKFFELYGRNFGYDKLGISLS 282 (514)
T ss_pred chhHHHHHHHHHHhhcccccccccchHHHHHHHHHHHHhhcccccCCccchhcccchHHHHHHHHhccccCchhhceecc
Confidence 99999999999999998755 688999988888777776 333333333332 7788888887332222 233322
Q ss_pred CCCCCCCChhHHHhhh----hcCCEEEeCCCCceeeccCCCHHHHHHHHHHHHHHHHHhhc
Q 002406 312 PKGQIGVSKEEKLQYK----EAFPVVICDPSAQVNLAFRMTSVGFCELQDEAASTLQCMDK 368 (927)
Q Consensus 312 ~~~~~~~~~~~~~~~~----~~f~vvf~D~sg~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~ 368 (927)
.. .+.++.+....+. +.+..-.-||---.|=.++.+ ..+.+++.+-..+...|-.
T Consensus 283 ~~-g~~~~~~~~~~~~~~~~~~~~LsieDP~~P~ndigr~s-~~~~~v~~~F~~af~~l~~ 341 (514)
T KOG1906|consen 283 LG-GEYVSKELTGFFNNSLERPGSLSIEDPVDPTNDIGRSS-FNFSQVKGAFAYAFKVLTN 341 (514)
T ss_pred CC-cccccHHhhhhhcccccCCCccccCCCCCccccccccc-ccHHHHHHHHHHHHHHHhh
Confidence 11 1122221111111 122222234433333333444 5566677777777776643
No 16
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=94.67 E-value=2.8 Score=49.38 Aligned_cols=228 Identities=14% Similarity=0.193 Sum_probs=139.7
Q ss_pred HHHHHHHHHHHHHHHhcc-CCCCeeeeecccCCcccccccCCCCCCCCCccccccccccCCCCCCccCcEEEEEEeccCC
Q 002406 568 SASLLEAFEVLSKRLHLI-EDIPLKISSVQPLDSAFRFTSVFPPEPHPLANERHTVSRLHKLTPSCIQPLEVMIQLEGSG 646 (927)
Q Consensus 568 ~~~v~~af~~L~k~Lr~L-~~LPL~I~~V~p~sp~lRytsv~pp~p~~~~~~~~~~~~~~~~~p~~~~pi~vvlqfE~Sg 646 (927)
...+.+..+++...|+.. .+.|.. ..|..+.++-|+|-+-. . .=+||.|-| ..
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 346777788888777764 456666 78888888889997621 0 136899999 44
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhcc--CC-eeeecCCceeeeccceeEEEEEeccchhHHHhhhcccccccccchhh
Q 002406 647 NWPMDHVAIEKTKSAFLIKIGESLQNRW--GM-TCSATEDDADIFMSGYAFRLKILHERGLSLVKSENGNKAKRVYSTDK 723 (927)
Q Consensus 647 kWPddl~AIq~~K~AF~lkIae~L~~~~--~~-~~~v~~d~lDV~~~G~~FRl~I~~~rE~~Ll~~~~~~~~~~~~~~~~ 723 (927)
..|. +-+++. .+.|++.+.+.+ +. .-.+...|+-+.++||--=++-++..+- | .+.++ ..++
T Consensus 71 ~~~~--e~L~~~----gl~i~~~~~~~~~~~~~~~yaeHpyv~~~~~G~~VDiVPcy~v~~------~-~~~~s--aVDR 135 (447)
T PRK13300 71 DTSR--EELEEK----GLEIGKEVAKELLGDYEERYAEHPYVTGEIDGFEVDIVPCYKVES------G-EEIIS--AVDR 135 (447)
T ss_pred CCCH--HHHHHH----HHHHHHHHHHhhCCcceeeeccCceEEEEECCEEEEEEeeEEccC------c-Ccccc--cccC
Confidence 5553 233332 345555554442 11 1234455677777888777776764311 1 11111 1122
Q ss_pred hHHHhhhHHHHHHHHHhcCCC-hhHHHHHHHHHHHhcCCC------CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHH
Q 002406 724 ILFIRGQHASMINGLQGRYPV-FGPVVRVAKRWAASHLFS------ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLR 796 (927)
Q Consensus 724 ~~~~~p~h~~~i~~l~~r~pa-f~~tvRLaKRWl~shlLs------~hi~eE~vELLva~vfl~p~p~~~P~S~~~GFlR 796 (927)
.|.|+..|.. |.-. +.--|||+|+|+.+..+. ..|+-=++||||++ | -||.-
T Consensus 136 ----tp~H~~fv~~---rl~~~~~d~VRLlK~f~k~~gvYGsE~k~~GFSGYl~ELLv~~-y-------------G~F~~ 194 (447)
T PRK13300 136 ----TPFHTKYVKE---RLKGKLEDEVRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIH-Y-------------GSFEN 194 (447)
T ss_pred ----chHHHHHHHH---hhhhhHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHH-h-------------CCHHH
Confidence 2678887654 2222 778999999999998773 35888999999999 2 48999
Q ss_pred HHHHHhcCCCCCCeEEEeCCCCCCHHhHHHHHHHHHHhhhcccccccCCCCeEEEEeCCCCCCCccccCCCCHHHHHHHH
Q 002406 797 FLRLLAEYDWTFSALVVDINNDFGPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRLV 876 (927)
Q Consensus 797 fL~lLa~~DW~~~PLiVd~~~~lt~~~~~~i~~~F~~~R~~~~~dp~~~~p~~fIaT~~D~~g~~wT~~~Ps~~v~~Rl~ 876 (927)
.|.-.++| + -|.+||+.+..+.. .| ..+++|.=|-|+.-. --.++-..++.
T Consensus 195 ~l~~a~~w--~-~~~~I~~~~~~~~~-------~f--------------~~PlvViDPvDp~RN-----VAaa~S~~~~~ 245 (447)
T PRK13300 195 VLKAASKW--K-PPVKIDLEKHGKEY-------KF--------------DDPLVVIDPVDPNRN-----VAAALSLENLA 245 (447)
T ss_pred HHHHHHhC--C-CCceEeccccCccc-------cC--------------CCCEEEeCCCCCcch-----HHHHcCHHHHH
Confidence 99999985 4 46889887553221 11 246888877777632 22233334444
Q ss_pred HHHHHHHHHH
Q 002406 877 AYARSSANLL 886 (927)
Q Consensus 877 ~LAk~s~~~l 886 (927)
.+--+|-..|
T Consensus 246 ~fv~aar~fL 255 (447)
T PRK13300 246 TFILAAREFL 255 (447)
T ss_pred HHHHHHHHHH
Confidence 4444555554
No 17
>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=94.00 E-value=1.7 Score=47.40 Aligned_cols=132 Identities=17% Similarity=0.268 Sum_probs=89.1
Q ss_pred hhhccChHHHHHHHHHHhhChHHHHHHHHHHHHHHHhcCCCccCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHH
Q 002406 217 ILEDMFLEDNAEYVEKTISRWKELGEALILLKVWARQRSSIYVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLD 296 (927)
Q Consensus 217 il~D~~~~~~l~~l~~~~~~~~~f~dA~~LlkvWl~QRg~~~~~~gf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~ 296 (927)
.+..+....|.+...+.....++.+--++++|= ++||- .+...++++.+=.|+-|.+..+.-+..+|....||-+++
T Consensus 107 cl~aLaalRhakWFq~~a~~l~s~~~viRIlrD-l~~R~--p~w~~L~~W~leLL~~~~i~~~~~~~~l~~g~a~RRvle 183 (248)
T PF07528_consen 107 CLSALAALRHAKWFQARANGLQSCVIVIRILRD-LRQRV--PTWQPLSSWALELLVEKAISNNSSRQPLSPGDAFRRVLE 183 (248)
T ss_pred HHHHHHHHHHhHHHHHHhccCCCcceehhhHHH-HHHhC--CCCCCCChhHHHHHHHHHeeeCCCCCCCChHHHHHHHHH
Confidence 334445667888888766665555444444442 45552 223445666555566666655555667899999999999
Q ss_pred HHhcCCCCCCceeecCCCCCCCChhHHHhhhhcCCEEEeCCC--CceeeccCCCHHHHHHHHHHHHHHHHHhhccCCCcc
Q 002406 297 FIATSKLWNRGLYFPPKGQIGVSKEEKLQYKEAFPVVICDPS--AQVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGF 374 (927)
Q Consensus 297 fLa~~d~~~~~i~~~~~~~~~~~~~~~~~~~~~f~vvf~D~s--g~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~~~~d~F 374 (927)
.|| .|+.+... +. +.||+ +..|++..||.-..+.+-.-|+..|.++.- +++
T Consensus 184 ~la------sGillp~~-----------------~g-l~DPcE~~~~~~~~~lt~qq~e~it~sAQ~~LRllaf---gq~ 236 (248)
T PF07528_consen 184 CLA------SGILLPGS-----------------PG-LRDPCEKDPVDVLDTLTLQQREDITSSAQTALRLLAF---GQI 236 (248)
T ss_pred HHh------CceecCCC-----------------CC-CcCCCCCCCceeeccCCHHHHHHHHHHHHHHHHHHHh---cCc
Confidence 998 36666422 11 35775 489999999999999999999999999964 344
Q ss_pred cccc
Q 002406 375 EETF 378 (927)
Q Consensus 375 ~~lF 378 (927)
..++
T Consensus 237 ~kvL 240 (248)
T PF07528_consen 237 HKVL 240 (248)
T ss_pred ceec
Confidence 4443
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=93.70 E-value=0.6 Score=44.47 Aligned_cols=108 Identities=18% Similarity=0.215 Sum_probs=69.3
Q ss_pred HHHHHHHHHHHhcCCC---ccCCCchhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCCCCCC
Q 002406 242 EALILLKVWARQRSSI---YVHDCLNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKGQIGV 318 (927)
Q Consensus 242 dA~~LlkvWl~QRg~~---~~~~gf~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~~~~~ 318 (927)
|-++|||..++--|.+ ....||+|++-=+|+.+- .=|+.+++..|+ | +.|+.+...+...
T Consensus 1 ddVrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~y-------------GsF~~~l~~a~~--W-~~~~~Id~~~~~~- 63 (114)
T PF09249_consen 1 DDVRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHY-------------GSFENVLEAAAK--W-KPPVVIDLEDHGE- 63 (114)
T ss_dssp HHHHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHHH-------------SSHHHHHHHHTT-----TTEEEETT-TTE-
T ss_pred ChhHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHHH-------------CCHHHHHHHHHh--c-CCCeEEccCccch-
Confidence 4588999999999854 447999999877776653 349999999884 4 3466665442111
Q ss_pred ChhHHHhhhhcCCEEEeCCCC-ceeeccCCCHHHHHHHHHHHHHHHHHhhccCCCcc
Q 002406 319 SKEEKLQYKEAFPVVICDPSA-QVNLAFRMTSVGFCELQDEAASTLQCMDKCGDGGF 374 (927)
Q Consensus 319 ~~~~~~~~~~~f~vvf~D~sg-~~Nl~~~~t~~s~~~L~~eA~~tl~~L~~~~~d~F 374 (927)
....| .-|+|++||.- .-|++|.+|...+.+.++.|+.= |.+.+.+-|
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 34888899954 89999999999999999998764 445444433
No 19
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=93.60 E-value=0.63 Score=58.28 Aligned_cols=168 Identities=14% Similarity=0.094 Sum_probs=107.0
Q ss_pred HHHHHHHHHHhhChHHHHHHHHHHHHHHHhcCCCccCCCchhHHHHHHHHHHhh-ccccCcCCcHHHHHHHHHHHHhcCC
Q 002406 224 EDNAEYVEKTISRWKELGEALILLKVWARQRSSIYVHDCLNGYLISILLSYLVS-LDKINNSMKALQILRVVLDFIATSK 302 (927)
Q Consensus 224 ~~~l~~l~~~~~~~~~f~dA~~LlkvWl~QRg~~~~~~gf~gf~~s~lla~Ll~-~~~l~~~~SsyQifr~~l~fLa~~d 302 (927)
-.|...|+...+.+|.|.-+++|.|-|+.-.=+. ||+..-.+=.|+|+++. .+....-.|..--|=.+++|||++|
T Consensus 805 p~ht~aL~~l~qsh~~ys~vvrLaKrWl~shLL~---~h~~De~iELLva~lf~~p~p~~~psS~~~gFlRfL~llS~~d 881 (1121)
T KOG2054|consen 805 PLHTLALQSLSQSHPFYSSVVRLAKRWLGSHLLS---GHHLDEAIELLVAALFLKPGPLVPPSSPENGFLRFLSLLSTWD 881 (1121)
T ss_pred HHHHHHHHHHhhcccchhHHHHHHHHHHHHHhhc---cchHHHHHHHHHHHHhcCccCCCCCCCcchhHHHHHHHHhcCc
Confidence 4677889999999999999999999999877443 45556667778888876 3444555677778999999999999
Q ss_pred CCCCceeecCCCCCCCChhHHH----hh---hhcCCE--EEeCCCCceeeccCCCHHHHHHHHH--HHHHHHHHhhccCC
Q 002406 303 LWNRGLYFPPKGQIGVSKEEKL----QY---KEAFPV--VICDPSAQVNLAFRMTSVGFCELQD--EAASTLQCMDKCGD 371 (927)
Q Consensus 303 ~~~~~i~~~~~~~~~~~~~~~~----~~---~~~f~v--vf~D~sg~~Nl~~~~t~~s~~~L~~--eA~~tl~~L~~~~~ 371 (927)
|...|+.+..+. ..+..... .| ++..|. |..+-++.-|-..+.+++..-+.+- -|+.++++++....
T Consensus 882 W~~~PLIvd~nn--~~~ed~~~e~~e~f~s~R~~lp~m~vit~yD~~~~~~t~~~P~~~v~~r~~alar~sl~ll~k~~p 959 (1121)
T KOG2054|consen 882 WKFDPLIVDFNN--GFPEDERSELEEKFISARKQLPPMVVITPYDHLGSKFTRTSPNQIVLNRLVALARESLKLLEKQAP 959 (1121)
T ss_pred ccCCceEEEcCC--CCcHHHHHHHHHHHhhhcccCCceEEeeccccccccccccCchHHHHHHHHHhhhhhHHhhccccc
Confidence 998898876543 12222221 11 223443 3344455444444455655444443 45788888876432
Q ss_pred Cccccccccccccc---ccCcEEEEeec
Q 002406 372 GGFEETFLTKIDFP---AKYDYCVRLNL 396 (927)
Q Consensus 372 d~F~~lFl~~~~~~---~~fD~~~~i~~ 396 (927)
..=-.+++-..-|. ..||.++.+..
T Consensus 960 ~~~~t~~~~~~lf~~~L~~yd~vi~~~~ 987 (1121)
T KOG2054|consen 960 GEIKTIVRPTSLFRENLSPYDAVIQLEP 987 (1121)
T ss_pred ccchhhhhhhhhhhcccccccchhcccc
Confidence 22112222222332 58998887764
No 20
>PTZ00418 Poly(A) polymerase; Provisional
Probab=92.31 E-value=1.4 Score=53.38 Aligned_cols=169 Identities=14% Similarity=0.151 Sum_probs=109.1
Q ss_pred hHHHHHHHHHhcCCChhHHHHHHHHHHHhcCCC----CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCC
Q 002406 730 QHASMINGLQGRYPVFGPVVRVAKRWAASHLFS----ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYD 805 (927)
Q Consensus 730 ~h~~~i~~l~~r~paf~~tvRLaKRWl~shlLs----~hi~eE~vELLva~vfl~p~p~~~P~S~~~GFlRfL~lLa~~D 805 (927)
+-+..|..+--....|-.+.|-+|.|...+.+. |++.--.+-+|||.|-- -+| ..++.+=.-||.+..++|+
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 455555566566778999999999999999874 57788999999999953 233 4778888899999999999
Q ss_pred CCCCeEEEeCCCCCC-HHhHHHHHHHHHHhhhcccccccCCCCeEEEEeCCCCCCCccccCCCCHHHHHHHHHHHHHHHH
Q 002406 806 WTFSALVVDINNDFG-PEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRLVAYARSSAN 884 (927)
Q Consensus 806 W~~~PLiVd~~~~lt-~~~~~~i~~~F~~~R~~~~~dp~~~~p~~fIaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~s~~ 884 (927)
|.+ |+++.--.+-. .+. ...|.-|... .+|......|-|.||.=|.-.. ...=+..-++.|+.==+.+.+
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 76553211100 000 0012222211 1344456789999997665322 234445566667666667777
Q ss_pred HHHHHhhccCCCcccccccccccCCCCCccccc
Q 002406 885 LLTKLILEDQTDSCRWEGQVTLPTSPSFPVRSK 917 (927)
Q Consensus 885 ~l~~~~~~~~~~~~~~~~lF~~pl~~~~~~~~~ 917 (927)
++++...+ +..+|..||.|. -|+-+|+
T Consensus 385 i~~~i~~~---~~~~W~~Lfep~---~Ff~~Yk 411 (593)
T PTZ00418 385 IIKYIEKN---SENTWTNVLEPL---DFFTSYK 411 (593)
T ss_pred HHHHHHhc---CCCCHHHHcCCc---chhhhcc
Confidence 77653221 256899999854 3555554
No 21
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=91.91 E-value=12 Score=43.74 Aligned_cols=184 Identities=17% Similarity=0.196 Sum_probs=112.0
Q ss_pred HHHHHHHHHHHHHHHhcc-CCCCeeeeecccCCcccccccCCCCCCCCCccccccccccCCCCCCccCcEEEEEEeccCC
Q 002406 568 SASLLEAFEVLSKRLHLI-EDIPLKISSVQPLDSAFRFTSVFPPEPHPLANERHTVSRLHKLTPSCIQPLEVMIQLEGSG 646 (927)
Q Consensus 568 ~~~v~~af~~L~k~Lr~L-~~LPL~I~~V~p~sp~lRytsv~pp~p~~~~~~~~~~~~~~~~~p~~~~pi~vvlqfE~Sg 646 (927)
.+.+....++|...|+.. .+.+.. ..|.-+.+.-|+|-+-- -.=|||.|-|. .
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 345666777777776654 233322 46777777778876520 01368999984 3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhccCC---eeeecCCceeeeccceeEEEEEeccchhHHHhhhcccccccccchhh
Q 002406 647 NWPMDHVAIEKTKSAFLIKIGESLQNRWGM---TCSATEDDADIFMSGYAFRLKILHERGLSLVKSENGNKAKRVYSTDK 723 (927)
Q Consensus 647 kWPddl~AIq~~K~AF~lkIae~L~~~~~~---~~~v~~d~lDV~~~G~~FRl~I~~~rE~~Ll~~~~~~~~~~~~~~~~ 723 (927)
..| +..--...+.|++.+.+. |. ...+...|+-+.++||--=++-++..+ .|. +.++ ..++
T Consensus 70 ~~~------~e~l~~~gl~i~~~~~~~-~~~~~~~yaeHpYv~~~~~G~~VDiVPcy~v~------~g~-~~~t--aVDR 133 (408)
T TIGR03671 70 DTS------REELEEYGLEIGHEVLKR-GGNYEERYAEHPYVSGEIEGFEVDVVPCYKVE------SGE-EIIS--AVDR 133 (408)
T ss_pred CCC------HHHHHHHHHHHHHHHHhh-CCCHhheeccCceEEEEEccEEEEEEeeEEcc------CcC-eeec--cccC
Confidence 333 223334456666666543 22 222344567777777766666666621 111 1111 1122
Q ss_pred hHHHhhhHHHHHHHHHhcCCChhHHHHHHHHHHHhcCCC------CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHH
Q 002406 724 ILFIRGQHASMINGLQGRYPVFGPVVRVAKRWAASHLFS------ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRF 797 (927)
Q Consensus 724 ~~~~~p~h~~~i~~l~~r~paf~~tvRLaKRWl~shlLs------~hi~eE~vELLva~vfl~p~p~~~P~S~~~GFlRf 797 (927)
.|.|+..+..=-.. -+.--|||+|+|+....+. ..|+-=++||||++ | -||.-.
T Consensus 134 ----tp~H~~fv~~rl~~--~~~d~VRLlK~f~k~igvYGsE~~~~GFSGYl~ELLv~~-y-------------G~F~~~ 193 (408)
T TIGR03671 134 ----TPFHTRYVLERLDG--KLRDDVRLLKQFLKGIGVYGSELKTRGFSGYLCELLVIH-Y-------------GSFENV 193 (408)
T ss_pred ----chHHHHHHHHhhhh--hHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHH-h-------------CCHHHH
Confidence 26788876542221 1778999999999998763 35888999999999 2 488999
Q ss_pred HHHHhcCCCCCCeEEEeCC
Q 002406 798 LRLLAEYDWTFSALVVDIN 816 (927)
Q Consensus 798 L~lLa~~DW~~~PLiVd~~ 816 (927)
|.-.++ |+ .+.++|+.
T Consensus 194 l~~a~~--wk-~~~~id~~ 209 (408)
T TIGR03671 194 LKAASK--WK-PGVVIDIE 209 (408)
T ss_pred HHHHHh--cC-CCeEEecC
Confidence 999987 44 57888775
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=91.44 E-value=0.85 Score=44.86 Aligned_cols=83 Identities=20% Similarity=0.238 Sum_probs=58.2
Q ss_pred ceeeEeeeeecccccCCCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhhccCCCCCceEeecCCCCCcceeE
Q 002406 81 KTFKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVL 160 (927)
Q Consensus 81 ~~v~vvGS~~l~t~~k~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~~~~~~v~~~~~~~d~~kPil 160 (927)
..|-+.|||+-+|.+++...||++|.|+..... .-....-++..|...|.+.... ...-...+|.+
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 467799999999999999999999999987653 1124455778888888764211 11223455677
Q ss_pred EEEeCCCCCCCCCeEEEEEecC
Q 002406 161 VVYPAVKSVEAPGFFVRIIPTA 182 (927)
Q Consensus 161 ~l~p~~~~~~~~~~~iRi~~~~ 182 (927)
.|.-.+ .++.|-|.|+.
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=91.01 E-value=1.1 Score=42.19 Aligned_cols=79 Identities=25% Similarity=0.220 Sum_probs=56.7
Q ss_pred ceeeEeeeeecccccCCCCceeEEEecCccccCcccccccchhHHHHhHHHHHHHhhccCCCCCceEeecCCCCCcceeE
Q 002406 81 KTFKIGGSYSINCVVKPAVNVDLFVGLPKECFHEKDYLNHRYHAKRCLYLCVIKKHLKSSPSFDKVEWSAMQNEARKPVL 160 (927)
Q Consensus 81 ~~v~vvGS~~l~t~~k~~~~VDl~V~mP~~~fq~KDylN~RY~~KRA~YLa~ia~~L~~~~~~~~v~~~~~~~d~~kPil 160 (927)
..+.+.||++.|+..+ +..||++|..|.. ......++..+++.|++.+.+.++. .--+++.|++
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 4578999999988664 6799999999976 1244567788999998876443333 3367899999
Q ss_pred EEEeCCCCCCCCCeEEEEEe
Q 002406 161 VVYPAVKSVEAPGFFVRIIP 180 (927)
Q Consensus 161 ~l~p~~~~~~~~~~~iRi~~ 180 (927)
.+.-.. +++.+.|-.
T Consensus 84 k~~~~~-----~~i~~Dis~ 98 (114)
T cd05402 84 KFVDKP-----TGIEVDISF 98 (114)
T ss_pred EEEEcC-----CCeEEEEEc
Confidence 887652 246666654
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=88.42 E-value=2.4 Score=46.22 Aligned_cols=101 Identities=20% Similarity=0.059 Sum_probs=81.1
Q ss_pred hhHHHHHHHHHhcCCChhHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCC-C
Q 002406 729 GQHASMINGLQGRYPVFGPVVRVAKRWAASHLFSACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDW-T 807 (927)
Q Consensus 729 p~h~~~i~~l~~r~paf~~tvRLaKRWl~shlLs~hi~eE~vELLva~vfl~p~p~~~P~S~~~GFlRfL~lLa~~DW-~ 807 (927)
-+|+.+-+.-++..++.-..+|+.|--.+-.---..+++=.+||||-++..+ .|-..|-++..+|-|+|++||+==. .
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 4899999999999999999999999887776555678999999999998764 3456788999999999999997432 2
Q ss_pred CCeEEEeCC--------CCCCHHhHHHHHHH
Q 002406 808 FSALVVDIN--------NDFGPEDFKVINDN 830 (927)
Q Consensus 808 ~~PLiVd~~--------~~lt~~~~~~i~~~ 830 (927)
..|=|.|+- +.||.+++++|...
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
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=87.74 E-value=3.2 Score=48.73 Aligned_cols=150 Identities=17% Similarity=0.203 Sum_probs=96.6
Q ss_pred ChhHHHHHHHHHHHhcCCC----CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCCCCCeEEEeCCCCC
Q 002406 744 VFGPVVRVAKRWAASHLFS----ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDWTFSALVVDINNDF 819 (927)
Q Consensus 744 af~~tvRLaKRWl~shlLs----~hi~eE~vELLva~vfl~p~p~~~P~S~~~GFlRfL~lLa~~DW~~~PLiVd~~~~l 819 (927)
-|..|-|-.|-|.-.|... |++---.-=+|||.+ .+=+| =.+|.+=.-||...+++|.|- .|++++.-++-
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 4778899999999999863 467788889999998 33333 345566677888899999997 88888775432
Q ss_pred CHHhHHHHHHHHHHhhhcccccccCCCCeEEEEeCCCC-CCCccccCCCCHHHHHHHHHHHHHHHHHHHHHhhccCCCcc
Q 002406 820 GPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDK-ASEAWTTCSPNFTELKRLVAYARSSANLLTKLILEDQTDSC 898 (927)
Q Consensus 820 t~~~~~~i~~~F~~~R~~~~~dp~~~~p~~fIaT~~D~-~g~~wT~~~Ps~~v~~Rl~~LAk~s~~~l~~~~~~~~~~~~ 898 (927)
+-. +.-|-.. .+|..+...|=|.||-=| .++..+ -|.--..-|+.==+.+++...+-. . ...
T Consensus 289 ~L~--------~~VWdPr--~n~~DryHlMPIITPAyP~~nsthN---VS~ST~~Vi~~Ef~~g~~I~~~i~-~---~k~ 351 (562)
T KOG2245|consen 289 NLN--------LPVWDPR--VNPSDRYHLMPIITPAYPQMNSTHN---VSRSTLKVITEEFKRGLEICDDIE-L---NKL 351 (562)
T ss_pred ccC--------ccccCCC--CCCCCcceecccccCCccccccccc---ccHHHHHHHHHHHHHHHHHHHHHH-h---ccc
Confidence 211 1222111 245566678999999544 333333 333344444444455555554432 2 267
Q ss_pred cccccccccCCCCCcccccc
Q 002406 899 RWEGQVTLPTSPSFPVRSKQ 918 (927)
Q Consensus 899 ~~~~lF~~pl~~~~~~~~~~ 918 (927)
+|..||..+ .|+.||++
T Consensus 352 ~W~~LFE~~---~FF~rYk~ 368 (562)
T KOG2245|consen 352 DWSDLFELY---NFFSRYKH 368 (562)
T ss_pred cHHHHhhhh---HHHHHHhh
Confidence 999999854 46666654
No 26
>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=85.62 E-value=5.7 Score=41.50 Aligned_cols=124 Identities=22% Similarity=0.225 Sum_probs=75.7
Q ss_pred hHHHHHHHHHHHHHHHhcCCC-ccCCC-chhHHHHHHHHHHhhccccCcCCcHHHHHHHHHHHHhcCCCCCCceeecCCC
Q 002406 237 WKELGEALILLKVWARQRSSI-YVHDC-LNGYLISILLSYLVSLDKINNSMKALQILRVVLDFIATSKLWNRGLYFPPKG 314 (927)
Q Consensus 237 ~~~f~dA~~LlkvWl~QRg~~-~~~~g-f~gf~~s~lla~Ll~~~~l~~~~SsyQifr~~l~fLa~~d~~~~~i~~~~~~ 314 (927)
..-+++=++|.|-|.+|=.-. ...++ -..|.+..|+.|..++|.=...++--|-||.||+.|.+..- =-|+-...
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 467899999999999876422 11223 46799999999999988777888999999999999975421 12222111
Q ss_pred CCCCChhH-----HHhhhhcCCEEEeCCCC-ceeeccCCCHHHHHHHHHHHHHHHHHh
Q 002406 315 QIGVSKEE-----KLQYKEAFPVVICDPSA-QVNLAFRMTSVGFCELQDEAASTLQCM 366 (927)
Q Consensus 315 ~~~~~~~~-----~~~~~~~f~vvf~D~sg-~~Nl~~~~t~~s~~~L~~eA~~tl~~L 366 (927)
-+..++. .......-||+ +||.- +-|+..+ ..+.+++|.+||+..++..
T Consensus 118 -Y~f~~~~v~~~l~~qL~~~RPvI-LDPAdPtnNV~~~-~~~~W~~la~eA~~wl~~~ 172 (190)
T PF10421_consen 118 -YDFEDETVRNYLQSQLKKPRPVI-LDPADPTNNVAGG-NRWCWDLLAQEAAEWLSSP 172 (190)
T ss_dssp ---SSSHHHHHHHHHHHTSSS-EE-B-TT-TT-BTT-S--HHHHHHHHHHHHHHTTSG
T ss_pred -CCCcCHHHHHHHHHhhccCCCce-eCCCCCCCccccC-CccchHHHHHHHHHHhcCc
Confidence 1112222 23445566876 78855 6666655 5689999999999998755
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=66.79 E-value=7 Score=40.83 Aligned_cols=120 Identities=19% Similarity=0.242 Sum_probs=62.3
Q ss_pred hHHHHHHHHHHHhcCCC----CC-CcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCCCCCeEEEeCCCCCC
Q 002406 746 GPVVRVAKRWAASHLFS----AC-LVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDWTFSALVVDINNDFG 820 (927)
Q Consensus 746 ~~tvRLaKRWl~shlLs----~h-i~eE~vELLva~vfl~p~p~~~P~S~~~GFlRfL~lLa~~DW~~~PLiVd~~~~lt 820 (927)
-.-+||+|+|-....-- +. -+.=++|||++|++-+- .-..-.+-.-||--+|.||..+.- -.+.=+-+-++.
T Consensus 45 K~LIrLVKhWy~~~~~~~~~~~~lPpsYaLELLtIyAWE~g-~~~~~F~~a~gfrtVLeLi~~y~~--LcIyWt~~Y~f~ 121 (190)
T PF10421_consen 45 KNLIRLVKHWYQQCKKKKCGGGSLPPSYALELLTIYAWEQG-CGAEDFSTAEGFRTVLELIQKYEQ--LCIYWTVYYDFE 121 (190)
T ss_dssp HHHHHHHHHHHHHHHCC--HTT-S--HHHHHHHHHHHHHHH-T-SSS--HHHHHHHHHHHHHCGGG---EE---SS--SS
T ss_pred HHHHHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHhc-CCCcCcchhhhHhHHHHHHhCcce--eEEEecccCCCc
Confidence 34589999999886543 33 35789999999999764 222334677899888999988652 122223334454
Q ss_pred HHhHHH-HHHHHHHhhhcccccccCCCCeEEEEeCCCCCCCccccCCCCHHHHHHHHHHHHHHHHHHH
Q 002406 821 PEDFKV-INDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRLVAYARSSANLLT 887 (927)
Q Consensus 821 ~~~~~~-i~~~F~~~R~~~~~dp~~~~p~~fIaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~s~~~l~ 887 (927)
.+.+.+ +...+... +| .|-=|-||++... +-...= --.||++|..-+.
T Consensus 122 ~~~v~~~l~~qL~~~-----------RP--vILDPAdPtnNV~---~~~~~~---W~~la~eA~~wl~ 170 (190)
T PF10421_consen 122 DETVRNYLQSQLKKP-----------RP--VILDPADPTNNVA---GGNRWC---WDLLAQEAAEWLS 170 (190)
T ss_dssp SHHHHHHHHHHHTSS-----------S---EEB-TT-TT-BTT----S-HHH---HHHHHHHHHHHTT
T ss_pred CHHHHHHHHHhhccC-----------CC--ceeCCCCCCCccc---cCCccc---hHHHHHHHHHHhc
Confidence 444433 22222222 23 3555667776542 221112 3456666666654
No 28
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=57.81 E-value=32 Score=39.16 Aligned_cols=161 Identities=17% Similarity=0.158 Sum_probs=94.6
Q ss_pred HHHHHHHHHhcCCChhHHHHHHHHHHHhcCCC----CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCC
Q 002406 731 HASMINGLQGRYPVFGPVVRVAKRWAASHLFS----ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDW 806 (927)
Q Consensus 731 h~~~i~~l~~r~paf~~tvRLaKRWl~shlLs----~hi~eE~vELLva~vfl~p~p~~~P~S~~~GFlRfL~lLa~~DW 806 (927)
.+.-|-.|--.-..|..+.|-.|-|....... ++.-.-+--++||.+ .+-+ |-.+..+-..||..+|++|+|
T Consensus 193 VTDeiL~LVP~~~vF~~ALRaIK~WAqRRavYaN~~GfpGGVAwam~VARi-CQLY---PNA~S~vIv~kFF~ils~WnW 268 (552)
T COG5186 193 VTDEILNLVPSVKVFHSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVARI-CQLY---PNASSFVIVCKFFEILSSWNW 268 (552)
T ss_pred ehHHHHHhCCchHHHHHHHHHHHHHHHhhhhhccccCCcchHHHHHHHHHH-Hhhc---cCcchHhHHHHHHHHHHhcCC
Confidence 34444444444445777889999999887653 345667788888887 2322 235667788999999999999
Q ss_pred CCCeEEEeCCCCCCHHhHHHHHHHHHHhhhcccccccCCCCeEEEEeCCCCCCCcccc---CCCCHHHHHHHHHHHHHHH
Q 002406 807 TFSALVVDINNDFGPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTT---CSPNFTELKRLVAYARSSA 883 (927)
Q Consensus 807 ~~~PLiVd~~~~lt~~~~~~i~~~F~~~R~~~~~dp~~~~p~~fIaT~~D~~g~~wT~---~~Ps~~v~~Rl~~LAk~s~ 883 (927)
- +|+|+-+-.+.+-+- .-|-. ..=|+.+..-|=|.||-=|+-.. |. .....+|+.-++.--
T Consensus 269 P-qPviLkPieDgplqv--------rvWnP--KvYpsDk~HRMPvITPAYPSMCA-THNit~STq~vIl~EfvRa~---- 332 (552)
T COG5186 269 P-QPVILKPIEDGPLQV--------RVWNP--KVYPSDKYHRMPVITPAYPSMCA-THNITNSTQHVILMEFVRAH---- 332 (552)
T ss_pred C-CCeEeeeccCCCeeE--------EeeCC--ccCcccccccCccccCCchhhhh-hccccchhhhhHHHHHHHHH----
Confidence 6 888886644433221 01110 01234444566677775544221 22 234466666665433
Q ss_pred HHHHHHhhccCCCcccccccccccCCCCCcccccc
Q 002406 884 NLLTKLILEDQTDSCRWEGQVTLPTSPSFPVRSKQ 918 (927)
Q Consensus 884 ~~l~~~~~~~~~~~~~~~~lF~~pl~~~~~~~~~~ 918 (927)
+.+.+- +. ...+|..||.- .-|+.||+.
T Consensus 333 ~I~~di-~~---n~~~w~~lFek---~DFF~RYk~ 360 (552)
T COG5186 333 KILSDI-ER---NALDWRRLFEK---SDFFSRYKL 360 (552)
T ss_pred HhhhhH-hh---ccccHHHHHHh---hhHHHHHhH
Confidence 333221 11 25789999984 346666653
No 29
>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=57.18 E-value=19 Score=34.55 Aligned_cols=97 Identities=21% Similarity=0.322 Sum_probs=61.2
Q ss_pred HHHHHHHHHhcCCC------CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHHHHHHHhcCCCCCCeEEEeCCCCCCHH
Q 002406 749 VRVAKRWAASHLFS------ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLRFLRLLAEYDWTFSALVVDINNDFGPE 822 (927)
Q Consensus 749 vRLaKRWl~shlLs------~hi~eE~vELLva~vfl~p~p~~~P~S~~~GFlRfL~lLa~~DW~~~PLiVd~~~~lt~~ 822 (927)
|||+|+.+-+.... ..||-=+.|||+++- -||.-+|+-.+ +|+ -|.+||+.+.-+.
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 89999999988763 358889999999875 37889999998 576 5999999732110
Q ss_pred hHHHHHHHHHHhhhcccccccCCCCeEEEEeCCCCCCCccccCCCCHHHHHHHHHHHHHHHHHHH
Q 002406 823 DFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRLVAYARSSANLLT 887 (927)
Q Consensus 823 ~~~~i~~~F~~~R~~~~~dp~~~~p~~fIaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~s~~~l~ 887 (927)
.++ -.-+++|.-|-|+.- +--..+-++++..+.-+|-..++
T Consensus 65 -----------~~~--------f~~PlvviDPvDp~R-----NVAAalS~~~~~~fv~~ar~fl~ 105 (114)
T PF09249_consen 65 -----------SKK--------FDDPLVVIDPVDPNR-----NVAAALSLENLAEFVHAAREFLK 105 (114)
T ss_dssp ------------EE--------E-SS-EEEETTEEEE-----ETTTTS-HHHHHHHHHHHHHHHH
T ss_pred -----------hhh--------cCCCeEEcCCCCCCc-----hHhHhcCHHHHHHHHHHHHHHHH
Confidence 011 124688888999874 33344555666665555555553
No 30
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=52.65 E-value=13 Score=34.67 Aligned_cols=29 Identities=28% Similarity=0.463 Sum_probs=23.9
Q ss_pred ceeeEeeeeecccccCCCCceeEEEecCcc
Q 002406 81 KTFKIGGSYSINCVVKPAVNVDLFVGLPKE 110 (927)
Q Consensus 81 ~~v~vvGS~~l~t~~k~~~~VDl~V~mP~~ 110 (927)
+++.|.|||+ +.-.+|+..||++|+.=..
T Consensus 25 ~~~~vFGS~a-RgE~~~~SDIDILVef~~~ 53 (97)
T COG1669 25 KRVAVFGSYA-RGEQKPDSDIDILVEFEPG 53 (97)
T ss_pred ceEEEeeeee-cCCCCCCCCceeEEeecCC
Confidence 4688999999 5568889999999987554
No 31
>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=43.29 E-value=27 Score=28.18 Aligned_cols=27 Identities=19% Similarity=0.140 Sum_probs=21.5
Q ss_pred CCceeeEeeeeecccccCCCCceeEEEe
Q 002406 79 KPKTFKIGGSYSINCVVKPAVNVDLFVG 106 (927)
Q Consensus 79 ~P~~v~vvGS~~l~t~~k~~~~VDl~V~ 106 (927)
.+..+-+.|||+-|+ .++...||++|.
T Consensus 16 ~~~~v~lfGS~arg~-~~~~SDIDi~v~ 42 (49)
T cd05397 16 PGYEIVVYGSLVRGL-LKKSSDIDLACV 42 (49)
T ss_pred CCcEEEEECCcCCCC-CCCCCCEEEEEE
Confidence 356788999999876 466778999986
No 32
>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=41.50 E-value=32 Score=30.41 Aligned_cols=32 Identities=22% Similarity=0.268 Sum_probs=25.8
Q ss_pred CCceeeEeeeeecccccCCCCceeEEEecCccc
Q 002406 79 KPKTFKIGGSYSINCVVKPAVNVDLFVGLPKEC 111 (927)
Q Consensus 79 ~P~~v~vvGS~~l~t~~k~~~~VDl~V~mP~~~ 111 (927)
....|-+.||++-|... +...||++|.++...
T Consensus 17 ~i~~i~LfGS~arg~~~-~~SDiDl~vi~~~~~ 48 (93)
T cd05403 17 GVEKVYLFGSYARGDAR-PDSDIDLLVIFDDPL 48 (93)
T ss_pred CccEEEEEeeeecCCCC-CCCCeeEEEEeCCCC
Confidence 35678899999998765 677899999998764
No 33
>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]
Probab=35.09 E-value=2.2e+02 Score=34.25 Aligned_cols=91 Identities=18% Similarity=0.250 Sum_probs=60.7
Q ss_pred HHHHHHhhhcCcccccccCCCCeEEEEeccCCcccccchHHHHHHHHHHHcCCCCCCcEEEecccchhhhccCCCCccch
Q 002406 488 EALRFRKFWGEKAELRRFKDGTIAESTVWESEQWTRHLILKGIIEYVLLRHLSLSKENVVQIVDQLDFSLLHGAKDLVSF 567 (927)
Q Consensus 488 eA~~FR~FWG~KsELRRFkDGsI~EsVvW~~~~~~r~~I~~~Iv~yiL~~H~~i~~~~i~~~~~~~d~~l~~~~~~~~~~ 567 (927)
.|.+|++|||+-- |=--+.---+|-+.|+... +.-.+.+++-+|+.|..-.+.+|-.+ . ++
T Consensus 202 ~a~Kfq~yf~n~P-ll~vpg~~PvEi~Yt~e~e---rDylEaairtV~qih~~ee~GDilvF------L---------tg 262 (699)
T KOG0925|consen 202 DAEKFQRYFGNAP-LLAVPGTHPVEIFYTPEPE---RDYLEAAIRTVLQIHMCEEPGDILVF------L---------TG 262 (699)
T ss_pred chHHHHHHhCCCC-eeecCCCCceEEEecCCCC---hhHHHHHHHHHHHHHhccCCCCEEEE------e---------cC
Confidence 4789999999742 1122233456778887654 35678999999999997444444432 1 13
Q ss_pred HHHHHHHHHHHHHHHhccC--CCCeeeeeccc
Q 002406 568 SASLLEAFEVLSKRLHLIE--DIPLKISSVQP 597 (927)
Q Consensus 568 ~~~v~~af~~L~k~Lr~L~--~LPL~I~~V~p 597 (927)
.+.+-+|...+.+..-+|. ..||+|.-+.|
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 3456678888888887773 78888776664
No 34
>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=32.17 E-value=30 Score=30.84 Aligned_cols=31 Identities=23% Similarity=0.300 Sum_probs=25.7
Q ss_pred CceeeEeeeeecccccCCCCceeEEEecCccc
Q 002406 80 PKTFKIGGSYSINCVVKPAVNVDLFVGLPKEC 111 (927)
Q Consensus 80 P~~v~vvGS~~l~t~~k~~~~VDl~V~mP~~~ 111 (927)
...|-+.||++-|+.. +...||++|..+...
T Consensus 14 ~~~v~lfGS~a~g~~~-~~SDIDl~i~~~~~~ 44 (93)
T PF01909_consen 14 VAEVYLFGSYARGDAT-PDSDIDLLIILDEPE 44 (93)
T ss_dssp TEEEEEEHHHHHTSSC-TTSCEEEEEEESSTS
T ss_pred CCEEEEECCcccCcCC-CCCCEEEEEEeCCcc
Confidence 5678899999998754 458999999999875
No 35
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=29.83 E-value=3.5e+02 Score=33.05 Aligned_cols=134 Identities=14% Similarity=0.145 Sum_probs=86.8
Q ss_pred HHhhChHHHHHHHHHHHHHHHhcCCCc-cCCCch-hHHHHHHHHHHhhccc-----------------------------
Q 002406 232 KTISRWKELGEALILLKVWARQRSSIY-VHDCLN-GYLISILLSYLVSLDK----------------------------- 280 (927)
Q Consensus 232 ~~~~~~~~f~dA~~LlkvWl~QRg~~~-~~~gf~-gf~~s~lla~Ll~~~~----------------------------- 280 (927)
.....-+.|+-.|.++|.|+..++... ..|+++ .+.+++++.|-+|+..
T Consensus 254 ~~~~~d~r~~~L~~~vk~wa~~~~~~d~~~g~~~s~ysl~lmvi~fLq~~~~~ilp~l~~l~~~~~~~~~~~~~~~~~~~ 333 (596)
T KOG2277|consen 254 NYSEIDPRVRPLVLLVKHWAKEKGLNDAKPGGLNSSYSLTLMVIHFLQTLSPPILPPLSKLLPESDSNDKPVVKKKVLCS 333 (596)
T ss_pred HhHhcCCCcchHhHHHHHHHHhccCCCCCCCceeccccHHHHHHHHHHhcCCcCCCchhhhchhcccccccchhhhhhhc
Confidence 334444699999999999999999654 457787 5888888888776210
Q ss_pred ----------cCcCCcHH-HHHHHHHHHHh-cCCCCCCceeecCCCCCCCChhHHHhhhhcCCEEEeCCCC-ceeeccCC
Q 002406 281 ----------INNSMKAL-QILRVVLDFIA-TSKLWNRGLYFPPKGQIGVSKEEKLQYKEAFPVVICDPSA-QVNLAFRM 347 (927)
Q Consensus 281 ----------l~~~~Ssy-Qifr~~l~fLa-~~d~~~~~i~~~~~~~~~~~~~~~~~~~~~f~vvf~D~sg-~~Nl~~~~ 347 (927)
.....+++ .++-+++.|.+ .-|+.++.|.+..... .... ...+. ..+..+-||-. ..|+-..+
T Consensus 334 ~~~~~~~~~~~~~~~~~l~~l~~~f~~yy~~~Fdf~~~~I~~r~~~~--l~~~-~~~~~-~~~l~i~dp~~~~~n~~~~~ 409 (596)
T KOG2277|consen 334 FLRVFQRNPSNSQNTGSLGELLLGFFSYYASLFDFRKNAISIRRGRA--LKRA-KKIKS-KKFLCIEDPFEVSHNADAGV 409 (596)
T ss_pred cccccccccccccccchHHHHHHHHHHHHhhhcccccceeeeeeccc--cccc-chhhh-ccceeeccccccccCccccc
Confidence 11222222 35667777878 6788777776654321 1100 00111 22333456544 45888999
Q ss_pred CHHHHHHHHHHHHHHHHHhhcc
Q 002406 348 TSVGFCELQDEAASTLQCMDKC 369 (927)
Q Consensus 348 t~~s~~~L~~eA~~tl~~L~~~ 369 (927)
+.-....++.+.+.+...+.+.
T Consensus 410 ~~~~~~~i~~~~~~~~~~~~~~ 431 (596)
T KOG2277|consen 410 TLKVLLLIQDEFQESRRVFKDV 431 (596)
T ss_pred hHHHHHHHHHHHHHHHHHhhhh
Confidence 9999999999999999988764
No 36
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=27.86 E-value=42 Score=31.93 Aligned_cols=75 Identities=13% Similarity=0.117 Sum_probs=41.0
Q ss_pred chHHHHHHHHHHHcCCCCCCcEEEecccchhhhccCCCCccchHHHHHHHHHHHHHHHhccCCCCeeeeecccCCccccc
Q 002406 525 LILKGIIEYVLLRHLSLSKENVVQIVDQLDFSLLHGAKDLVSFSASLLEAFEVLSKRLHLIEDIPLKISSVQPLDSAFRF 604 (927)
Q Consensus 525 ~I~~~Iv~yiL~~H~~i~~~~i~~~~~~~d~~l~~~~~~~~~~~~~v~~af~~L~k~Lr~L~~LPL~I~~V~p~sp~lRy 604 (927)
.+-++++.|+|++|+|+.-++-.+..+..-......+. ...+|-|.|..+- .|.-+==.=-+.++-||+++-
T Consensus 20 ~vWQ~llt~LL~~HYGLtLNDT~f~de~vI~~hidaGI-------s~~~AVN~LVeKY-~LvRiD~~gFs~~~qsP~l~~ 91 (114)
T PF06755_consen 20 EVWQQLLTYLLEQHYGLTLNDTPFSDETVIQEHIDAGI-------SPADAVNFLVEKY-ELVRIDRNGFSWQEQSPYLTA 91 (114)
T ss_pred HHHHHHHHHHHHHhcCCccCCCccchHHHHHHHHHhCC-------CHHHHHHHHHHHH-hhhhcCCcccCccCCCchhhH
Confidence 36689999999999998866655432211111111111 2445666666543 221111122255778888877
Q ss_pred ccC
Q 002406 605 TSV 607 (927)
Q Consensus 605 tsv 607 (927)
.++
T Consensus 92 ~Di 94 (114)
T PF06755_consen 92 IDI 94 (114)
T ss_pred HHH
Confidence 765
No 37
>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=24.86 E-value=31 Score=34.91 Aligned_cols=27 Identities=44% Similarity=0.833 Sum_probs=18.8
Q ss_pred HHHHHHHHHHhcCCCCCCcHHHHHHHHHHhhcCCCCC
Q 002406 748 VVRVAKRWAASHLFSACLVEEAVELLVAYLFLKPLPF 784 (927)
Q Consensus 748 tvRLaKRWl~shlLs~hi~eE~vELLva~vfl~p~p~ 784 (927)
+||| |||+.++-...+| | |+.-+|.||
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 9999998655433 2 555677776
No 38
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=24.37 E-value=5.1e+02 Score=30.66 Aligned_cols=226 Identities=19% Similarity=0.232 Sum_probs=132.3
Q ss_pred HHHHHHHHHHHHHHHhccC-CCCeeeeecccCCcccccccCCCCCCCCCccccccccccCCCCCCccCcEEEEEEeccCC
Q 002406 568 SASLLEAFEVLSKRLHLIE-DIPLKISSVQPLDSAFRFTSVFPPEPHPLANERHTVSRLHKLTPSCIQPLEVMIQLEGSG 646 (927)
Q Consensus 568 ~~~v~~af~~L~k~Lr~L~-~LPL~I~~V~p~sp~lRytsv~pp~p~~~~~~~~~~~~~~~~~p~~~~pi~vvlqfE~Sg 646 (927)
...+...-++|...+.++- ++++ ...|-=+.++-|.|=+- .+ .=|||-|-|
T Consensus 21 ~~~~~~~~e~l~~~~~~~~~e~~~-~aev~lVGS~AkgTwL~--------gd---------------~DIDvFi~F---- 72 (443)
T COG1746 21 RKKLKEVAEELRERINEIIEELGI-DAEVVLVGSYAKGTWLR--------GD---------------HDIDVFIAF---- 72 (443)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCC-cceEEEEeecccCcccC--------CC---------------cceeEEEEC----
Confidence 4467777788888887773 4555 33444455556666431 00 135777766
Q ss_pred CCCCC--HHHHHHHHHHHHHHHHHHHhhcc-CCeeeecCCceeeeccceeEEEEEeccchhHHHhhhcccccccccchhh
Q 002406 647 NWPMD--HVAIEKTKSAFLIKIGESLQNRW-GMTCSATEDDADIFMSGYAFRLKILHERGLSLVKSENGNKAKRVYSTDK 723 (927)
Q Consensus 647 kWPdd--l~AIq~~K~AF~lkIae~L~~~~-~~~~~v~~d~lDV~~~G~~FRl~I~~~rE~~Ll~~~~~~~~~~~~~~~~ 723 (927)
|.| .+-+++. -+.|+...-+.. +-...+..-|+-...+||--=+.-+|.-|-. . +. +...++
T Consensus 73 --p~d~~~eel~~~----GL~ig~~~l~~~~~~~~YAeHPYV~g~v~G~eVDvVPCy~v~~~------~-~~--~sAVDR 137 (443)
T COG1746 73 --PKDTSEEELEEK----GLEIGREVLKRGNYEERYAEHPYVTGEVDGYEVDVVPCYKVEDG------E-KI--ISAVDR 137 (443)
T ss_pred --CCCCCHHHHHHH----HHHHHHHHhcCCchhhhhccCCeeEEEEccEEEEEEecccccCc------c-cc--cccccC
Confidence 444 4443332 234444443321 1112233445667777876666666653211 1 11 111122
Q ss_pred hHHHhhhHHHHHHH-HHhcCCChhHHHHHHHHHHHhcCCC------CCCcHHHHHHHHHHhhcCCCCCCCCCchhhHHHH
Q 002406 724 ILFIRGQHASMING-LQGRYPVFGPVVRVAKRWAASHLFS------ACLVEEAVELLVAYLFLKPLPFNVPCSRVTGFLR 796 (927)
Q Consensus 724 ~~~~~p~h~~~i~~-l~~r~paf~~tvRLaKRWl~shlLs------~hi~eE~vELLva~vfl~p~p~~~P~S~~~GFlR 796 (927)
.|.||..+.+ |-.+-- -=|||+|+.+-+-... ..||-=+.|||+.+- -+|.-
T Consensus 138 ----TplHt~yv~e~L~~~~~---deVrLLK~FlK~iGvYGaE~rt~GFSGYL~ELLII~y--------------GsFe~ 196 (443)
T COG1746 138 ----TPLHTRYVEEHLKGRQK---DEVRLLKQFLKGIGVYGAELRTQGFSGYLCELLIIHY--------------GSFEN 196 (443)
T ss_pred ----cchhHHHHHHHhcccch---hHHHHHHHHHhccCccceeeeeccchHHHHHHHHhhh--------------ccHHH
Confidence 2568877655 222211 4799999999987763 358888999999774 25777
Q ss_pred HHHHHhcCCCCCCeEEEeCCCCCCHHhHHHHHHHHHHhhhcccccccCCCCeEEEEeCCCCCCCccccCCCCHHHHHHHH
Q 002406 797 FLRLLAEYDWTFSALVVDINNDFGPEDFKVINDNFMSSRKASEENVQNVNPALFLATAYDKASEAWTTCSPNFTELKRLV 876 (927)
Q Consensus 797 fL~lLa~~DW~~~PLiVd~~~~lt~~~~~~i~~~F~~~R~~~~~dp~~~~p~~fIaT~~D~~g~~wT~~~Ps~~v~~Rl~ 876 (927)
+|+--++ |+- |.+||+.+- .|... .--+|+|.-|-||.- +--.++-++|+.
T Consensus 197 vl~~a~~--wrp-~~~ID~~~~---------------~~e~f------~d~PliVvDPVDP~R-----NVAAalSl~~la 247 (443)
T COG1746 197 VLKAASR--WRP-GKIIDLEGH---------------KRERF------EDEPLIVVDPVDPKR-----NVAAALSLENLA 247 (443)
T ss_pred HHHHHhc--cCC-CeEEeccch---------------hhhcc------CCCCeEecCCCCCcc-----chhhhcCHHHHH
Confidence 7777776 874 499999754 12111 112799999999984 434556777777
Q ss_pred HHHHHHHHHH
Q 002406 877 AYARSSANLL 886 (927)
Q Consensus 877 ~LAk~s~~~l 886 (927)
.+--+|-..|
T Consensus 248 ~f~~aar~FL 257 (443)
T COG1746 248 RFVHAAREFL 257 (443)
T ss_pred HHHHHHHHHh
Confidence 7777776766
Done!