Query 004767
Match_columns 732
No_of_seqs 252 out of 721
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 12:34:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004767.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004767hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2245 Poly(A) polymerase and 100.0 2E-142 4E-147 1158.0 41.4 481 5-495 11-502 (562)
2 PTZ00418 Poly(A) polymerase; P 100.0 4E-135 1E-139 1136.4 53.4 512 7-527 50-573 (593)
3 COG5186 PAP1 Poly(A) polymeras 100.0 1E-123 2E-128 978.3 35.9 482 6-494 4-531 (552)
4 PF04928 PAP_central: Poly(A) 100.0 6.9E-73 1.5E-77 586.0 22.2 253 7-357 2-254 (254)
5 COG5260 TRF4 DNA polymerase si 100.0 3.1E-30 6.8E-35 282.9 24.5 261 26-340 56-342 (482)
6 PF04926 PAP_RNA-bind: Poly(A) 100.0 1.6E-31 3.6E-36 258.2 9.1 133 358-491 1-155 (157)
7 KOG1906 DNA polymerase sigma [ 100.0 5.5E-28 1.2E-32 270.0 24.2 267 21-340 57-341 (514)
8 cd05402 NT_PAP_TUTase Nucleoti 99.8 1.6E-18 3.6E-23 158.0 13.3 98 49-163 1-101 (114)
9 KOG2277 S-M checkpoint control 99.7 6.8E-17 1.5E-21 184.8 20.3 250 42-341 127-431 (596)
10 TIGR03671 cca_archaeal CCA-add 99.6 7.1E-12 1.5E-16 138.4 33.1 341 33-454 4-363 (408)
11 PRK13300 tRNA CCA-pyrophosphor 99.5 5.8E-12 1.3E-16 140.7 30.9 343 32-454 4-366 (447)
12 PF03813 Nrap: Nrap protein; 99.1 1.1E-08 2.4E-13 124.6 27.6 288 91-398 1-363 (972)
13 COG1746 CCA1 tRNA nucleotidylt 99.1 3.5E-08 7.6E-13 108.8 27.9 345 29-454 5-367 (443)
14 KOG2054 Nucleolar RNA-associat 98.4 5.5E-06 1.2E-10 98.9 16.0 269 83-372 147-464 (1121)
15 smart00572 DZF domain in DSRM 98.3 4.1E-05 8.8E-10 80.3 18.1 213 86-338 5-229 (246)
16 PF03828 PAP_assoc: Cid1 famil 97.7 2.9E-05 6.4E-10 63.6 2.8 55 254-312 1-59 (60)
17 cd05400 NT_2-5OAS_ClassI-CCAas 97.6 0.00053 1.1E-08 65.1 11.1 77 83-162 27-110 (143)
18 cd05397 NT_Pol-beta-like Nucle 97.5 0.00019 4E-09 57.5 4.8 26 83-108 17-42 (49)
19 PF01909 NTP_transf_2: Nucleot 97.3 0.00032 6.9E-09 61.2 4.3 32 83-114 14-45 (93)
20 PF09249 tRNA_NucTransf2: tRNA 96.7 0.0044 9.4E-08 58.3 6.9 93 214-328 3-97 (114)
21 cd05403 NT_KNTase_like Nucleot 96.7 0.0031 6.8E-08 54.4 5.5 31 84-114 19-49 (93)
22 PF03813 Nrap: Nrap protein; 96.2 0.043 9.2E-07 68.1 13.5 155 193-356 668-839 (972)
23 PF14091 DUF4269: Domain of un 95.9 0.088 1.9E-06 52.1 11.3 117 86-229 18-144 (152)
24 COG1669 Predicted nucleotidylt 95.5 0.052 1.1E-06 50.0 7.3 46 51-112 8-53 (97)
25 PF07528 DZF: DZF domain; Int 95.2 0.83 1.8E-05 48.6 16.5 209 89-338 2-231 (248)
26 COG1708 Predicted nucleotidylt 93.8 0.098 2.1E-06 47.5 5.0 28 83-110 26-53 (128)
27 PRK13746 aminoglycoside resist 93.6 0.13 2.9E-06 54.9 6.1 31 85-115 30-60 (262)
28 PF10421 OAS1_C: 2'-5'-oligoad 92.0 0.38 8.3E-06 49.2 6.7 47 207-253 41-88 (190)
29 PRK02098 phosphoribosyl-dephos 90.2 0.57 1.2E-05 49.1 6.0 33 83-115 120-158 (221)
30 cd00141 NT_POLXc Nucleotidyltr 89.8 4 8.7E-05 44.5 12.4 113 82-234 159-277 (307)
31 TIGR03135 malonate_mdcG holo-A 89.3 0.69 1.5E-05 47.7 5.7 33 83-115 108-146 (202)
32 cd05401 NT_GlnE_GlnD_like Nucl 83.9 4.4 9.6E-05 39.8 7.9 48 82-129 54-101 (172)
33 COG1665 Predicted nucleotidylt 83.3 0.26 5.7E-06 52.9 -1.0 27 86-112 124-150 (315)
34 PF14792 DNA_pol_B_palm: DNA p 82.8 2.2 4.8E-05 39.9 5.0 53 82-135 23-78 (112)
35 KOG2054 Nucleolar RNA-associat 79.0 11 0.00023 47.2 10.1 122 195-323 806-936 (1121)
36 COG2844 GlnD UTP:GlnB (protein 77.5 7.6 0.00016 47.6 8.3 56 55-114 42-97 (867)
37 KOG3793 Transcription factor N 74.2 1.3E+02 0.0027 33.1 15.3 212 24-268 38-264 (362)
38 PF03445 DUF294: Putative nucl 74.1 18 0.00039 34.9 8.5 48 82-129 48-96 (138)
39 PRK05007 PII uridylyl-transfer 69.4 16 0.00035 45.6 8.7 57 53-113 54-110 (884)
40 PF10620 MdcG: Phosphoribosyl- 66.2 9.4 0.0002 39.7 5.0 40 83-123 116-161 (213)
41 PRK00227 glnD PII uridylyl-tra 64.8 16 0.00034 44.5 7.1 65 48-128 6-70 (693)
42 PRK03059 PII uridylyl-transfer 64.1 14 0.00031 45.9 6.8 54 52-111 36-89 (856)
43 KOG2534 DNA polymerase IV (fam 61.7 32 0.00069 38.3 8.1 50 81-131 169-218 (353)
44 PRK01759 glnD PII uridylyl-tra 60.7 27 0.00059 43.4 8.4 56 53-112 30-85 (854)
45 PRK08609 hypothetical protein; 59.1 59 0.0013 38.7 10.4 109 82-234 174-283 (570)
46 PF03710 GlnE: Glutamate-ammon 56.7 96 0.0021 32.8 10.6 47 83-129 127-179 (247)
47 PF10127 Nuc-transf: Predicted 56.0 9.6 0.00021 39.9 3.0 26 85-110 22-47 (247)
48 PRK01293 phosphoribosyl-dephos 56.0 27 0.00058 36.5 6.1 44 83-128 109-158 (207)
49 PF09970 DUF2204: Nucleotidyl 52.4 51 0.0011 33.4 7.4 76 83-164 16-95 (181)
50 smart00483 POLXc DNA polymeras 52.3 1.6E+02 0.0035 32.6 11.9 30 82-112 163-192 (334)
51 PRK03381 PII uridylyl-transfer 47.8 55 0.0012 40.4 8.0 29 83-111 57-85 (774)
52 PRK04374 PII uridylyl-transfer 46.5 63 0.0014 40.5 8.3 29 83-111 72-100 (869)
53 PRK00275 glnD PII uridylyl-tra 46.5 67 0.0014 40.4 8.6 32 82-113 77-108 (895)
54 PF03281 Mab-21: Mab-21 protei 45.9 4E+02 0.0086 28.4 16.4 97 207-333 190-289 (292)
55 COG2413 Predicted nucleotidylt 43.6 47 0.001 34.9 5.5 27 85-111 39-65 (228)
56 PHA02603 nrdC.11 hypothetical 42.5 15 0.00033 40.8 2.1 24 86-109 6-29 (330)
57 TIGR01693 UTase_glnD [Protein- 42.4 79 0.0017 39.3 8.3 31 82-112 42-72 (850)
58 PF12633 Adenyl_cycl_N: Adenyl 41.1 30 0.00066 36.1 3.8 30 84-114 98-128 (204)
59 PRK14109 bifunctional glutamin 34.3 86 0.0019 39.9 7.0 48 82-129 722-773 (1007)
60 COG3541 Predicted nucleotidylt 32.6 21 0.00046 38.2 1.2 18 89-106 16-33 (248)
61 COG1796 POL4 DNA polymerase IV 32.0 76 0.0016 35.4 5.2 71 84-163 181-251 (326)
62 PF10281 Ish1: Putative stress 31.8 37 0.00081 25.8 2.1 31 28-59 6-36 (38)
63 PF07357 DRAT: Dinitrogenase r 31.5 19 0.00042 38.8 0.6 21 373-393 95-115 (262)
64 PRK14109 bifunctional glutamin 29.4 1.6E+02 0.0036 37.5 8.3 48 82-129 214-265 (1007)
65 COG1391 GlnE Glutamine synthet 26.4 4E+02 0.0087 33.9 10.4 45 85-129 173-225 (963)
66 PRK05092 PII uridylyl-transfer 24.6 2.1E+02 0.0045 36.2 7.9 29 83-111 105-133 (931)
67 PRK11072 bifunctional glutamin 24.2 2E+02 0.0043 36.6 7.6 48 82-129 153-208 (943)
68 PF04439 Adenyl_transf: Strept 23.7 53 0.0012 35.7 2.3 79 86-164 24-108 (282)
69 PRK11072 bifunctional glutamin 23.5 2E+02 0.0044 36.5 7.5 59 70-129 667-736 (943)
No 1
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=100.00 E-value=1.6e-142 Score=1157.98 Aligned_cols=481 Identities=59% Similarity=1.022 Sum_probs=462.2
Q ss_pred CCccccccCCCCCCCCChHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCc
Q 004767 5 NGQRLGITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANA 84 (732)
Q Consensus 5 ~~~~~Gvt~Pis~~~Pt~~D~~~t~eL~~~L~~~~l~pS~eE~~~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~ 84 (732)
.++.||||+|||+++||++|.++|.+|+++|+++|+||++||..+|++||++|++||++||+++++++|++++++.+++|
T Consensus 11 ~~~~~Gvt~PiS~a~p~~~d~~lt~~L~~~L~~~g~fEs~eEt~~R~~VL~~L~~iVk~wVk~vs~~k~~p~~~~~~agg 90 (562)
T KOG2245|consen 11 STKSYGVTQPISTAGPTEADIALTQELIKTLKNEGLFESKEETQRREEVLGKLNQIVKEWVKKVSEQKGLPDGMIENAGG 90 (562)
T ss_pred ccccccccCCcccCCCcHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhhhhhcCc
Confidence 35899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeeeeecCCCCCCCCceEEeecCCCCCchhhHHHHHHHHHhcCCCceeeEeecCCcccEEEEEecCeeeeEEeeecc
Q 004767 85 KIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLS 164 (732)
Q Consensus 85 kI~~FGSy~lGv~~p~SDID~lcv~P~~v~r~~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~ 164 (732)
+|+||||||||||+||||||+|||+|+|++|+ |||..|.++|+++++|++|++|++|+||||||+|+||+|||+||+++
T Consensus 91 kIftfGSYRLGVhg~GADIDtLcV~Prhv~R~-DFF~sf~~mL~~~~eVteL~~V~dAfVPiikfKf~GI~IDllfArL~ 169 (562)
T KOG2245|consen 91 KIFTFGSYRLGVHGPGADIDTLCVGPRHVSRS-DFFTSFYDMLKERPEVTELHAVEDAFVPIIKFKFDGIEIDLLFARLA 169 (562)
T ss_pred eEEeccceeecccCCCCCcceeeeccccccHH-HHHHHHHHHHhcCccccccccccccccceEEEEecCeeeeeeehhcc
Confidence 99999999999999999999999999999995 99999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCCchhhhccchhhhhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCcChHHHHHHHH
Q 004767 165 LWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVA 244 (732)
Q Consensus 165 ~~~ip~~ldl~~~~lL~~lde~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~LGG~swalLVa 244 (732)
+++||+++||+|+++|+++||+|+||||||||||+||+|||+.+.||.+|||||+|||+||||+|.+|||||++||||||
T Consensus 170 l~~VP~dldl~ddslLknlDe~~vrSLNGcRVtdqiL~LVPn~~~F~~tLRaiKlWAKrrgVYsN~~GF~GGV~wA~LVA 249 (562)
T KOG2245|consen 170 LPVVPEDLDLSDDSLLKNLDERCVRSLNGCRVTDQILKLVPNQENFRITLRAIKLWAKRRGVYSNVMGFLGGVAWAMLVA 249 (562)
T ss_pred cccCCCcccccchHhhhcccHHHHHHhcCcCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcccccccccccchHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhCCCCCHHHHHHHHHHHhccCCCCCceeecccccCCCCccccCCCCCCCCCCCceeEeCCCCCCCCcccccChhhH
Q 004767 245 RICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTL 324 (732)
Q Consensus 245 ~vcQlyPnas~~~LL~~FF~~Ys~wdW~~pV~l~~i~~G~l~~~vWdP~~~~~dr~hlMpIiTP~~P~~Nsa~NVs~sTl 324 (732)
|+||+||||++++|+.+||.+|++|+||+||+|+.+++|.++++||||+.|+.||||+|||||||||+||+|||||+||+
T Consensus 250 RiCQLYPNA~~s~Lv~kfF~ifs~W~WP~PVlL~~ie~~~L~~~VWdPr~n~~DryHlMPIITPAyP~~nsthNVS~ST~ 329 (562)
T KOG2245|consen 250 RICQLYPNASPSTLVAKFFRVFSQWNWPNPVLLKPIEEGNLNLPVWDPRVNPSDRYHLMPIITPAYPQMNSTHNVSRSTL 329 (562)
T ss_pred HHHccCCCcchHHHHHHHHHHHhhccCCCceEeccccccccCccccCCCCCCCCcceecccccCCcccccccccccHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhccCCCCcccccCCcchhhhccceEEEEeeecChhhhhhhhhHHHHHHHHHHHHHhhccccc
Q 004767 325 RIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNM 404 (732)
Q Consensus 325 ~vI~~EF~RA~~Il~~i~~~~~~~~W~~Lfep~~Ff~~Yk~yL~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~ 404 (732)
++|.+||+||++||++|+.++. +|.+|||+++||.+|||||+|+++|.++|++.+|.||||||+|+|+.+||++ ..+
T Consensus 330 ~Vi~~Ef~~g~~I~~~i~~~k~--~W~~LFE~~~FF~rYk~yl~i~~~A~~~ed~l~w~G~vESriR~Lv~klE~~-~~i 406 (562)
T KOG2245|consen 330 KVITEEFKRGLEICDDIELNKL--DWSDLFELYNFFSRYKHYLQITASAATEEDLLKWVGWVESRIRQLVLKLERN-QVI 406 (562)
T ss_pred HHHHHHHHHHHHHHHHHHhccc--cHHHHhhhhHHHHHHhhHheeeeeccChHHHhhhhhHHHHHHHHHHHHHHhh-cce
Confidence 9999999999999999999998 9999999999999999999999999999999999999999999999999996 467
Q ss_pred eeeccCCCCCCCCCC-----CceEEEEEeeEecCCCCCCCCcccchHHHHHHHHHHHH----hhccCCCC--cEEEEEEe
Q 004767 405 LQCHPHPGDFSDKSK-----PLYCSYFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVS----MYTLRKPG--MQISVAHV 473 (732)
Q Consensus 405 l~~hp~P~~f~~~~~-----~~~~~ffIGL~~~~~~~~~~~~~~Dl~~~v~eF~~~v~----~~~~~~~~--m~i~v~~v 473 (732)
+.|||+|+.|.++.. .|...+||||...+. .++||+..+++|...++ .++.++.| |++.+.|+
T Consensus 407 ~~ahp~P~~f~~~~~~~~~~~~~~~~~igl~~~e~------~~~Dlt~~iq~f~~~v~~q~~~~~~~~~g~~~~~~~~~~ 480 (562)
T KOG2245|consen 407 LIAHPNPKKFKDTYNCPLEEDPESLWFIGLEFDEN------VKIDLTKDIQSFKKNVERQAVNLTLIKAGCDVEIDFGHV 480 (562)
T ss_pred EEecCCcccccccccCCcccchhHhhhhccccccc------ccchhhhhHHHhhhhhhhcceeeeeeecccccccccccc
Confidence 899999999987642 356679999987653 34999999999999888 67778899 77888899
Q ss_pred cCCCCCCccCCCCCCCCCCCCC
Q 004767 474 TRRNLPNFVFPGGVRPSRPSKG 495 (732)
Q Consensus 474 kr~~LP~~v~~~~~~~~~~~~~ 495 (732)
||++|+.++++...+..|..+.
T Consensus 481 krr~l~~~~~~~~l~~~k~~~~ 502 (562)
T KOG2245|consen 481 KRRSLIQTITKEFLRLCKQYKK 502 (562)
T ss_pred cccccccccCHHHhhHHHhhcc
Confidence 9999999999998888775553
No 2
>PTZ00418 Poly(A) polymerase; Provisional
Probab=100.00 E-value=4.4e-135 Score=1136.38 Aligned_cols=512 Identities=44% Similarity=0.828 Sum_probs=472.7
Q ss_pred ccccccCCCCCCCCChHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEE
Q 004767 7 QRLGITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKI 86 (732)
Q Consensus 7 ~~~Gvt~Pis~~~Pt~~D~~~t~eL~~~L~~~~l~pS~eE~~~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI 86 (732)
..||||+|||+++||++|++.+++|+++|+++|+|||+||.++|++||++|+++|++|+++++.++|++++++.+++++|
T Consensus 50 ~~~Gvt~Pis~~~Pt~~d~~~s~~L~~~L~~~~~fes~ee~~kR~~vL~~L~~iv~~wv~~vs~~k~~~~~~~~~~~g~I 129 (593)
T PTZ00418 50 LSYGVTDPISLNGPTEEDLKLSNELINLLKSYNLYETEEGKKKRERVLGSLNKLVREFVVEASIEQGINEEEASQISGKL 129 (593)
T ss_pred cccCCCCCccCCCCChHHHhhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhHHhcCCeEE
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeeeecCCCCCCCCceEEeecCCCCCchhhHHHHHHHHHhcCCCceeeEeecCCcccEEEEEecCeeeeEEeeecccc
Q 004767 87 FTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLW 166 (732)
Q Consensus 87 ~~FGSy~lGv~~p~SDID~lcv~P~~v~r~~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~ 166 (732)
+|||||+||||+|+||||+|||+|.|++|+ +||..|+++|+++++|++|++|++|+||||||+++||+|||+||+++..
T Consensus 130 ~tfGSYrLGV~~pgSDID~L~V~P~~vtre-dFF~~f~~~L~~~~~V~eL~~V~~A~VPiIk~~~~GI~iDL~fa~l~~~ 208 (593)
T PTZ00418 130 FTFGSYRLGVVAPGSDIDTLCLAPRHITRE-SFFSDFYAKLQQDPNITKLQPVPDAYTPVIKFVYDGIDIDLLFANLPLP 208 (593)
T ss_pred EEeccccccCCCCCCcccEEEECCCCCCHH-HHHHHHHHHHhcCCCcceeeccCccccCeEEEEECCEEEeeeecccCCC
Confidence 999999999999999999999999999995 9999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCchh-hhccchhhhhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCcChHHHHHHHHH
Q 004767 167 VIPEDLDISQDS-ILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVAR 245 (732)
Q Consensus 167 ~ip~~ldl~~~~-lL~~lde~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~LGG~swalLVa~ 245 (732)
.||+++++.+++ +|+++|++++|||||+||+|+|+++||+.+.||.+|||||+|||+||||+|++||||||+|||||||
T Consensus 209 ~vp~~~~~l~d~~lL~nlde~s~rSLNG~Rvtd~Il~lVPn~~~Fr~aLR~IKlWAkrRGIYsNv~GflGGV~wAILvAR 288 (593)
T PTZ00418 209 TIPDCLNSLDDDYILRNVDEKTVRSLNGCRVADLILASVPNKDYFRTTLRFIKLWAKRRGIYSNVLGYLGGVSWAILTAR 288 (593)
T ss_pred CCCccccccCchhhhhcCCHHHhhhhccHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccccccccccchHHHHHHHHH
Confidence 999999988776 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCCCHHHHHHHHHHHhccCCCCCceeeccccc-----CCCCccccCCCCCCCCCCCceeEeCCCCCCCCcccccC
Q 004767 246 ICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEE-----GSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVS 320 (732)
Q Consensus 246 vcQlyPnas~~~LL~~FF~~Ys~wdW~~pV~l~~i~~-----G~l~~~vWdP~~~~~dr~hlMpIiTP~~P~~Nsa~NVs 320 (732)
+||+|||+++++||.+||.+|++|+||+||+|+.+++ |.++++||||+.|++|++|+||||||+||+||+|||||
T Consensus 289 VCQLyPna~~s~Lv~~FF~iys~W~Wp~PV~L~~i~~~~~~~g~~~~~VWdPr~~~~dr~h~MPIITPayP~mNst~nVt 368 (593)
T PTZ00418 289 ICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKEVPNIPGLMNFKVWDPRVNPQDRAHLMPIITPAFPSMNSTHNVT 368 (593)
T ss_pred HHHhCCCCCHHHHHHHHHHHhhcCCCCCCeEcccccccccCCcccCCcccCCCCCcccccccCCeecCCCCCcccccccc
Confidence 9999999999999999999999999999999999875 77889999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHh-ccCCCCcccccCCcchhhhccceEEEEeeecChhhhhhhhhHHHHHHHHHHHHHhh
Q 004767 321 TSTLRIMMDEFQRGHEICEAMEK-NEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIER 399 (732)
Q Consensus 321 ~sTl~vI~~EF~RA~~Il~~i~~-~~~~~~W~~Lfep~~Ff~~Yk~yL~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~ 399 (732)
.+|+++|++||+||++|+++|.. ++. +|++||+|++||.+|++||+|++.+.+++++..|.||||||||.|+.+||+
T Consensus 369 ~sT~~vI~~Ef~Ra~~i~~~i~~~~~~--~W~~Lfep~~Ff~~Yk~yl~V~v~a~~~~~~~~w~G~VESRlR~Lv~~LE~ 446 (593)
T PTZ00418 369 YTTKRVITEEFKRAHEIIKYIEKNSEN--TWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKKLET 446 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCC--CHHHHcCCcchhhhcceEEEEEEEECCHHHhhhhhhHHHHHHHHHHHHhhc
Confidence 99999999999999999999987 666 999999999999999999999999999999999999999999999999998
Q ss_pred ccccceeeccCCCCCCCCC--CCceEEEEEeeEecCCCCCCCCcccchHHHHHHHHHHHHhhc---cCCCCcEEEEEEec
Q 004767 400 HTYNMLQCHPHPGDFSDKS--KPLYCSYFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYT---LRKPGMQISVAHVT 474 (732)
Q Consensus 400 ~~~~~l~~hp~P~~f~~~~--~~~~~~ffIGL~~~~~~~~~~~~~~Dl~~~v~eF~~~v~~~~---~~~~~m~i~v~~vk 474 (732)
. +.+.+||||++|.+.. ..|+++|||||+++..... +.+++||+.++++|++.|++|. .|+++|+|+|+|||
T Consensus 447 ~--~~i~~~p~P~~f~~~~~~~~~~~~ffIGL~~~~~~~~-~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~~i~v~~Vk 523 (593)
T PTZ00418 447 L--NNLKIRPYPKFFKYQDDGWDYASSFFIGLVFFSKNVY-NNSTFDLRYAIRDFVDIINNWPEMEKYPDQIDINIKYLK 523 (593)
T ss_pred c--CCceEeecCcccccCCCCceeEEEEEEeEeeccCCCC-CCceEecHHHHHHHHHHHHhhhhcccCCCCceEEEEEee
Confidence 5 3367899999998765 4688999999998765432 3458999999999999999886 36889999999999
Q ss_pred CCCCCCccCCCCCCCCCCCCCcccccccccccCCCCCCCCCCCcccccccccc
Q 004767 475 RRNLPNFVFPGGVRPSRPSKGTWDSRRALERKVSSHTKPGADDGRKRKQTDDN 527 (732)
Q Consensus 475 r~~LP~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 527 (732)
+++||+|||+.|.++.+..|... ..+..+...++|.|.....+.++.+++
T Consensus 524 ~~~Lp~~v~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~ 573 (593)
T PTZ00418 524 KSQLPAFVLSQTPEEPVKTKANT---KTNTSSATTSGQSGSSGSTSNSNSNES 573 (593)
T ss_pred hHhCCHhhccCCCcCCCcccccc---ccccccccccccccccCcccCCCCCcc
Confidence 99999999998877665555322 223334444556666555555554443
No 3
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=100.00 E-value=1.1e-123 Score=978.27 Aligned_cols=482 Identities=45% Similarity=0.834 Sum_probs=461.5
Q ss_pred CccccccCCCCCCCCChHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcE
Q 004767 6 GQRLGITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAK 85 (732)
Q Consensus 6 ~~~~Gvt~Pis~~~Pt~~D~~~t~eL~~~L~~~~l~pS~eE~~~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~k 85 (732)
.++||||+|||+.+.|+++.+++.+|+++|+..|+|+++.|.+.|.+||+.|+.++++|+.+++.++|+++.|+.+++++
T Consensus 4 ~k~~GiTgP~ST~~aTe~En~Ln~~li~eLk~~g~FE~~~E~~~Rv~VL~~Lq~~~~eFV~~vs~~K~m~dgmar~aGGK 83 (552)
T COG5186 4 KKKYGITGPLSTREATEEENRLNGELIKELKERGFFEDDKEGQTRVRVLGKLQFMVREFVARVSRNKGMGDGMARPAGGK 83 (552)
T ss_pred cccccccCCcccccccHHHhhhhHHHHHHHHHcCCcCCchhhhhHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCce
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeeeeecCCCCCCCCceEEeecCCCCCchhhHHHHHHHHHhcCCCceeeEeecCCcccEEEEEecCeeeeEEeeeccc
Q 004767 86 IFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSL 165 (732)
Q Consensus 86 I~~FGSy~lGv~~p~SDID~lcv~P~~v~r~~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~ 165 (732)
|+||||||||||+||||||+|||.|.|++|+ |||..|..+|++.++++++.+|++|+||||||+|+||+|||.||++..
T Consensus 84 IFTyGSYRLGVhgpGsDIDtLvvVPkHVsR~-dFFt~f~~~Lrer~ei~eva~vpDAfVPIIK~KF~GIsIDLifARLs~ 162 (552)
T COG5186 84 IFTYGSYRLGVHGPGSDIDTLVVVPKHVSRS-DFFTHFYEELRERPEIEEVAKVPDAFVPIIKLKFQGISIDLIFARLSI 162 (552)
T ss_pred eeeecceeeeccCCCCCcceEEEecccccHH-HHHHHHHHHhccCcchhhhccCCcccceeEEEEecCccceeeeeeccC
Confidence 9999999999999999999999999999995 999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCchhhhccchhhhhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCcChHHHHHHHHH
Q 004767 166 WVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVAR 245 (732)
Q Consensus 166 ~~ip~~ldl~~~~lL~~lde~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~LGG~swalLVa~ 245 (732)
+++|..|+++|+++|++|||+|++||||.||||+||++||+...|+.+||+||+||+||.||.|.+||+||++|+|||||
T Consensus 163 P~Vp~~l~Lsd~nLLk~~dEkcilsLNGtRVTDeiL~LVP~~~vF~~ALRaIK~WAqRRavYaN~~GfpGGVAwam~VAR 242 (552)
T COG5186 163 PVVPDGLNLSDDNLLKSMDEKCILSLNGTRVTDEILNLVPSVKVFHSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVAR 242 (552)
T ss_pred CcCCCcccccchhhhhcchHHHHHhhcCceehHHHHHhCCchHHHHHHHHHHHHHHHhhhhhccccCCcchHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCCCHHHHHHHHHHHhccCCCCCceeecccccCCCCccccCCCCCCCCCCCceeEeCCCCCCCCcccccChhhHH
Q 004767 246 ICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLR 325 (732)
Q Consensus 246 vcQlyPnas~~~LL~~FF~~Ys~wdW~~pV~l~~i~~G~l~~~vWdP~~~~~dr~hlMpIiTP~~P~~Nsa~NVs~sTl~ 325 (732)
+||||||++...++.+||+++++|+||+||+|++|++|.++.++|||+.|++|++|+||||||+||+||.|||||.||..
T Consensus 243 iCQLYPNA~S~vIv~kFF~ils~WnWPqPviLkPieDgplqvrvWnPKvYpsDk~HRMPvITPAYPSMCATHNit~STq~ 322 (552)
T COG5186 243 ICQLYPNASSFVIVCKFFEILSSWNWPQPVILKPIEDGPLQVRVWNPKVYPSDKYHRMPVITPAYPSMCATHNITNSTQH 322 (552)
T ss_pred HHhhccCcchHhHHHHHHHHHHhcCCCCCeEeeeccCCCeeEEeeCCccCcccccccCccccCCchhhhhhccccchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCCcccccCCcchhhhccceEEEEeeecChhhhhhhhhHHHHHHHHHHHHHhhccccce
Q 004767 326 IMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNML 405 (732)
Q Consensus 326 vI~~EF~RA~~Il~~i~~~~~~~~W~~Lfep~~Ff~~Yk~yL~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l 405 (732)
+|..||-||.+|+.+|+.+.. +|..||+.++||.+||+||.|++.+.++|++.+|.|+||||+|.|+.+||... .++
T Consensus 323 vIl~EfvRa~~I~~di~~n~~--~w~~lFek~DFF~RYk~yleitA~s~~~E~~lKW~GlvESKiR~Lv~klE~vd-~i~ 399 (552)
T COG5186 323 VILMEFVRAHKILSDIERNAL--DWRRLFEKSDFFSRYKLYLEITAMSSCEEDFLKWEGLVESKIRILVSKLEAVD-DIL 399 (552)
T ss_pred hHHHHHHHHHHhhhhHhhccc--cHHHHHHhhhHHHHHhHhhhhhhhhcchhhhhhhhhHHHHHHHHHHHHHHHhh-hhh
Confidence 999999999999999998877 99999999999999999999999999999999999999999999999999764 678
Q ss_pred eeccCCCCCCCC--------------------------------------------CCCceEEEEEeeEecCCCCCCCCc
Q 004767 406 QCHPHPGDFSDK--------------------------------------------SKPLYCSYFMGLQRKQGVPVGEGE 441 (732)
Q Consensus 406 ~~hp~P~~f~~~--------------------------------------------~~~~~~~ffIGL~~~~~~~~~~~~ 441 (732)
.|||||+.|... ...|++.|||||+.... ..++
T Consensus 400 ~AhPF~K~F~~~y~c~~Ee~~e~i~~~~~~~~a~~s~d~~kl~~d~~~eees~~d~~k~y~tt~yIgld~~~~---~~~k 476 (552)
T COG5186 400 YAHPFPKAFRKVYNCVAEESIEKIGSGVTLEVAYESTDHEKLANDTVPEEESMEDGMKVYCTTFYIGLDVIPV---KPGK 476 (552)
T ss_pred hcCcCChhhhhhcCCccHHHHHHHhcccceeehhhccchhhhccccCchhhhhccccceeeeEEEEEEEeeec---CCCc
Confidence 899999999610 02378899999997643 3367
Q ss_pred ccchHHHHHHHHHHHHhhccCC-CCcEEEEEEecCCCCCCccCC-CCCCCCCCCC
Q 004767 442 QFDIRLTVKEFKQAVSMYTLRK-PGMQISVAHVTRRNLPNFVFP-GGVRPSRPSK 494 (732)
Q Consensus 442 ~~Dl~~~v~eF~~~v~~~~~~~-~~m~i~v~~vkr~~LP~~v~~-~~~~~~~~~~ 494 (732)
++||..++++|.+.|+.|++++ .+|.|.|+.+|+.+||+-||. |+.||+..+|
T Consensus 477 kvdi~~p~~EF~elcr~~d~gd~~~mni~v~~~K~~dlpdeVF~~geerPs~~sK 531 (552)
T COG5186 477 KVDIEQPVKEFIELCREYDEGDASGMNIEVNSLKRKDLPDEVFYPGEERPSNSSK 531 (552)
T ss_pred eeeeeccHHHHHHHHHHhhccccceeeeehhhccccCCchhhcCCCccCcccccc
Confidence 8999999999999999998776 579999999999999999995 7778876555
No 4
>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=100.00 E-value=6.9e-73 Score=586.02 Aligned_cols=253 Identities=62% Similarity=1.102 Sum_probs=203.0
Q ss_pred ccccccCCCCCCCCChHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEE
Q 004767 7 QRLGITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKI 86 (732)
Q Consensus 7 ~~~Gvt~Pis~~~Pt~~D~~~t~eL~~~L~~~~l~pS~eE~~~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI 86 (732)
++||||+|||+++||+.|++.+++|+++|+++++|||+||.++|++||++|++++++|+++
T Consensus 2 ~~~Gvt~PIS~~~Pt~~Dl~~s~~L~~~l~~~~~~es~ee~~~R~~vl~~L~~iv~~wv~~------------------- 62 (254)
T PF04928_consen 2 KQYGVTKPISLAPPTEKDLKRSASLEEFLKDYGLFESEEEEQKREEVLRKLQQIVKEWVKQ------------------- 62 (254)
T ss_dssp GGGSTT--S------HHHHHHHHHHHHHHHHCT-S--HHHHHHHHHHHHHHHHHHHHHHHH-------------------
T ss_pred CccCCCCCccCCCCChhhHHhHHHHHHHHHHcCCCCChHHHhHHHHHHHHHHHHHHHHHHh-------------------
Confidence 7899999999999999999999999999999999999999999999999999999999853
Q ss_pred EEeeeeecCCCCCCCCceEEeecCCCCCchhhHHHHHHHHHhcCCCceeeEeecCCcccEEEEEecCeeeeEEeeecccc
Q 004767 87 FTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLW 166 (732)
Q Consensus 87 ~~FGSy~lGv~~p~SDID~lcv~P~~v~r~~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~ 166 (732)
...
T Consensus 63 -----------------------------------------------------------------------------~~~ 65 (254)
T PF04928_consen 63 -----------------------------------------------------------------------------ALP 65 (254)
T ss_dssp -----------------------------------------------------------------------------SSS
T ss_pred -----------------------------------------------------------------------------hhc
Confidence 456
Q ss_pred ccCCCCCCCchhhhccchhhhhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCcChHHHHHHHHHH
Q 004767 167 VIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARI 246 (732)
Q Consensus 167 ~ip~~ldl~~~~lL~~lde~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~LGG~swalLVa~v 246 (732)
++|+++++.++++|+++|++|++||||+||+++|+++||+.+.||.++||||+|||+||||+|++||||||+||||||++
T Consensus 66 ~~p~~l~~~~~~~l~~ld~~s~~sLnG~Rv~~~il~~Vp~~~~Fr~~lR~IK~WAk~RGIYsn~~GylGGI~waILvArv 145 (254)
T PF04928_consen 66 RVPEDLDLLDDDPLRNLDEASVRSLNGVRVTDYILRLVPNQETFRTALRFIKLWAKRRGIYSNVFGYLGGIHWAILVARV 145 (254)
T ss_dssp SB-TT--TT-GGGGTT--HHHHHHHHHHHHHHHHHCTSS-HHHHHHHHHHHHHHHHHTT-B-CCCTSB-HHHHHHHHHHH
T ss_pred CCCcccccCCchhhhCCCHhhccCcccccHHHHHHHHCCCHHHHHHHHHHHHHHHHHccccchhhccchHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhCCCCCHHHHHHHHHHHhccCCCCCceeecccccCCCCccccCCCCCCCCCCCceeEeCCCCCCCCcccccChhhHHH
Q 004767 247 CQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRI 326 (732)
Q Consensus 247 cQlyPnas~~~LL~~FF~~Ys~wdW~~pV~l~~i~~G~l~~~vWdP~~~~~dr~hlMpIiTP~~P~~Nsa~NVs~sTl~v 326 (732)
||+|||+++++||.+||.+|++|+|++||+|+.+.++.+++++|+|+.+.+|+.|+|||+||+||+||+|+|||.+|+++
T Consensus 146 cql~Pn~~~~~ll~~FF~~ys~W~W~~PV~l~~~~~~~~~~~~w~p~~~~~~~~~~MpIiTP~yP~~Nst~nVt~st~~~ 225 (254)
T PF04928_consen 146 CQLYPNASPSTLLSRFFQIYSQWDWPNPVVLDPIEDGPLGFKVWNPRLYPRDRRHLMPIITPAYPSMNSTYNVTRSTLRI 225 (254)
T ss_dssp HHHSTT--HHHHHHHHHHHHHCS-TTS-EESS-----SSSCGS--TTT-HHHHC-SS-EE-SSSS--BTTTT--HHHHHH
T ss_pred HHHCccccccchHHHHHHHhcCCCCCCceeecccccCcccccCCCCCCCCCCcccceeEccCCCCccccccccCHHHHHH
Confidence 99999999999999999999999999999999999998999999999988899999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhccCCCCcccccCCc
Q 004767 327 MMDEFQRGHEICEAMEKNEADVDWDTLFEPF 357 (732)
Q Consensus 327 I~~EF~RA~~Il~~i~~~~~~~~W~~Lfep~ 357 (732)
|++||+||+++++++..++. +|++||+|+
T Consensus 226 i~~Ef~ra~~i~~~~~~~~~--~W~~L~e~~ 254 (254)
T PF04928_consen 226 IREEFQRAHEILSEILKGGA--SWSDLFEPH 254 (254)
T ss_dssp HHHHHHHHHHHHHHHHTTSS---HHHCT---
T ss_pred HHHHHHHHHHHHHHHHcCCC--CHHHHcCCC
Confidence 99999999999999998777 999999985
No 5
>COG5260 TRF4 DNA polymerase sigma [DNA replication, recombination, and repair]
Probab=99.97 E-value=3.1e-30 Score=282.86 Aligned_cols=261 Identities=23% Similarity=0.320 Sum_probs=207.6
Q ss_pred HhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCCCCCceE
Q 004767 26 MRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDT 105 (732)
Q Consensus 26 ~~t~eL~~~L~~~~l~pS~eE~~~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDID~ 105 (732)
.++.+|.+++. .+.|+.+|.++|...|++|++++++- + .++.+++|||+.+|+++|+||||+
T Consensus 56 ~lt~el~~~y~--~I~ps~eEl~~R~~~leklr~~lk~~---------~-------pda~l~vFGS~~t~L~l~~SDiDl 117 (482)
T COG5260 56 ELTSELLEFYD--YIAPSDEELKRRKALLEKLRTLLKKE---------F-------PDADLKVFGSTETGLALPKSDIDL 117 (482)
T ss_pred HHHHHHHHHHH--hhCCCHHHHHHHHHHHHHHHHHHHHh---------C-------CccceeEecccccccccCcccccE
Confidence 44555555554 36799999999999999999999762 1 356899999999999999999999
Q ss_pred EeecCCCCCchhhHHHHHHHHHhcCCCceeeEeecCCcccEEEEEe--cCeeeeEEeeeccccccCCCCCCCchhhhccc
Q 004767 106 LCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKF--SGVSIDLLYARLSLWVIPEDLDISQDSILQNA 183 (732)
Q Consensus 106 lcv~P~~v~r~~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~--~GI~iDLsfa~l~~~~ip~~ldl~~~~lL~~l 183 (732)
+++.+....++..--..++..|.......++.+|..||||||||.+ .|+.|||+|++.
T Consensus 118 ~I~s~~~~~~et~~~~~l~~~l~~~~~~~~~~~v~tarVPIIKl~d~~s~l~~Disfn~~-------------------- 177 (482)
T COG5260 118 CIISDPRGYKETRNAGSLASHLFKKNLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNT-------------------- 177 (482)
T ss_pred EEecCCccccccccHHHHHHHHHHhccCeeeEEEEecccceEEEecCccceEEEeecCch--------------------
Confidence 8888665543211112455555555677889999999999999998 589999999885
Q ss_pred hhhhhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCcChHHHHHHHHHHHHhCCC-----------
Q 004767 184 DEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPN----------- 252 (732)
Q Consensus 184 de~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~LGG~swalLVa~vcQlyPn----------- 252 (732)
+|++.|..++.++-..+++|+|+.+||+||++|.+++...|+|+||++.+||..++|++|.
T Consensus 178 --------~~~~~akl~~~~~~~~P~lrpLvliIKhwl~~R~ln~~~~GtL~sy~i~cmV~sfLq~~~~~~~~~~~~~~~ 249 (482)
T COG5260 178 --------NGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPFLFFDNGLLSP 249 (482)
T ss_pred --------hHHHHHHHHHHHHhcCcccchHHHHHHHHHHHHhhcccccCcchhhhhHHHHHHHHHhCCccccccccccch
Confidence 5788899999999999999999999999999999999999999999999999999999982
Q ss_pred -------CCHHHHHHHHHHHhc-cCCCCCceeecccccC-CC-C--ccccCCCCCCCCCCCceeEeCCC-CCCCCccccc
Q 004767 253 -------AVPSMLVSRFFRVYT-QWRWPNPVLLCAIEEG-SL-G--LQVWDPRRNPKDKYHLMPIITPA-YPCMNSSYNV 319 (732)
Q Consensus 253 -------as~~~LL~~FF~~Ys-~wdW~~pV~l~~i~~G-~l-~--~~vWdP~~~~~dr~hlMpIiTP~-~P~~Nsa~NV 319 (732)
..++.|+..||++|+ .|+|..-++. +..| .+ . -+.|--. -+...++|++|. .+..+++.
T Consensus 250 l~~~~~~~~lgvLf~dFf~~yG~~f~Y~~~~~s--i~~g~~~~~K~e~g~~~~----~~p~~LsiqdP~td~n~~~~a-- 321 (482)
T COG5260 250 LKYNKNIDNLGVLFDDFFELYGKSFNYSLVVLS--INSGDFYLPKYEKGWLKP----SKPNSLSIQDPGTDRNNDISA-- 321 (482)
T ss_pred hhccccccccchHHHHHHHHhccccChhheEEE--ecCCceeeehhhcccccc----cCCCcEeecCCCCCccccccc--
Confidence 257899999999999 8999875543 4445 21 1 1234211 113679999999 55555443
Q ss_pred ChhhHHHHHHHHHHHHHHHHH
Q 004767 320 STSTLRIMMDEFQRGHEICEA 340 (732)
Q Consensus 320 s~sTl~vI~~EF~RA~~Il~~ 340 (732)
...+...|+.+|.+|.+++.+
T Consensus 322 ~s~~ik~i~~~F~~aF~lls~ 342 (482)
T COG5260 322 VSFNIKDIKAAFIRAFELLSN 342 (482)
T ss_pred ccchHHHHHHHHHHHHHHHhh
Confidence 456799999999999998864
No 6
>PF04926 PAP_RNA-bind: Poly(A) polymerase predicted RNA binding domain; InterPro: IPR007010 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 that specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analogue at 2.5 A resolution 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 C-terminal domain unexpectedly folds into a compact domain reminiscent of the RNA-recognition motif fold. The three invariant aspartates of the catalytic triad ligate two of the three active site metals. One of these metals also contacts the adenine ring. Furthermore, conserved, catalytically important residues contact the nucleotide. These contacts, taken together with metal coordination of the adenine base, provide a structural basis for ATP selection by poly(A) polymerase. ; GO: 0003723 RNA binding, 0004652 polynucleotide adenylyltransferase activity, 0043631 RNA polyadenylation, 0005634 nucleus; PDB: 2O1P_A 2HHP_A 3C66_B 1FA0_A 2Q66_A 1Q79_A 1Q78_A 1F5A_A.
Probab=99.97 E-value=1.6e-31 Score=258.23 Aligned_cols=133 Identities=40% Similarity=0.774 Sum_probs=105.3
Q ss_pred chhhhccceEEEEeeecChhhhhhhhhHHHHHHHHHHHHHhhccccceeeccCCCCCC-------------------CCC
Q 004767 358 TFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPHPGDFS-------------------DKS 418 (732)
Q Consensus 358 ~Ff~~Yk~yL~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~~hp~P~~f~-------------------~~~ 418 (732)
+||.+|||||+|+|+|.+++++.+|.||||||||.|+.+||+.. .+..|||||+.|. ...
T Consensus 1 ~FF~~Yk~yl~I~~~a~~~~~~~~W~G~VESrlR~Lv~~LE~~~-~i~~ahp~pk~f~~~~~~~~~~~~~~~~~~~~~~~ 79 (157)
T PF04926_consen 1 DFFSRYKHYLQIDVSAKNEEDHRKWSGWVESRLRHLVQKLERNP-GIKLAHPFPKRFERVYECSEQADENNDEEEEEDPE 79 (157)
T ss_dssp -HHHH-SEEEEEEEEECSHHHHHHHHHHHHCCHHHHHHHHHTST-TEEEEEE-SS-EEEEEE-EBECTTCTTSHHCHCTS
T ss_pred ChhHhCceeEEEEEEeCCHHHHHHhhhHHHHHHHHHHHHHccCC-CeeEecCCCCccccccccccccccccccccccCCC
Confidence 69999999999999999999999999999999999999999875 4778999999998 122
Q ss_pred CCceEEEEEeeEecCCCCCCCCcccchHHHHHHHHHHHHhhcc---CCCCcEEEEEEecCCCCCCccCCCCCCCCC
Q 004767 419 KPLYCSYFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYTL---RKPGMQISVAHVTRRNLPNFVFPGGVRPSR 491 (732)
Q Consensus 419 ~~~~~~ffIGL~~~~~~~~~~~~~~Dl~~~v~eF~~~v~~~~~---~~~~m~i~v~~vkr~~LP~~v~~~~~~~~~ 491 (732)
..++++|||||++........++++||+.++++|++.|++|+. +.++|+|+|+||||++||++||+++.++.+
T Consensus 80 ~~~~~~~fIGL~~~~~~~~~~~~~~dL~~~i~~F~~~v~~~~~~~~~~~~m~i~i~~vk~~~Lp~~v~~~~~~r~~ 155 (157)
T PF04926_consen 80 NEYTSSFFIGLEFDSKESNEGSKKLDLTYAIQEFKDLVRNWEKYYYDEEGMDISISHVKRSQLPDFVFEEGEKRPK 155 (157)
T ss_dssp EEEEEEEEEEEEE--SSSS---S-EE-HHHHHHHHHHHHCCCCTTC-TTTEEEEEEEEEHHHHGGGGS-TTS----
T ss_pred ceeEEEEEEEEEECCCCccccceEEehHHHHHHHHHHHHhhhccccCCCccEEEEEEechHHCChhhhcccCcCCC
Confidence 4588999999999876544334679999999999999999877 567899999999999999999998876654
No 7
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=99.96 E-value=5.5e-28 Score=270.03 Aligned_cols=267 Identities=20% Similarity=0.301 Sum_probs=211.5
Q ss_pred ChHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCCC
Q 004767 21 TDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPG 100 (732)
Q Consensus 21 t~~D~~~t~eL~~~L~~~~l~pS~eE~~~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~ 100 (732)
.+.=..+++++..+++ .+.||.+|.+.|.++++++++.|++- + .+++|++||||.+|+++|+
T Consensus 57 ~~~s~~l~~eI~~fv~--~l~pt~~e~~~R~~~~~~i~~~v~~~---------~-------~~a~v~~FGS~~tglyLP~ 118 (514)
T KOG1906|consen 57 NLVSERLRNEILDFVQ--YLIPTPEEIEVRSELVEKIRDVVKQK---------W-------PDASVYVFGSVPTGLYLPD 118 (514)
T ss_pred chhHHHHHHHHHHHHH--HhcCCchHHHHHHHHHHHHHHHHHHh---------c-------ccceeEEeeeeeccccccc
Confidence 3344466677777776 48899999999999999999988741 1 3689999999999999999
Q ss_pred CCceEEeecCCCCCchhhHHHHHHHHHhc--CCCceeeEeecCCcccEEEEEe--cCeeeeEEeeeccccccCCCCCCCc
Q 004767 101 ADIDTLCVGPRHATREEDFFGELHQMLTE--MPEVTELHPVPDAHVPVMKFKF--SGVSIDLLYARLSLWVIPEDLDISQ 176 (732)
Q Consensus 101 SDID~lcv~P~~v~r~~dFf~~l~~~L~~--~~~V~~l~~I~~ArVPIIKf~~--~GI~iDLsfa~l~~~~ip~~ldl~~ 176 (732)
||||+++.++....++ +....+.-++.. ...-..+..|..|+||||||+. .+|.|||+|++.
T Consensus 119 sDIDl~v~~~~~~~~e-~~~~~~~l~~~~e~~~~~~~v~~v~karvpiik~~d~~s~i~vDISFn~~------------- 184 (514)
T KOG1906|consen 119 SDIDLVVLSKFLNDKE-DRAVKLELALELEEDNSAFHVKVVQKARVPIIKFKDPVSNIHVDISFNQT------------- 184 (514)
T ss_pred cceEEEEecccccCch-hhHHHHHHHHhhhhccccceEEEeeeeeeeeEEeecCccceEEEeeeccc-------------
Confidence 9999999999766653 555555444443 3333568889999999999997 699999999986
Q ss_pred hhhhccchhhhhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCcChHHHHHHHHHHHHhCCCC---
Q 004767 177 DSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNA--- 253 (732)
Q Consensus 177 ~~lL~~lde~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~LGG~swalLVa~vcQlyPna--- 253 (732)
||||.++.|..++-+.+.+|.++.++|+|...|++++...|+++||++++||..++|++|..
T Consensus 185 ---------------~G~~aa~~i~~~~~~~p~~~~lvlvlk~fl~~r~ln~v~tGgisSyal~~Lv~~fl~l~~~~~s~ 249 (514)
T KOG1906|consen 185 ---------------NGVKAAKFIKDFLRDHPFLRSLVLVLKQFLYERRLNGVHTGGISSYALELLVLSFLQLHPRSKSG 249 (514)
T ss_pred ---------------CchhHHHHHHHHHhcCccchhHHHHHHHHHHhhcccccccccchHHHHHHHHHHHHhhcccccCC
Confidence 68999999999999999999999999999999999999999999999999999999999864
Q ss_pred ------CHHHHHHHHHHHhc-cCCCCC-ceeecccccCC-CC--ccccCCCCCCCCCCCceeEeCCCCCCCCcccccChh
Q 004767 254 ------VPSMLVSRFFRVYT-QWRWPN-PVLLCAIEEGS-LG--LQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTS 322 (732)
Q Consensus 254 ------s~~~LL~~FF~~Ys-~wdW~~-pV~l~~i~~G~-l~--~~vWdP~~~~~dr~hlMpIiTP~~P~~Nsa~NVs~s 322 (732)
.++.||.+||++|+ +|.+.. -|.+. ..|. .+ ...|- .+...+...+.|+||..|..+.++ +..
T Consensus 250 ~~~~~~~~~vll~~f~e~yG~~f~~~k~~i~~~--~~g~~~~~~~~~~~--~~~~~~~~~LsieDP~~P~ndigr--~s~ 323 (514)
T KOG1906|consen 250 RLAVLKNLGVLLIKFFELYGRNFGYDKLGISLS--LGGEYVSKELTGFF--NNSLERPGSLSIEDPVDPTNDIGR--SSF 323 (514)
T ss_pred ccchhcccchHHHHHHHHhccccCchhhceecc--CCcccccHHhhhhh--cccccCCCccccCCCCCccccccc--ccc
Confidence 36789999999999 777665 23221 1121 11 11121 122245567999999999877764 235
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 004767 323 TLRIMMDEFQRGHEICEA 340 (732)
Q Consensus 323 Tl~vI~~EF~RA~~Il~~ 340 (732)
.+..|+.+|..|+.++..
T Consensus 324 ~~~~v~~~F~~af~~l~~ 341 (514)
T KOG1906|consen 324 NFSQVKGAFAYAFKVLTN 341 (514)
T ss_pred cHHHHHHHHHHHHHHHhh
Confidence 688899999999998754
No 8
>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=99.78 E-value=1.6e-18 Score=158.00 Aligned_cols=98 Identities=43% Similarity=0.822 Sum_probs=87.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCCCCCceEEeecCCC-CCchhhHHHHHHHHH
Q 004767 49 SREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRH-ATREEDFFGELHQML 127 (732)
Q Consensus 49 ~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~-v~r~~dFf~~l~~~L 127 (732)
.|++++++|++++++|. .++++++|||+++|+++|+||||+++..|.. ... ..++..+.+.|
T Consensus 1 ~r~~i~~~l~~~i~~~~----------------~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~~~~~-~~~l~~l~~~l 63 (114)
T cd05402 1 KREEVLDRLQELIKEWF----------------PGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDR-EDFLRKLAKLL 63 (114)
T ss_pred CHHHHHHHHHHHHHHHC----------------CCCEEEEecccccCCCCCCCCeeEEEEeCCCCccH-HHHHHHHHHHH
Confidence 38899999999999863 3588999999999999999999999999876 333 47999999999
Q ss_pred hcCCCceeeEeecCCcccEEEEEec--CeeeeEEeeec
Q 004767 128 TEMPEVTELHPVPDAHVPVMKFKFS--GVSIDLLYARL 163 (732)
Q Consensus 128 ~~~~~V~~l~~I~~ArVPIIKf~~~--GI~iDLsfa~l 163 (732)
++...+.++..|.+|+||||||.+. |++|||+|++.
T Consensus 64 ~~~~~~~~~~~i~~ArVPiik~~~~~~~i~~Dis~~~~ 101 (114)
T cd05402 64 KKSGEVVEVEPIINARVPIIKFVDKPTGIEVDISFNNL 101 (114)
T ss_pred HhCCCceeeEEeccCCCCEEEEEEcCCCeEEEEEcccc
Confidence 9988888999999999999999998 99999999874
No 9
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=99.74 E-value=6.8e-17 Score=184.84 Aligned_cols=250 Identities=21% Similarity=0.339 Sum_probs=186.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCCCCCceEEeecCCCC--C----c
Q 004767 42 ESQEEAVSREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRHA--T----R 115 (732)
Q Consensus 42 pS~eE~~~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v--~----r 115 (732)
+...+...|...+..++.++..- .+ .....+..|||..+|+....+|+| +|+.-... . .
T Consensus 127 ~~~~~~~~~~~~~~~l~~~~~~~---------~p-----~~~~~~~~~gs~~~~~~~~~~d~d-~~~~~~~~~~~~~~~~ 191 (596)
T KOG2277|consen 127 LPHSDVKTRKLILDKLRALASLL---------FP-----DSILSLYLFGSSDLGLGERSSDLD-LCVDFTSSFLSFEKIK 191 (596)
T ss_pred CCccccchHHHHHHHHHHHHHHh---------cC-----CCcceeeccCcccccccccccCcc-eeecccccccccchhh
Confidence 45556666667777777766542 11 122336799999999999999999 66643221 1 1
Q ss_pred hhhHHHHHHHHHhcCCC--ceeeEeecCCcccEEEEEe--cCeeeeEEeeeccccccCCCCCCCchhhhccchhhhhhhc
Q 004767 116 EEDFFGELHQMLTEMPE--VTELHPVPDAHVPVMKFKF--SGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSL 191 (732)
Q Consensus 116 ~~dFf~~l~~~L~~~~~--V~~l~~I~~ArVPIIKf~~--~GI~iDLsfa~l~~~~ip~~ldl~~~~lL~~lde~svrSL 191 (732)
...++..++++|....+ +..++.|..|+||||||.+ .++++|+++.+..
T Consensus 192 ~~~~~~l~~~~~~~~~~~~~~~~~~i~~A~vPiik~~~~~~~~~~d~s~~n~~--------------------------- 244 (596)
T KOG2277|consen 192 GLEILKLLAKCLASLLEEGVREVQQILSARVPIIKFNDSGSGLECDLSVNNSD--------------------------- 244 (596)
T ss_pred hHHHHHHHHHHHHhccccccceeeeeeecCCCEEEecCCCCCCceeeeeccch---------------------------
Confidence 13556777888887543 8889999999999999966 5799999998752
Q ss_pred chhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCcC-hHHHHHHHHHHHHhCCC------------------
Q 004767 192 NGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLG-GINWALLVARICQLYPN------------------ 252 (732)
Q Consensus 192 NG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~LG-G~swalLVa~vcQlyPn------------------ 252 (732)
|.+.+..+..+...+.+|+.|...||+||+++++++...|.+. +|++.+||++++|.++.
T Consensus 245 -~~~nS~ll~~~~~~d~r~~~L~~~vk~wa~~~~~~d~~~g~~~s~ysl~lmvi~fLq~~~~~ilp~l~~l~~~~~~~~~ 323 (596)
T KOG2277|consen 245 -AILNSQLLRNYSEIDPRVRPLVLLVKHWAKEKGLNDAKPGGLNSSYSLTLMVIHFLQTLSPPILPPLSKLLPESDSNDK 323 (596)
T ss_pred -hhhhhHHHHHhHhcCCCcchHhHHHHHHHHhccCCCCCCCceeccccHHHHHHHHHHhcCCcCCCchhhhchhcccccc
Confidence 2334444444455567999999999999999999999999998 69999999999998631
Q ss_pred -------------------------CCHHHHHHHHHHHhc-cCCCCCceeecccccCCCCccccCCCCCCCCCCCceeEe
Q 004767 253 -------------------------AVPSMLVSRFFRVYT-QWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPII 306 (732)
Q Consensus 253 -------------------------as~~~LL~~FF~~Ys-~wdW~~pV~l~~i~~G~l~~~vWdP~~~~~dr~hlMpIi 306 (732)
.+++.|+..||.||+ .|+|++-++- ++.|......|.. .....+.|+
T Consensus 324 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~f~~yy~~~Fdf~~~~I~--~r~~~~l~~~~~~-----~~~~~l~i~ 396 (596)
T KOG2277|consen 324 PVVKKKVLCSFLRVFQRNPSNSQNTGSLGELLLGFFSYYASLFDFRKNAIS--IRRGRALKRAKKI-----KSKKFLCIE 396 (596)
T ss_pred cchhhhhhhccccccccccccccccchHHHHHHHHHHHHhhhcccccceee--eeecccccccchh-----hhccceeec
Confidence 035689999999999 8999997652 3333211100111 112469999
Q ss_pred CCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHH
Q 004767 307 TPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAM 341 (732)
Q Consensus 307 TP~~P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~~i 341 (732)
+|++...|.+..++......|+.+|+.+..++...
T Consensus 397 dp~~~~~n~~~~~~~~~~~~i~~~~~~~~~~~~~~ 431 (596)
T KOG2277|consen 397 DPFEVSHNADAGVTLKVLLLIQDEFQESRRVFKDV 431 (596)
T ss_pred cccccccCccccchHHHHHHHHHHHHHHHHHhhhh
Confidence 99999999999999999999999999999998753
No 10
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=99.56 E-value=7.1e-12 Score=138.38 Aligned_cols=341 Identities=20% Similarity=0.244 Sum_probs=207.3
Q ss_pred HHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCC-CCCceEEeecCC
Q 004767 33 KYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGP-GADIDTLCVGPR 111 (732)
Q Consensus 33 ~~L~~~~l~pS~eE~~~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p-~SDID~lcv~P~ 111 (732)
+.|+. +-||+||.++-+++.++|...+++++++. ...++++.|||++-|.+++ +||||++++.|.
T Consensus 4 ~vl~~--i~Ps~eE~~~~~~~~~~l~~~l~~~~~e~------------~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~~ 69 (408)
T TIGR03671 4 EVLER--IKPTEEEREKLKKVADELIARLEEIIEEL------------GVDAEVVLVGSYARGTWLKGDRDIDIFILFPK 69 (408)
T ss_pred HHhhh--cCCCHHHHHHHHHHHHHHHHHHHHHHHhc------------CCcceEEEEeeEecCCccCCCCceeEEEEeCC
Confidence 44443 67999999999999999998888876441 1347999999999999999 899999999988
Q ss_pred CCCchhhH---HHHHHHHHhcC-CCceeeEeecCCcccEEEEEecCeeeeEEeeeccccccCCCCCCCch-hhhccchhh
Q 004767 112 HATREEDF---FGELHQMLTEM-PEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQD-SILQNADEQ 186 (732)
Q Consensus 112 ~v~r~~dF---f~~l~~~L~~~-~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~~ip~~ldl~~~-~lL~~lde~ 186 (732)
...++ ++ ...+...+.+. +.. ...-|-=|-++..+.|++|||.=|-- +.+- .+...+|-
T Consensus 70 ~~~~e-~l~~~gl~i~~~~~~~~~~~----~~~yaeHpYv~~~~~G~~VDiVPcy~----------v~~g~~~~taVDR- 133 (408)
T TIGR03671 70 DTSRE-ELEEYGLEIGHEVLKRGGNY----EERYAEHPYVSGEIEGFEVDVVPCYK----------VESGEEIISAVDR- 133 (408)
T ss_pred CCCHH-HHHHHHHHHHHHHHhhCCCH----hheeccCceEEEEEccEEEEEEeeEE----------ccCcCeeeccccC-
Confidence 77763 33 11233333221 111 14467779999999999999984321 1111 11111111
Q ss_pred hhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCC--CCCCcChHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 004767 187 TVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSN--VAGFLGGINWALLVARICQLYPNAVPSMLVSRFFR 264 (732)
Q Consensus 187 svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn--~~G~LGG~swalLVa~vcQlyPnas~~~LL~~FF~ 264 (732)
| ..-+++++...- +.|+..+|++|.|+|.-|+|++ ..++++||..=||++++ .+-..++..+
T Consensus 134 t------p~H~~fv~~rl~--~~~~d~VRLlK~f~k~igvYGsE~~~~GFSGYl~ELLv~~y------G~F~~~l~~a-- 197 (408)
T TIGR03671 134 T------PFHTRYVLERLD--GKLRDDVRLLKQFLKGIGVYGSELKTRGFSGYLCELLVIHY------GSFENVLKAA-- 197 (408)
T ss_pred c------hHHHHHHHHhhh--hhHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHh------CCHHHHHHHH--
Confidence 0 112345544432 3488999999999999999964 57889999999999994 2333333333
Q ss_pred HhccCCCCCceeecccccCCCCccccCCCCCCCCCCCceeEeCCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHhc
Q 004767 265 VYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKN 344 (732)
Q Consensus 265 ~Ys~wdW~~pV~l~~i~~G~l~~~vWdP~~~~~dr~hlMpIiTP~~P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~~i~~~ 344 (732)
++ |..++.+ .+... .... -...+.|+||.+|..|+|..+|..++..+...-+++.+ .
T Consensus 198 --~~--wk~~~~i-d~~~~-------~~~~----f~~PlvViDPvDp~RNVAaalS~~~~~~fv~aar~fl~-------~ 254 (408)
T TIGR03671 198 --SK--WKPGVVI-DIEEH-------GTKK----FDDPLVVIDPVDPKRNVAAALSLENLARFILAARMFLK-------N 254 (408)
T ss_pred --Hh--cCCCeEE-ecCcc-------cccc----CCCCEEEeCCCCCcchHHHHcCHHHHHHHHHHHHHHHH-------C
Confidence 33 4445554 22211 1110 12479999999999999999999888877765444432 2
Q ss_pred cCCCCcccccCCc-----chh---hhc-cceEEEEeeecChhhhhhhhhHHHHHHHHHHHHHhhccccceeeccCCCCCC
Q 004767 345 EADVDWDTLFEPF-----TFF---EAY-KNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPHPGDFS 415 (732)
Q Consensus 345 ~~~~~W~~Lfep~-----~Ff---~~Y-k~yL~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~~hp~P~~f~ 415 (732)
. =..+|.|. ++- .+- .+.+.|.....+.-+=.- -|-++--.+.|...||+....++....|-
T Consensus 255 P----s~~fF~p~~~~~~~~~~~l~~r~t~~~~~~f~~p~~v~Dil-~pQl~r~~~~i~~~L~~~gF~v~r~~~~~---- 325 (408)
T TIGR03671 255 P----SLEFFFPPEIEPEEFLERLERRGTTLLAIVFRTPDVVDDIL-YPQLERSGRSLVKLLEREGFEVLRYGVWA---- 325 (408)
T ss_pred C----CHHHcCCCCCChHHHHHHHhhcCcEEEEEEeCCCCCCccch-hHHHHHHHHHHHHHHHHCCCEEEEeeeec----
Confidence 2 22555442 111 222 234444444444322223 35666666677777887666556555552
Q ss_pred CCCCCceEEEEEeeEecCC--CCCCCCcccchHHHHHHHHH
Q 004767 416 DKSKPLYCSYFMGLQRKQG--VPVGEGEQFDIRLTVKEFKQ 454 (732)
Q Consensus 416 ~~~~~~~~~ffIGL~~~~~--~~~~~~~~~Dl~~~v~eF~~ 454 (732)
+.. .|+.++=|...+- .....|..+.-+.....|.+
T Consensus 326 ~~~---~~~l~~el~~~~lp~~~~h~GPpv~~~~~a~~F~~ 363 (408)
T TIGR03671 326 DEN---TCYLLLELESAELPRVKLHVGPPVWVRDHAEKFIE 363 (408)
T ss_pred CCC---eEEEEEEeeccccCCceeeeCCCccchhHHHHHHH
Confidence 222 1444545543221 11122445666566778886
No 11
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=99.54 E-value=5.8e-12 Score=140.68 Aligned_cols=343 Identities=19% Similarity=0.263 Sum_probs=203.6
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCC-CCCceEEeecC
Q 004767 32 EKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGP-GADIDTLCVGP 110 (732)
Q Consensus 32 ~~~L~~~~l~pS~eE~~~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p-~SDID~lcv~P 110 (732)
.+.|+. +-||++|.++-.++.+.|...+++++.+ .+. .++++.+|||+-|.+++ +||||++++.|
T Consensus 4 ~evl~~--i~Ps~eE~~~l~~~~~~l~~~L~~~~~~----~~~--------~~~V~l~GS~ArgT~L~GdsDIDIFv~fp 69 (447)
T PRK13300 4 EEVLER--IKPTEEEREKLKKVAEELIERLEEAIKE----LGL--------DAEVELVGSTARGTWLSGDRDIDIFVLFP 69 (447)
T ss_pred HHHHHh--cCCCHHHHHHHHHHHHHHHHHHHHHHHh----cCC--------ceEEEEEeeecCCcccCCCCceeEEEEeC
Confidence 344543 7799999999999999888888876643 221 37899999999999999 78999999998
Q ss_pred CCCCchhhH----HHHHHHHHhc-CCCceeeEeecCCcccEEEEEecCeeeeEEee-eccccccCCCCCCCchhhhccch
Q 004767 111 RHATREEDF----FGELHQMLTE-MPEVTELHPVPDAHVPVMKFKFSGVSIDLLYA-RLSLWVIPEDLDISQDSILQNAD 184 (732)
Q Consensus 111 ~~v~r~~dF----f~~l~~~L~~-~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa-~l~~~~ip~~ldl~~~~lL~~ld 184 (732)
....++ ++ .......++. .+. ..++ -|-=|-++..+.|++|||.=| .+.. + ..+...+|
T Consensus 70 ~~~~~e-~L~~~gl~i~~~~~~~~~~~-~~~~---yaeHpyv~~~~~G~~VDiVPcy~v~~---~-------~~~~saVD 134 (447)
T PRK13300 70 KDTSRE-ELEEKGLEIGKEVAKELLGD-YEER---YAEHPYVTGEIDGFEVDIVPCYKVES---G-------EEIISAVD 134 (447)
T ss_pred CCCCHH-HHHHHHHHHHHHHHHhhCCc-ceee---eccCceEEEEECCEEEEEEeeEEccC---c-------Cccccccc
Confidence 877763 22 1122223333 222 2333 478899999999999999844 2210 0 11111112
Q ss_pred hhhhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCC--CCCCcChHHHHHHHHHHHHhCCCCCHHHHHHHH
Q 004767 185 EQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSN--VAGFLGGINWALLVARICQLYPNAVPSMLVSRF 262 (732)
Q Consensus 185 e~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn--~~G~LGG~swalLVa~vcQlyPnas~~~LL~~F 262 (732)
-. ..-+.+|+... .+.++..+|++|.|.|.-|+|++ ..++++||..=||++++ .+-..+|..+
T Consensus 135 Rt-------p~H~~fv~~rl--~~~~~d~VRLlK~f~k~~gvYGsE~k~~GFSGYl~ELLv~~y------G~F~~~l~~a 199 (447)
T PRK13300 135 RT-------PFHTKYVKERL--KGKLEDEVRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHY------GSFENVLKAA 199 (447)
T ss_pred Cc-------hHHHHHHHHhh--hhhHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHh------CCHHHHHHHH
Confidence 10 11244555443 23488999999999999999964 57889999999999995 3434444433
Q ss_pred HHHhccCCCCCceeecccccCCCCccccCCCCCCCCCCCceeEeCCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHH
Q 004767 263 FRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAME 342 (732)
Q Consensus 263 F~~Ys~wdW~~pV~l~~i~~G~l~~~vWdP~~~~~dr~hlMpIiTP~~P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~~i~ 342 (732)
++|. -++.+. +++.. ... .-...+.|+||.+|..|+|.++|..++..+... |...|
T Consensus 200 ----~~w~--~~~~I~-~~~~~-------~~~---~f~~PlvViDPvDp~RNVAaa~S~~~~~~fv~a---ar~fL---- 255 (447)
T PRK13300 200 ----SKWK--PPVKID-LEKHG-------KEY---KFDDPLVVIDPVDPNRNVAAALSLENLATFILA---AREFL---- 255 (447)
T ss_pred ----HhCC--CCceEe-ccccC-------ccc---cCCCCEEEeCCCCCcchHHHHcCHHHHHHHHHH---HHHHH----
Confidence 3453 333332 12110 000 112479999999999999999998887766542 22222
Q ss_pred hccCCCCcccccCCcc-----h---hhh-ccceEEEEeeecChhhhhhhhhHHHHHHHHHHHHHhhccccceeeccCCCC
Q 004767 343 KNEADVDWDTLFEPFT-----F---FEA-YKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPHPGD 413 (732)
Q Consensus 343 ~~~~~~~W~~Lfep~~-----F---f~~-Yk~yL~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~~hp~P~~ 413 (732)
+.. =..+|.|.+ + +.+ =.+.+.|.....+.-+=.-| |-++--.+.|...||+....++...-|
T Consensus 256 ~~P----s~~fF~~~~~~~~~~~~~l~~R~t~~~~v~f~~p~~v~Dil~-pQl~r~~~~i~~~L~~~gF~v~~~~~~--- 327 (447)
T PRK13300 256 KNP----SLEFFFPSDLSPEEILEELERRGTTVLALEFPRPDIVEDILY-PQLERSLRSIVKLLEREGFEVLRSGAW--- 327 (447)
T ss_pred hCC----CHHhcCCCCCChHHHHHHHhhcCceEEEEEeCCCCCCccchh-HHHHHHHHHHHHHHHHCCCEEEEeeee---
Confidence 222 224444433 1 111 12444555555443333333 556666666777788766555555443
Q ss_pred CCCCCCCceEEEEEeeEecC--CCCCCCCcccchHHHHHHHHH
Q 004767 414 FSDKSKPLYCSYFMGLQRKQ--GVPVGEGEQFDIRLTVKEFKQ 454 (732)
Q Consensus 414 f~~~~~~~~~~ffIGL~~~~--~~~~~~~~~~Dl~~~v~eF~~ 454 (732)
.+.+ .|..++=|.... ......|.++..+.-...|.+
T Consensus 328 -~d~~---~~~l~~el~~~~lp~~~~h~GPpv~~~~~a~~F~~ 366 (447)
T PRK13300 328 -ADED---RAYLLLELEVAELPNVKLHIGPPVWVREHAENFIE 366 (447)
T ss_pred -cCCC---eEEEEEEeecccCCCeeeeeCCCcCchhhHHHHHH
Confidence 2211 244444443221 111122444555555778876
No 12
>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=99.14 E-value=1.1e-08 Score=124.57 Aligned_cols=288 Identities=17% Similarity=0.241 Sum_probs=187.1
Q ss_pred eeecCCCC---CCCCceEEeecCCCCCchhhH------------HHHHHHHH--hcCCCceeeE---eecCCcccEEEEE
Q 004767 91 SYRLGVHG---PGADIDTLCVGPRHATREEDF------------FGELHQML--TEMPEVTELH---PVPDAHVPVMKFK 150 (732)
Q Consensus 91 Sy~lGv~~---p~SDID~lcv~P~~v~r~~dF------------f~~l~~~L--~~~~~V~~l~---~I~~ArVPIIKf~ 150 (732)
||.++... ++-.||+.+..|..+-.++|| ...++..| .+...+.++. .-.+.+-||+.+.
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 56666654 467999999999866443333 33567777 2233333333 2367888999988
Q ss_pred ec-----C------eeeeEEeeecccc-----ccC------------------CCCCCCchhhhccchhhhhhhcchhhh
Q 004767 151 FS-----G------VSIDLLYARLSLW-----VIP------------------EDLDISQDSILQNADEQTVRSLNGCRV 196 (732)
Q Consensus 151 ~~-----G------I~iDLsfa~l~~~-----~ip------------------~~ldl~~~~lL~~lde~svrSLNG~Rv 196 (732)
-. + +.|-|..+..... -.| ..-...|..+|.++-. ..-
T Consensus 81 p~~~~~~~~~~~~~~~iRi~~~~~~~~F~~~rl~P~rnnvR~~~~~~~~~~~~~pTP~YNssIL~D~~~--------~~~ 152 (972)
T PF03813_consen 81 PKGKKDSDDFSKTKFRIRIIPSIPSDTFPLSRLAPSRNNVRPSWFDEEDSSSLPPTPHYNSSILEDMLM--------EEH 152 (972)
T ss_pred ECCccccccccCCcEEEEEEecCCcccCCHHhcCCCCCccCcCcccccccCCCCCCCcchHHHHHHHhH--------HHH
Confidence 42 2 4555554431100 001 0112345556554422 112
Q ss_pred HHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCC-CCCcChHHHHHHHHHHHHh---------CCCCCHHHHHHHHHHHh
Q 004767 197 TDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNV-AGFLGGINWALLVARICQL---------YPNAVPSMLVSRFFRVY 266 (732)
Q Consensus 197 td~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~-~G~LGG~swalLVa~vcQl---------yPnas~~~LL~~FF~~Y 266 (732)
..++.+..-..+.|+.++.++|.||++||+.+.. .|++||+-|++|+++.+|- .+..+.-+|+..+..+.
T Consensus 153 l~~l~~~~~~~p~f~dA~iLlkvWl~QRg~~~~~~~~Gf~~f~~s~lla~Ll~~g~~~~~~~l~~~mSsyQlFr~~l~fL 232 (972)
T PF03813_consen 153 LKYLHEASKSSPAFRDACILLKVWLRQRGFGSGISQGGFGGFEWSMLLAYLLQGGGRNGKKKLSKSMSSYQLFRAVLQFL 232 (972)
T ss_pred HHHHHHHHhcCHHHHHHHHHHHHHHhcCCCCcccCCCCcchHHHHHHHHHHHcCCCccCCcccCCCCCHHHHHHHHHHHH
Confidence 3455555566799999999999999999998865 5889999999999999976 34567889999999999
Q ss_pred ccCCC-CCceeecccccCCCCccccCCCCCCCCCCCceeEeCCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHhcc
Q 004767 267 TQWRW-PNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNE 345 (732)
Q Consensus 267 s~wdW-~~pV~l~~i~~G~l~~~vWdP~~~~~dr~hlMpIiTP~~P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~~i~~~~ 345 (732)
+..|| .+|+.++.-.+.......| .+.+....+|| .-.+|.+.+++.++++.++.|-+++.++|.+-. .
T Consensus 233 A~~d~~~~~l~~~~~~~~~~~~~~~-------~~~~~~vf~D~-sg~~Nl~~~ms~~s~~~L~~eA~~tl~lL~~~~--~ 302 (972)
T PF03813_consen 233 ATTDLSKKPLFFKSSSDSTESLEEF-------HSAFDPVFVDP-SGGLNLLAKMSPSSYEELQHEAKLTLELLDDSS--D 302 (972)
T ss_pred hccccccCceEEecCCCccchhhhh-------hccCCeEEEeC-CCCEEEEEcCCHHHHHHHHHHHHHHHHHhcccc--c
Confidence 99999 5688776543211111111 12345666777 456999999999999999999999999886421 1
Q ss_pred CCCCcccccC-C-cchhhhccceEEEE---e----eecChhhhhhhhhHHHHHHHHHHH-HHh
Q 004767 346 ADVDWDTLFE-P-FTFFEAYKNYLRID---I----SAENADDLRNWKGWVESRLRQLTL-KIE 398 (732)
Q Consensus 346 ~~~~W~~Lfe-p-~~Ff~~Yk~yL~I~---v----~a~~~e~~~~w~GwVESRlR~Lv~-~LE 398 (732)
. ..+.+|- + ..+..+|.+++.|. . ......+...|..++..++-.|+. .|-
T Consensus 303 d--~F~~lFl~~~~~~~~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lL~raLg 363 (972)
T PF03813_consen 303 D--GFDSLFLTKVDPPALRFDHVLRISPDSLLSSFSPDESLDFLSFSNYLLRKIYRLLKRALG 363 (972)
T ss_pred c--chhhhhcccCCcccccCCEEEEEcchhhcccccccccccccchhHHHHHHHHHHHHHHHH
Confidence 2 5677774 4 45678999999991 1 112223334454556667766653 454
No 13
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=99.12 E-value=3.5e-08 Score=108.83 Aligned_cols=345 Identities=19% Similarity=0.221 Sum_probs=202.0
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCC-CCCceEEe
Q 004767 29 RKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGP-GADIDTLC 107 (732)
Q Consensus 29 ~eL~~~L~~~~l~pS~eE~~~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p-~SDID~lc 107 (732)
+.|.+.|+. +.||+||.++=+++.+.|...+++. +.+.|+ ++.+...||++=|.|++ +.|||+.|
T Consensus 5 ~~l~evl~~--i~P~~eE~~~~~~~~e~l~~~~~~~----~~e~~~--------~aev~lVGS~AkgTwL~gd~DIDvFi 70 (443)
T COG1746 5 EVLEEVLKR--IKPTEEERKKLKEVAEELRERINEI----IEELGI--------DAEVVLVGSYAKGTWLRGDHDIDVFI 70 (443)
T ss_pred HHHHHHHHH--cCCCHHHHHHHHHHHHHHHHHHHHH----HHhcCC--------cceEEEEeecccCcccCCCcceeEEE
Confidence 345566664 6799999988888888877777653 344444 58899999999999999 68999999
Q ss_pred ecCCCCCchhhH----HHHHHHHHhcCCCceeeEeecCCcccEEEEEecCeeeeEEeeeccccccCCCCCCCchhhhccc
Q 004767 108 VGPRHATREEDF----FGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNA 183 (732)
Q Consensus 108 v~P~~v~r~~dF----f~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~~ip~~ldl~~~~lL~~l 183 (732)
..|....++ .. +......|.+ .+ -.+.-|-=|-+.-.++|+++|+.=|-.... ++ .+...+
T Consensus 71 ~Fp~d~~~e-el~~~GL~ig~~~l~~-~~----~~~~YAeHPYV~g~v~G~eVDvVPCy~v~~--~~-------~~~sAV 135 (443)
T COG1746 71 AFPKDTSEE-ELEEKGLEIGREVLKR-GN----YEERYAEHPYVTGEVDGYEVDVVPCYKVED--GE-------KIISAV 135 (443)
T ss_pred ECCCCCCHH-HHHHHHHHHHHHHhcC-Cc----hhhhhccCCeeEEEEccEEEEEEecccccC--cc-------cccccc
Confidence 999887764 22 2223334442 11 125568889999999999999985532100 11 011111
Q ss_pred hhhhhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCC--CCCCcChHHHHHHHHHHHHhCCCCCHHHHHHH
Q 004767 184 DEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSN--VAGFLGGINWALLVARICQLYPNAVPSMLVSR 261 (732)
Q Consensus 184 de~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn--~~G~LGG~swalLVa~vcQlyPnas~~~LL~~ 261 (732)
|-.- -=+.++..-+-.. -+.=+|.+|.+.|.=|+|++ ..++++||.-=||++++ -.
T Consensus 136 DRTp-------lHt~yv~e~L~~~--~~deVrLLK~FlK~iGvYGaE~rt~GFSGYL~ELLII~y-------------Gs 193 (443)
T COG1746 136 DRTP-------LHTRYVEEHLKGR--QKDEVRLLKQFLKGIGVYGAELRTQGFSGYLCELLIIHY-------------GS 193 (443)
T ss_pred cCcc-------hhHHHHHHHhccc--chhHHHHHHHHHhccCccceeeeeccchHHHHHHHHhhh-------------cc
Confidence 1100 0123333333221 12347899999999999996 46889999999999987 23
Q ss_pred HHHHhccCC-CCCceeecccccCCCCccccCCCCCCCCCCCceeEeCCCCCCCCcccccChhhHHHHHHHHHHHHHHHHH
Q 004767 262 FFRVYTQWR-WPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEA 340 (732)
Q Consensus 262 FF~~Ys~wd-W~~pV~l~~i~~G~l~~~vWdP~~~~~dr~hlMpIiTP~~P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~~ 340 (732)
|=...-... |.-+++|. +. .|..... .| ..|-|+||.+|..|+|.+||..++..+. -|.+ .
T Consensus 194 Fe~vl~~a~~wrp~~~ID-~~-------~~~~e~f-~d--~PliVvDPVDP~RNVAAalSl~~la~f~----~aar---~ 255 (443)
T COG1746 194 FENVLKAASRWRPGKIID-LE-------GHKRERF-ED--EPLIVVDPVDPKRNVAAALSLENLARFV----HAAR---E 255 (443)
T ss_pred HHHHHHHHhccCCCeEEe-cc-------chhhhcc-CC--CCeEecCCCCCccchhhhcCHHHHHHHH----HHHH---H
Confidence 333333222 77776542 22 1211111 11 2799999999999999999987766544 2333 2
Q ss_pred HHhccCCCCcccccCCcc--------hhhhccceEEEEeeecChhhhhhhhhHHHHHHHHHHHHHhhccccceeeccCCC
Q 004767 341 MEKNEADVDWDTLFEPFT--------FFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPHPG 412 (732)
Q Consensus 341 i~~~~~~~~W~~Lfep~~--------Ff~~Yk~yL~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~~hp~P~ 412 (732)
.+++.+ ...|.|.. ...+=.+-+.+..-..+.-+ ...-+-++---+.|...||...+.++..+-|-
T Consensus 256 FL~~PS----~efF~p~~~~~~~~~~~~~rgt~v~~l~~~~pd~vd-DilypQl~r~~~~l~r~Le~~gF~vl~~~~~~- 329 (443)
T COG1746 256 FLKNPS----PEFFFPRKPKPLLLSKLRRRGTHVLALVFPKPDLVD-DILYPQLERTARSLFRALEEEGFRVLRSGVWS- 329 (443)
T ss_pred HhcCCC----hhhcCCCCcCcccccchhhcCceEEEEEeCCCCCCc-chhhHHHHHHHHHHHHHHHHcCCEEeeeeeee-
Confidence 333322 23333321 11122233344444444322 23447777777788888888766656555552
Q ss_pred CCCCCCCCceEEEEEeeEecCCC--CCCCCcccchHHHHHHHHH
Q 004767 413 DFSDKSKPLYCSYFMGLQRKQGV--PVGEGEQFDIRLTVKEFKQ 454 (732)
Q Consensus 413 ~f~~~~~~~~~~ffIGL~~~~~~--~~~~~~~~Dl~~~v~eF~~ 454 (732)
|... ++.-|+=++...-. ....|.+..-..+++ |.+
T Consensus 330 ---D~~~--~~~v~~E~~~~~l~~i~~r~GPp~~~e~a~r-F~~ 367 (443)
T COG1746 330 ---DESE--RIYVLLELESKELPRIELRVGPPVWTEHAVR-FIE 367 (443)
T ss_pred ---cCCc--ceEEEEEEecccccceeeecCCCccchhHHH-HHH
Confidence 2221 34555555432110 111133344466776 876
No 14
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=98.38 E-value=5.5e-06 Score=98.87 Aligned_cols=269 Identities=19% Similarity=0.267 Sum_probs=166.3
Q ss_pred CcEEE-EeeeeecCCC-CCCCCceEEeecCCCCCchhhH------------HHHHHHHHhcCCCceeeEee---cCCccc
Q 004767 83 NAKIF-TFGSYRLGVH-GPGADIDTLCVGPRHATREEDF------------FGELHQMLTEMPEVTELHPV---PDAHVP 145 (732)
Q Consensus 83 ~~kI~-~FGSy~lGv~-~p~SDID~lcv~P~~v~r~~dF------------f~~l~~~L~~~~~V~~l~~I---~~ArVP 145 (732)
.+++. ..||+.+|.. .|+.-+|+++..|+..-.++|+ +..+...|.+.+....+... .+-.-|
T Consensus 147 p~~v~~vv~sal~~~~~~P~i~vDvll~mP~e~~~~kd~ln~Ryf~kra~yla~~~~hl~e~l~~~~~~f~~~n~d~~~p 226 (1121)
T KOG2054|consen 147 PAQVTKVVGSALLGTCLRPDISVDVLLTMPREILQQKDGLNQRYFRKRALYLAYLAHHLLEDLLFGSLEFSYTNGDHLKP 226 (1121)
T ss_pred ccccceeeeecccCcccCCcchhhhhhhhhHHhhcCcccccccccchHHHHHHHHHHHHHhccccceeeecccCCccccc
Confidence 34555 5566666544 6889999999998754322233 33344444444433233322 245568
Q ss_pred EEEEEecCeeeeEEeeeccccccCCCCC-CCchhhhccchhhhhhhcchhhh--------------------------HH
Q 004767 146 VMKFKFSGVSIDLLYARLSLWVIPEDLD-ISQDSILQNADEQTVRSLNGCRV--------------------------TD 198 (732)
Q Consensus 146 IIKf~~~GI~iDLsfa~l~~~~ip~~ld-l~~~~lL~~lde~svrSLNG~Rv--------------------------td 198 (732)
|+.+.-.|-..|++-.+....-||..+. ..++.+|-++ ||+|. ..
T Consensus 227 il~i~~~~~~~~~~~~~~~~~li~~~~~~f~~~kllp~~--------~~ir~~~e~~e~ppTP~yN~svL~~~~le~~~q 298 (1121)
T KOG2054|consen 227 ILLIRPRGKDERLVTVRPPDFLIPCRLLPFKNNKLLPWY--------NGIRPAGEGSEEPPTPRYNTSVLEDQVLEEYLQ 298 (1121)
T ss_pred hhhccccCCccccccccCccccccccccccccccccchh--------cccCccccCCCCCCCCccchhHHHHHHHHHHHH
Confidence 8888776655555433322222222211 1122222111 11111 12
Q ss_pred HHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCcChHHHHHHHHHHHH---hCCCCCHHHHHHHHHHHhccCCCCC-c
Q 004767 199 QILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQ---LYPNAVPSMLVSRFFRVYTQWRWPN-P 274 (732)
Q Consensus 199 ~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~LGG~swalLVa~vcQ---lyPnas~~~LL~~FF~~Ys~wdW~~-p 274 (732)
++.+.....+.|+.++-..|.|+++|.. +-..|++||+-|++++++... ++-+.+..+++..-+++.+.|||.. -
T Consensus 299 ~L~K~~s~~~~f~da~~Llk~WlrqRs~-~~~~~gfg~f~~s~lvv~L~s~~ki~~~~S~yqvfR~vl~flat~dlt~~~ 377 (1121)
T KOG2054|consen 299 LLSKTLSSAKGFKDALALLKVWLRQRSL-DIGQGGFGGFLLSALVVYLVSTRKIHTTLSAYQVFRSVLQFLATTDLTVNG 377 (1121)
T ss_pred HHHHHHhhhhhHHHHHHHHHHHHHhhhh-hcccCcchHHHHHHHHHHHHhcCchhhcchHHHHHHHHHHHHhhhhhhccc
Confidence 3344445568899999999999999922 124788999999999998874 4566788899999999999999986 4
Q ss_pred eeecccccCCCCccccCCCCCCCCCCCceeEeCCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHhccCCCCccccc
Q 004767 275 VLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLF 354 (732)
Q Consensus 275 V~l~~i~~G~l~~~vWdP~~~~~dr~hlMpIiTP~~P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~~i~~~~~~~~W~~Lf 354 (732)
+-+++-. .+. |....-+..+....+|= .-..|...|++.++++.+++|.+-+..+|.+.... .++.+|
T Consensus 378 ~~l~~~~-~s~------~~~~~f~e~~~~~f~D~-s~~~NLc~~mt~s~y~~~q~ea~ltl~lL~~~~~~----~F~~IF 445 (1121)
T KOG2054|consen 378 ISLVPSS-PSL------PALADFHEGQLVTFIDS-SGHLNLCANMTASTYEQVQEEARLTLMLLDSRADD----GFSLIF 445 (1121)
T ss_pred eEeccCC-CCc------hhhhhhhhcceeeEecc-CCcchhhhhccHHHHHHHHHHHHHHHHHHhhhhhc----Ccceee
Confidence 4443210 000 10000112234444442 34689999999999999999999999999875432 577777
Q ss_pred -CCcchhhhccceEEEEee
Q 004767 355 -EPFTFFEAYKNYLRIDIS 372 (732)
Q Consensus 355 -ep~~Ff~~Yk~yL~I~v~ 372 (732)
++.+.|..|.|-+.+...
T Consensus 446 mtkip~~~~yDh~l~l~~~ 464 (1121)
T KOG2054|consen 446 MTKIPVFRAYDHVLHLSPL 464 (1121)
T ss_pred eecCCchhhhheeeecccc
Confidence 778899999998877654
No 15
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=98.29 E-value=4.1e-05 Score=80.28 Aligned_cols=213 Identities=17% Similarity=0.223 Sum_probs=148.8
Q ss_pred EEEeeeeecCCCCCCC-CceEEeecCCCCCchhhHHHHHH----HHHhcCCCceeeEeecCCcccEEEEEec--C--eee
Q 004767 86 IFTFGSYRLGVHGPGA-DIDTLCVGPRHATREEDFFGELH----QMLTEMPEVTELHPVPDAHVPVMKFKFS--G--VSI 156 (732)
Q Consensus 86 I~~FGSy~lGv~~p~S-DID~lcv~P~~v~r~~dFf~~l~----~~L~~~~~V~~l~~I~~ArVPIIKf~~~--G--I~i 156 (732)
+.-.||+.-|+.+.|. +.|+++++....|. .....+. +-|+...+=.....|..+.+|.++..+. + ...
T Consensus 5 V~rVG~~aKG~ll~Gd~~~~lVv~c~~~PT~--~ll~~v~~~l~e~l~~~~~~e~~~~~~~~~~~~~~~~i~ltSp~~r~ 82 (246)
T smart00572 5 VMRVGSFAKGTLLKGDNVAELVLLCKEKPTS--ELVARLARKLPEQLKAVTEDEALIIVTSTKEPTMEVGILITSPLARV 82 (246)
T ss_pred eEEeeeeccCceecCCCceeEEEEecCCCcH--HHHHHHHHHHHHHHhhcCcccceeeeeccCCCceeEEEEEecccccc
Confidence 6778999999999874 88999999877775 3445444 4444322112223466777788887763 1 223
Q ss_pred eEEeeeccccccCCCCCCCchhhhccch-hhhhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCcC
Q 004767 157 DLLYARLSLWVIPEDLDISQDSILQNAD-EQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLG 235 (732)
Q Consensus 157 DLsfa~l~~~~ip~~ldl~~~~lL~~ld-e~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~LG 235 (732)
+...+ .+|+++.-.+.. .-+| ..|+.+|-.+|-+.++.........|+.++|++|-|.++-..... |.
T Consensus 83 ~~~~~-----~~~~~~~~~~p~--~~ld~~~cl~aLAalRhakWFq~~a~~l~s~~iviRilKd~~~R~~~~~p----L~ 151 (246)
T smart00572 83 ELLIT-----TVPENLRKLDPE--DHLDRKKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQP----LS 151 (246)
T ss_pred ccccc-----ccCcccccCCcc--ccCCHHHHHHHHHHHHHhHHHHHhccCCcchhhHHHHHHHHHHhcccccc----cc
Confidence 33332 234443322211 1133 457888889999999999988888999999999999998765443 88
Q ss_pred hHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHhccCCCCCceeecccccCCCCccccCCCCCCCCCCCceeEeCCCCC-CC
Q 004767 236 GINWALLVARICQLYP-NAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYP-CM 313 (732)
Q Consensus 236 G~swalLVa~vcQlyP-nas~~~LL~~FF~~Ys~wdW~~pV~l~~i~~G~l~~~vWdP~~~~~dr~hlMpIiTP~~P-~~ 313 (732)
++.+=+++++.+-... ..++++-+.+||++.++ |.+ + |. ---|.||+.+ ..
T Consensus 152 ~w~iELl~~~~i~~~~~~l~~~~a~RR~fe~lAs--------------G~l-~----p~--------~~gI~DPce~~~~ 204 (246)
T smart00572 152 GWPLELLVEKAIGSARQPLGLGDAFRRVFECLAS--------------GIL-L----PG--------SPGLTDPCEKDNT 204 (246)
T ss_pred cccHHHHHHHHhccCCCCCCHHHHHHHHHHHHHh--------------ccC-c----CC--------CCCCcCCCCCCcc
Confidence 9999999999986332 24689999999999874 111 0 10 0237899997 88
Q ss_pred CcccccChhhHHHHHHHHHHHHHHH
Q 004767 314 NSSYNVSTSTLRIMMDEFQRGHEIC 338 (732)
Q Consensus 314 Nsa~NVs~sTl~vI~~EF~RA~~Il 338 (732)
|++...|....+.|...-+.|.+++
T Consensus 205 nv~~~lT~qqrd~It~sAQ~alRl~ 229 (246)
T smart00572 205 DALTALTLQQREDVTASAQTALRLL 229 (246)
T ss_pred cHHHhcCHHHHHHHHHHHHHHHHHH
Confidence 9988899888999998888888776
No 16
>PF03828 PAP_assoc: Cid1 family poly A polymerase; InterPro: IPR002058 These PAP/25A associated domains are found in uncharacterised eukaryotic proteins, a number of which are described as 'topoisomerase 1-related' though they appear to have little or no homology to topoisomerase 1. The signatures that define this group of sequences often occur towards the C terminus after the PAP/25A core domain IPR001201 from INTERPRO.; PDB: 2B4V_A 2B56_A 2B51_A 4EP7_B 2NOM_B 2Q0G_B 2Q0D_B 2Q0C_A 2Q0F_A 2Q0E_A ....
Probab=97.66 E-value=2.9e-05 Score=63.63 Aligned_cols=55 Identities=22% Similarity=0.404 Sum_probs=37.1
Q ss_pred CHHHHHHHHHHHhc-cCCCCCceeecccccCCC-C--ccccCCCCCCCCCCCceeEeCCCCCC
Q 004767 254 VPSMLVSRFFRVYT-QWRWPNPVLLCAIEEGSL-G--LQVWDPRRNPKDKYHLMPIITPAYPC 312 (732)
Q Consensus 254 s~~~LL~~FF~~Ys-~wdW~~pV~l~~i~~G~l-~--~~vWdP~~~~~dr~hlMpIiTP~~P~ 312 (732)
++++||..||+||+ .|||.+-|+. ++.|.. . ...|.. ....+...|+|+||+.|+
T Consensus 1 slg~Ll~~Ff~~Y~~~Fd~~~~~Is--i~~g~~~~k~~~~~~~--~~~~~~~~l~IeDP~~~~ 59 (60)
T PF03828_consen 1 SLGELLLGFFEYYGRKFDYENNVIS--IRNGGYFPKEEKNWSK--SRNQRKKRLCIEDPFDPS 59 (60)
T ss_dssp -HHHHHHHHHHHHHHTS-TTTEEEE--SSSSSEEEHHHHTGCH--CCCCECSSSEBBESSSTT
T ss_pred CHHHHHHHHHHHhCCcCCCCceEEE--ecCCceEEhhhccccc--cccCCCCeEEEECCCCCC
Confidence 57899999999999 9999997764 444542 1 234431 111235689999999885
No 17
>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=97.62 E-value=0.00053 Score=65.07 Aligned_cols=77 Identities=27% Similarity=0.371 Sum_probs=55.7
Q ss_pred CcEEEEeeeeecCCCCC-CCCceEEeecCCCCC----chhhHHHHHHHHHhcCCCceeeEeecCCcccEEEEEec--Cee
Q 004767 83 NAKIFTFGSYRLGVHGP-GADIDTLCVGPRHAT----REEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFS--GVS 155 (732)
Q Consensus 83 ~~kI~~FGSy~lGv~~p-~SDID~lcv~P~~v~----r~~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~--GI~ 155 (732)
...++.||||+.|...+ .||||++++.+.... ...+++..+...|.+...- .......-|.|.+.+. |++
T Consensus 27 ~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~~~~~~~~~~~~l~~~L~~~~~~---~~~~~~~~~~v~v~~~~~~~~ 103 (143)
T cd05400 27 VAEVFLQGSYARGTALRGDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEYYGA---NEEVKAQHRSVTVKFKGQGFH 103 (143)
T ss_pred ccEEEEEcceeCCCCCCCCCceeEEEEEcCcccccccCHHHHHHHHHHHHHHhcCc---ccccccCceEEEEEEcCCCeE
Confidence 46899999999999977 899999999876532 1236677777888764321 1112355578888886 899
Q ss_pred eeEEeee
Q 004767 156 IDLLYAR 162 (732)
Q Consensus 156 iDLsfa~ 162 (732)
|||+-+.
T Consensus 104 vDvvP~~ 110 (143)
T cd05400 104 VDVVPAF 110 (143)
T ss_pred EEEEEEe
Confidence 9997654
No 18
>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=97.46 E-value=0.00019 Score=57.51 Aligned_cols=26 Identities=35% Similarity=0.581 Sum_probs=24.1
Q ss_pred CcEEEEeeeeecCCCCCCCCceEEee
Q 004767 83 NAKIFTFGSYRLGVHGPGADIDTLCV 108 (732)
Q Consensus 83 ~~kI~~FGSy~lGv~~p~SDID~lcv 108 (732)
..+++.||||+.|.+.+.||||++|+
T Consensus 17 ~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 17 GYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred CcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 46899999999999999999998887
No 19
>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=97.26 E-value=0.00032 Score=61.20 Aligned_cols=32 Identities=34% Similarity=0.542 Sum_probs=29.3
Q ss_pred CcEEEEeeeeecCCCCCCCCceEEeecCCCCC
Q 004767 83 NAKIFTFGSYRLGVHGPGADIDTLCVGPRHAT 114 (732)
Q Consensus 83 ~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~ 114 (732)
...++.|||++.|.+.|+||||++++.+....
T Consensus 14 ~~~v~lfGS~a~g~~~~~SDIDl~i~~~~~~~ 45 (93)
T PF01909_consen 14 VAEVYLFGSYARGDATPDSDIDLLIILDEPED 45 (93)
T ss_dssp TEEEEEEHHHHHTSSCTTSCEEEEEEESSTSC
T ss_pred CCEEEEECCcccCcCCCCCCEEEEEEeCCccc
Confidence 47899999999999999999999999988765
No 20
>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=96.71 E-value=0.0044 Score=58.26 Aligned_cols=93 Identities=19% Similarity=0.319 Sum_probs=57.3
Q ss_pred HHHHHHHHHHcCCCCCC--CCCcChHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhccCCCCCceeecccccCCCCccccC
Q 004767 214 LRCMRFWAKRRGVYSNV--AGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWD 291 (732)
Q Consensus 214 lr~IK~WAK~RgIysn~--~G~LGG~swalLVa~vcQlyPnas~~~LL~~FF~~Ys~wdW~~pV~l~~i~~G~l~~~vWd 291 (732)
+|.+|.+.|.-|+|++- .++++||..=|||+++= + +...-+.-+ +|..++.|..-..+.. .+..
T Consensus 3 VrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~yG------s----F~~~l~~a~--~W~~~~~Id~~~~~~~-~~~f- 68 (114)
T PF09249_consen 3 VRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHYG------S----FENVLEAAA--KWKPPVVIDLEDHGEP-SKKF- 68 (114)
T ss_dssp HHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHHHS------S----HHHHHHHHT--T--TTEEEETT-TTE---EEE-
T ss_pred hHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHHHC------C----HHHHHHHHH--hcCCCeEEccCccchh-hhhc-
Confidence 68899999999999964 68899999999999872 2 223333334 5666776532211110 0111
Q ss_pred CCCCCCCCCCceeEeCCCCCCCCcccccChhhHHHHH
Q 004767 292 PRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMM 328 (732)
Q Consensus 292 P~~~~~dr~hlMpIiTP~~P~~Nsa~NVs~sTl~vI~ 328 (732)
...+.|+||.+|..|+|.+||..++..+.
T Consensus 69 --------~~PlvviDPvDp~RNVAAalS~~~~~~fv 97 (114)
T PF09249_consen 69 --------DDPLVVIDPVDPNRNVAAALSLENLAEFV 97 (114)
T ss_dssp ---------SS-EEEETTEEEEETTTTS-HHHHHHHH
T ss_pred --------CCCeEEcCCCCCCchHhHhcCHHHHHHHH
Confidence 24699999999999999999988766554
No 21
>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=96.70 E-value=0.0031 Score=54.39 Aligned_cols=31 Identities=35% Similarity=0.563 Sum_probs=28.1
Q ss_pred cEEEEeeeeecCCCCCCCCceEEeecCCCCC
Q 004767 84 AKIFTFGSYRLGVHGPGADIDTLCVGPRHAT 114 (732)
Q Consensus 84 ~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~ 114 (732)
..++.|||++.|-+.++||||++++.+....
T Consensus 19 ~~i~LfGS~arg~~~~~SDiDl~vi~~~~~~ 49 (93)
T cd05403 19 EKVYLFGSYARGDARPDSDIDLLVIFDDPLD 49 (93)
T ss_pred cEEEEEeeeecCCCCCCCCeeEEEEeCCCCC
Confidence 5799999999999999999999999887654
No 22
>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=96.24 E-value=0.043 Score=68.12 Aligned_cols=155 Identities=23% Similarity=0.399 Sum_probs=103.8
Q ss_pred hhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCcChHHHHHHHHHHH-HhCC---CCCHHHHHHHHHHHhcc
Q 004767 193 GCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARIC-QLYP---NAVPSMLVSRFFRVYTQ 268 (732)
Q Consensus 193 G~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~LGG~swalLVa~vc-QlyP---nas~~~LL~~FF~~Ys~ 268 (732)
..+-+..|..+.-..+.|..++|.+|.|...+-+ .|++.--..=||||++. +-+| +.++.+=+.+|.++-++
T Consensus 668 ~p~h~~~i~~l~~~~p~fs~tvRL~KrW~~shlL----s~~i~~E~vELlva~vfl~~~p~~~P~S~~~GFlRfL~lLs~ 743 (972)
T PF03813_consen 668 LPKHTSAIHGLHTRFPSFSPTVRLAKRWLSSHLL----SGHISEEAVELLVASVFLSPAPWSPPSSPQTGFLRFLHLLST 743 (972)
T ss_pred hHHHHHHHHHHHhhCCchhHHHHHHHHHHHhccC----cccCCHHHHHHHHHHHhcCCCCCCCCCCHhHHHHHHHHHHHh
Confidence 3445566666666788999999999999999977 56778889999999887 3344 45666667788888899
Q ss_pred CCCCC-ceeecccccCCC----------CccccCCCCCCCCCCCceeEeCCCCCCCCc--ccccChhhHHHHHHHHHHHH
Q 004767 269 WRWPN-PVLLCAIEEGSL----------GLQVWDPRRNPKDKYHLMPIITPAYPCMNS--SYNVSTSTLRIMMDEFQRGH 335 (732)
Q Consensus 269 wdW~~-pV~l~~i~~G~l----------~~~vWdP~~~~~dr~hlMpIiTP~~P~~Ns--a~NVs~sTl~vI~~EF~RA~ 335 (732)
|||.+ |+++.- . +.+ .+..|.. ..+......|.|.||.+|.-.. ...-+..-+++|+.--+.+.
T Consensus 744 ~dW~~~PLiVd~-~-~~l~~~~~~~i~~~f~~~R~-~dp~~~~p~~~IaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~sl 820 (972)
T PF03813_consen 744 WDWREEPLIVDF-N-NELTEEDRAEIETNFDAWRK-IDPAMNLPAMFIATPYDPEGSLWTRNGPSKVVAKRLTALAKASL 820 (972)
T ss_pred CCCCcCCEEEEC-C-CCCCHHHHHHHHHHHHHhhc-cCccccCCcEEEEeCCCCCCCEeECCCCCHHHHHHHHHHHHHHH
Confidence 99985 776532 2 111 1222321 1122334579999999985331 12344455677777666777
Q ss_pred HHHHHHHhccCCCCcccccCC
Q 004767 336 EICEAMEKNEADVDWDTLFEP 356 (732)
Q Consensus 336 ~Il~~i~~~~~~~~W~~Lfep 356 (732)
++++. .+-...+|..||.+
T Consensus 821 ~~l~~--~~~~~~~~~~lF~~ 839 (972)
T PF03813_consen 821 KLLEE--QGLSDLDWKSLFRP 839 (972)
T ss_pred HHHHh--cCCCCCCHHHhcCC
Confidence 77762 12123499999976
No 23
>PF14091 DUF4269: Domain of unknown function (DUF4269)
Probab=95.93 E-value=0.088 Score=52.06 Aligned_cols=117 Identities=21% Similarity=0.359 Sum_probs=74.3
Q ss_pred EEEeeeeecCCCCCCCCceEEeecCCCCCchhhHHHHHHHHHhcCCCceee-EeecCCcccEEEEEecCeeeeEEeeecc
Q 004767 86 IFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTEL-HPVPDAHVPVMKFKFSGVSIDLLYARLS 164 (732)
Q Consensus 86 I~~FGSy~lGv~~p~SDID~lcv~P~~v~r~~dFf~~l~~~L~~~~~V~~l-~~I~~ArVPIIKf~~~GI~iDLsfa~l~ 164 (732)
-...|...+|+..++||||++|.++.. +.|-..+.....+.++.+-- ..|..-..=+..|.+.|..|-|---..+
T Consensus 18 PiL~GTiPi~Idi~~SDLDIic~~~d~----~~F~~~l~~~f~~~~~f~~~~~~i~~~~~~~~~F~~~~~~~EiF~Q~~P 93 (152)
T PF14091_consen 18 PILVGTIPIGIDIPGSDLDIICEVPDP----EAFEQLLQSLFGQFEGFTIKEKTIRGEPSIVANFRYEGFPFEIFGQPIP 93 (152)
T ss_pred CEEecccccccCCCCCCccEEEEeCCH----HHHHHHHHHHhccCCCceeeeceeCCceeEEEEEEECCceEEEeecCCC
Confidence 345699999999999999999998853 23444444444444443211 2344555566788889988887432221
Q ss_pred ccccCCCCCCCchhhhccchhhhhhhcchhhhHHHHHHHcCCh-hhHHHHHHHHH--------HHHHHcCCCCC
Q 004767 165 LWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKI-QNFRTTLRCMR--------FWAKRRGVYSN 229 (732)
Q Consensus 165 ~~~ip~~ldl~~~~lL~~lde~svrSLNG~Rvtd~IlrlVP~~-~~FR~llr~IK--------~WAK~RgIysn 229 (732)
+..-||+|=..--.+++-.. +.||.-+|-+| +||+--||-++
T Consensus 94 -----------------------v~~QnayrHm~iE~rLL~~~g~~~r~~Ii~LK~~GlKTEPAFa~lLgL~GD 144 (152)
T PF14091_consen 94 -----------------------VEEQNAYRHMLIEHRLLELHGPSFREEIIELKESGLKTEPAFAKLLGLEGD 144 (152)
T ss_pred -----------------------hhhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHcCCcchHHHHHHhCCCCC
Confidence 23457777554334444444 78998888887 46666666544
No 24
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=95.47 E-value=0.052 Score=49.96 Aligned_cols=46 Identities=28% Similarity=0.451 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCCCCCceEEeecCCC
Q 004767 51 EEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRH 112 (732)
Q Consensus 51 ~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~ 112 (732)
+++++++...+++|. |. .++-.||||+=|=..|+||||+++-....
T Consensus 8 ~~~lr~~~~~l~~k~-------gv---------~~~~vFGS~aRgE~~~~SDIDILVef~~~ 53 (97)
T COG1669 8 KKILRKIKPELKEKY-------GV---------KRVAVFGSYARGEQKPDSDIDILVEFEPG 53 (97)
T ss_pred HHHHHHHHHHHHHHh-------CC---------ceEEEeeeeecCCCCCCCCceeEEeecCC
Confidence 344556666666553 32 57999999999999999999988866433
No 25
>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=95.24 E-value=0.83 Score=48.58 Aligned_cols=209 Identities=18% Similarity=0.247 Sum_probs=133.3
Q ss_pred eeeeecCCCCCCC-CceEEeecCCCCCchhhHHHHHHHHHhc----C-CC-ce---e-eEeecCCcccEEEEEe--cC--
Q 004767 89 FGSYRLGVHGPGA-DIDTLCVGPRHATREEDFFGELHQMLTE----M-PE-VT---E-LHPVPDAHVPVMKFKF--SG-- 153 (732)
Q Consensus 89 FGSy~lGv~~p~S-DID~lcv~P~~v~r~~dFf~~l~~~L~~----~-~~-V~---~-l~~I~~ArVPIIKf~~--~G-- 153 (732)
.||+.-|+.+.|. +.|+|+++..-.|. ++++.+.+.|.+ . +. |. + ...|...+.|.+...+ .+
T Consensus 2 VG~~aKGllL~Gd~~~eLVVlck~kPT~--~lL~~v~~~L~~~L~~~~~~ev~~~~e~~~~~~~~~~~~~~~~~~lts~~ 79 (248)
T PF07528_consen 2 VGSFAKGLLLKGDNDVELVVLCKEKPTK--ELLNRVAEKLPEQLKKVTPEEVTNSVEAAIIIDSCKEPKLEVGIDLTSPV 79 (248)
T ss_pred cceecCCceecCCceEeEEEEcCCCCcH--HHHHHHHHHHHHHHhhhCccccccchhhhhhhcccccccceeeEEecCCc
Confidence 5999999999875 89999999877775 566665555443 2 22 11 0 1112223335555544 22
Q ss_pred eeeeEEeeeccccccCCCCCCCchhhhccch-hhhhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCC
Q 004767 154 VSIDLLYARLSLWVIPEDLDISQDSILQNAD-EQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAG 232 (732)
Q Consensus 154 I~iDLsfa~l~~~~ip~~ldl~~~~lL~~ld-e~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G 232 (732)
+.+.+..+. .+++..-.+. -..+| ..|..+|-.+|=+.++.+........+.++|++|-..+|--- ++
T Consensus 80 ~r~~~~~~~-----~~~~~~~~dp--~~~Ld~~~cl~aLaalRhakWFq~~a~~l~s~~~viRIlrDl~~R~p~----w~ 148 (248)
T PF07528_consen 80 MRVRVLITT-----IPENLSKLDP--EDHLDRKKCLSALAALRHAKWFQARANGLQSCVIVIRILRDLRQRVPT----WQ 148 (248)
T ss_pred eEEEEeccc-----cCccccccCh--hhcCCHHHHHHHHHHHHHhHHHHHHhccCCCcceehhhHHHHHHhCCC----CC
Confidence 333333322 2333221111 11234 357788888999999999988888899999999999887533 55
Q ss_pred CcChHHHHHHHHHHHHhCCC---CCHHHHHHHHHHHhcc-CCCCCceeecccccCCCCccccCCCCCCCCCCCceeEeCC
Q 004767 233 FLGGINWALLVARICQLYPN---AVPSMLVSRFFRVYTQ-WRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITP 308 (732)
Q Consensus 233 ~LGG~swalLVa~vcQlyPn---as~~~LL~~FF~~Ys~-wdW~~pV~l~~i~~G~l~~~vWdP~~~~~dr~hlMpIiTP 308 (732)
-|+++.+=+|+-+..-.-|+ .++++-+.+||+..|. +=.|. . | -|.||
T Consensus 149 ~L~~W~leLL~~~~i~~~~~~~~l~~g~a~RRvle~lasGillp~----------~-------~-----------gl~DP 200 (248)
T PF07528_consen 149 PLSSWALELLVEKAISNNSSRQPLSPGDAFRRVLECLASGILLPG----------S-------P-----------GLRDP 200 (248)
T ss_pred CCChhHHHHHHHHHeeeCCCCCCCChHHHHHHHHHHHhCceecCC----------C-------C-----------CCcCC
Confidence 68888888887766653333 4689999999999773 11111 0 1 14567
Q ss_pred CC-CCCCcccccChhhHHHHHHHHHHHHHHH
Q 004767 309 AY-PCMNSSYNVSTSTLRIMMDEFQRGHEIC 338 (732)
Q Consensus 309 ~~-P~~Nsa~NVs~sTl~vI~~EF~RA~~Il 338 (732)
+. ...++..+.|..-...|..--|.+.+++
T Consensus 201 cE~~~~~~~~~lt~qq~e~it~sAQ~~LRll 231 (248)
T PF07528_consen 201 CEKDPVDVLDTLTLQQREDITSSAQTALRLL 231 (248)
T ss_pred CCCCCceeeccCCHHHHHHHHHHHHHHHHHH
Confidence 77 5677778888888888887666665554
No 26
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=93.81 E-value=0.098 Score=47.51 Aligned_cols=28 Identities=39% Similarity=0.557 Sum_probs=25.8
Q ss_pred CcEEEEeeeeecCCCCCCCCceEEeecC
Q 004767 83 NAKIFTFGSYRLGVHGPGADIDTLCVGP 110 (732)
Q Consensus 83 ~~kI~~FGSy~lGv~~p~SDID~lcv~P 110 (732)
...++.|||++-|=+.+.||||++++++
T Consensus 26 ~~~v~LfGS~arG~~~~~SDiDv~vv~~ 53 (128)
T COG1708 26 DLLIYLFGSYARGDFVKESDIDLLVVSD 53 (128)
T ss_pred CeEEEEEccCcccccccCCCeeEEEEcC
Confidence 5789999999999999999999999973
No 27
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=93.56 E-value=0.13 Score=54.89 Aligned_cols=31 Identities=29% Similarity=0.267 Sum_probs=27.8
Q ss_pred EEEEeeeeecCCCCCCCCceEEeecCCCCCc
Q 004767 85 KIFTFGSYRLGVHGPGADIDTLCVGPRHATR 115 (732)
Q Consensus 85 kI~~FGSy~lGv~~p~SDID~lcv~P~~v~r 115 (732)
.|+.|||++.|-..|.||||++++.....+.
T Consensus 30 ~vyLfGS~~~G~~~p~SDIDllvvv~~~l~~ 60 (262)
T PRK13746 30 AIHLYGSAVDGGLKPHSDIDLLVTVAVPLDE 60 (262)
T ss_pred EEEEECCcccCCCCCCCceeEEEEeCCCCCH
Confidence 5899999999999999999999998877653
No 28
>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=92.03 E-value=0.38 Score=49.25 Aligned_cols=47 Identities=11% Similarity=0.089 Sum_probs=33.2
Q ss_pred hhhHHHHHHHHHHHHHHcCCCCCC-CCCcChHHHHHHHHHHHHhCCCC
Q 004767 207 IQNFRTTLRCMRFWAKRRGVYSNV-AGFLGGINWALLVARICQLYPNA 253 (732)
Q Consensus 207 ~~~FR~llr~IK~WAK~RgIysn~-~G~LGG~swalLVa~vcQlyPna 253 (732)
....+.|+|.||+|-+...-.... -+-+.+|++-||+++.-..-...
T Consensus 41 P~klK~LIrLVKhWy~~~~~~~~~~~~lPpsYaLELLtIyAWE~g~~~ 88 (190)
T PF10421_consen 41 PTKLKNLIRLVKHWYQQCKKKKCGGGSLPPSYALELLTIYAWEQGCGA 88 (190)
T ss_dssp -HHHHHHHHHHHHHHHHHHCC--HTT-S--HHHHHHHHHHHHHHHT-S
T ss_pred CHHHHHHHHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHhcCCC
Confidence 467889999999999986665333 44577899999999999765443
No 29
>PRK02098 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=90.24 E-value=0.57 Score=49.06 Aligned_cols=33 Identities=27% Similarity=0.337 Sum_probs=27.4
Q ss_pred CcEEEEeeeee----cCC--CCCCCCceEEeecCCCCCc
Q 004767 83 NAKIFTFGSYR----LGV--HGPGADIDTLCVGPRHATR 115 (732)
Q Consensus 83 ~~kI~~FGSy~----lGv--~~p~SDID~lcv~P~~v~r 115 (732)
+..+.+|||+. +|+ -.++||||+|+-.+.....
T Consensus 120 g~~~gv~GS~a~qlaTG~~~l~~~SDLDLLi~~~~~~~~ 158 (221)
T PRK02098 120 GVDCRVFGSLAWQALTGLPYLSASSDLDLLWPLPAAAQI 158 (221)
T ss_pred CCcEEEeeehHHHHhhCCcccCCCCCeeEEEecCChhhH
Confidence 45799999999 999 6899999998888755444
No 30
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup 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. These three carboxylate residues are fairly well conserved in this
Probab=89.84 E-value=4 Score=44.49 Aligned_cols=113 Identities=24% Similarity=0.270 Sum_probs=70.8
Q ss_pred cCcEEEEeeeeecCCCCCCCCceEEeecCCCCCchhhHHHHHHHHHhcCCCceeeEeecCCcccEEEEEec------Cee
Q 004767 82 ANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFS------GVS 155 (732)
Q Consensus 82 ~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~r~~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~------GI~ 155 (732)
...++.+-||||=|-.+ .+|||+|+..+....+ .++..+...|.+.+.++.+.. .-..-....+. |+.
T Consensus 159 ~~~~v~i~GS~RRg~et-~gDiDilv~~~~~~~~--~~~~~v~~~l~~~~~~~~~~~---~g~~k~~~~~~~~~~~~~~r 232 (307)
T cd00141 159 PVLQVEIAGSYRRGKET-VGDIDILVTHPDATSR--GLLEKVVDALVELGFVTEVLS---KGDTKASGILKLPGGWKGRR 232 (307)
T ss_pred CceEEEEcccccCCCCc-cCCEEEEEecCCcccc--ccHHHHHHHHHhCCCeehhhh---CCCceEEEEEecCCCCCceE
Confidence 46789999999998765 4799988877765442 567788888888777644211 11122222222 899
Q ss_pred eeEEeeeccccccCCCCCCCchhhhccchhhhhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCc
Q 004767 156 IDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFL 234 (732)
Q Consensus 156 iDLsfa~l~~~~ip~~ldl~~~~lL~~lde~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~L 234 (732)
|||.++....+ .-.++-+.-+. . ..|-++.||++||..=+..|..
T Consensus 233 VDl~~~p~~~~------------------------------~~all~fTGs~-~---~nr~lR~~A~~~G~~L~~~GL~ 277 (307)
T cd00141 233 VDLRVVPPEEF------------------------------GAALLYFTGSK-Q---FNRALRRLAKEKGLKLNEYGLF 277 (307)
T ss_pred EEEEEeCHHHH------------------------------HHHHHHhhCCH-H---HHHHHHHHHHHcCCeeeccccc
Confidence 99998764211 01122222222 2 3566799999999877766654
No 31
>TIGR03135 malonate_mdcG holo-ACP synthase, malonate decarboxylase-specific. Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A. Members of this protein family are the phosphoribosyl-dephospho-CoA transferase specific to the malonate decarboxylase system. This enzyme can also be designated holo-ACP synthase (2.7.7.61). The corresponding component of the citrate lyase system, CitX, shows little or no sequence similarity to this family.
Probab=89.27 E-value=0.69 Score=47.75 Aligned_cols=33 Identities=21% Similarity=0.247 Sum_probs=27.6
Q ss_pred CcEEEEeeee----ecCC--CCCCCCceEEeecCCCCCc
Q 004767 83 NAKIFTFGSY----RLGV--HGPGADIDTLCVGPRHATR 115 (732)
Q Consensus 83 ~~kI~~FGSy----~lGv--~~p~SDID~lcv~P~~v~r 115 (732)
+..+.+|||+ .+|+ -.++||||+|+-.+....+
T Consensus 108 ~~~~gv~GS~~~qlaTg~~~~~~~SDLDLLi~~~~~~~~ 146 (202)
T TIGR03135 108 GVPWGVYGSAGWQLLTGLPYLHASSDLDLLLRAPSPLSL 146 (202)
T ss_pred CCcEEEecchHHHHhcCCcccCCCCCeeEEEcCCChhhH
Confidence 4579999999 8999 6899999998888865554
No 32
>cd05401 NT_GlnE_GlnD_like Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins. Escherichia coli GlnD and -E participate in the Glutamine synthetase (GS)/Glutamate synthase (GOGAT) pathway for the assimilation of ammonium nitrogen. In nitrogen sufficiency, GlnE adenylates GS, reducing GS activity; when nitrogen is limiting, GlnE deadenylates GS-AMP, restoring GS activity. When nitrogen is limiting, GlnD uridylylates the nitrogen regulatory protein PII to PII-UTP, and in nitrogen sufficiency, it removes the modifying groups. The activity of Escherichia coli GlnE is modulated by PII-proteins. PII-UMP promotes GlnE deadenylation activity, and PII promotes GlnE adenylation activity. Escherichia coli GlnE has two separate NT domains. The N-terminal NT domain catalyzes the deadenylylation of GS, and the C-terminal NT domain the adenylylation reaction. The majority of proteins in this family conta
Probab=83.86 E-value=4.4 Score=39.80 Aligned_cols=48 Identities=25% Similarity=0.396 Sum_probs=36.1
Q ss_pred cCcEEEEeeeeecCCCCCCCCceEEeecCCCCCchhhHHHHHHHHHhc
Q 004767 82 ANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTE 129 (732)
Q Consensus 82 ~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~r~~dFf~~l~~~L~~ 129 (732)
...-++.+|||+-+=-.+.||+|++++.+........+|..+.+.+.+
T Consensus 54 ~~~~~la~Gs~GR~E~~~~SD~D~~~v~~~~~~~~~~~~~~l~~~i~~ 101 (172)
T cd05401 54 VPFALLALGSYGRGELNPSSDQDLLLLYDDDGDEVAAYFEELAERLIK 101 (172)
T ss_pred CcEEEEEeCCcccCCcCCCcCcceEEEeCCCCchHHHHHHHHHHHHHH
Confidence 457899999999999999999999998865432123567666665554
No 33
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=83.31 E-value=0.26 Score=52.87 Aligned_cols=27 Identities=30% Similarity=0.348 Sum_probs=22.9
Q ss_pred EEEeeeeecCCCCCCCCceEEeecCCC
Q 004767 86 IFTFGSYRLGVHGPGADIDTLCVGPRH 112 (732)
Q Consensus 86 I~~FGSy~lGv~~p~SDID~lcv~P~~ 112 (732)
+=.-||..+|++..+||||+++.++.+
T Consensus 124 mGVTGSiL~gl~~~nSDIDfVVYG~~~ 150 (315)
T COG1665 124 MGVTGSILLGLYDENSDIDFVVYGQMW 150 (315)
T ss_pred ccccccccccccCCCCCceEEEEcHHH
Confidence 445699999999999999999999543
No 34
>PF14792 DNA_pol_B_palm: DNA polymerase beta palm ; PDB: 1RZT_A 3PML_A 2PFN_A 3HX0_K 3HWT_A 2GWS_E 2BCQ_A 3UPQ_A 2BCS_A 3UQ2_A ....
Probab=82.76 E-value=2.2 Score=39.88 Aligned_cols=53 Identities=30% Similarity=0.416 Sum_probs=39.5
Q ss_pred cCcEEEEeeeeecCCCCCCCCceEEeecCCCCCc---hhhHHHHHHHHHhcCCCcee
Q 004767 82 ANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATR---EEDFFGELHQMLTEMPEVTE 135 (732)
Q Consensus 82 ~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~r---~~dFf~~l~~~L~~~~~V~~ 135 (732)
.+..+..-||||=|-.+.+ |||+|+..|..... ...++..+...|.+..-++.
T Consensus 23 p~~~v~i~GSyRRGK~~~g-DiDiLIt~~~~~~~~~~~~~~l~~lv~~L~~~g~i~~ 78 (112)
T PF14792_consen 23 PGLEVEICGSYRRGKETSG-DIDILITHPDPSSVSKKLEGLLEKLVKRLEEKGFITD 78 (112)
T ss_dssp TT-EEEEEHHHHTT-SEES-SEEEEEEETTCSTTTCSTTCHHHHHHHHHHHTTSEEE
T ss_pred CCcEEEEccccccCCCcCC-CeEEEEeCCCcCcchhhHHHHHHHHHHHHHhCCeEEE
Confidence 4688999999999987765 99999988876542 13688899999988655543
No 35
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=78.95 E-value=11 Score=47.22 Aligned_cols=122 Identities=18% Similarity=0.297 Sum_probs=72.5
Q ss_pred hhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCcChHHHHHHHHHHHHh----CCCCCHHHHHHHHHHHhccCC
Q 004767 195 RVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQL----YPNAVPSMLVSRFFRVYTQWR 270 (732)
Q Consensus 195 Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~LGG~swalLVa~vcQl----yPnas~~~LL~~FF~~Ys~wd 270 (732)
|.+-.|..+...+..|-.++|.-|.|...+=+-+. .+ -=++=+|||...+. .|..++-.=+.+|..+-|+||
T Consensus 806 ~ht~aL~~l~qsh~~ys~vvrLaKrWl~shLL~~h---~~-De~iELLva~lf~~p~p~~~psS~~~gFlRfL~llS~~d 881 (1121)
T KOG2054|consen 806 LHTLALQSLSQSHPFYSSVVRLAKRWLGSHLLSGH---HL-DEAIELLVAALFLKPGPLVPPSSPENGFLRFLSLLSTWD 881 (1121)
T ss_pred HHHHHHHHHhhcccchhHHHHHHHHHHHHHhhccc---hH-HHHHHHHHHHHhcCccCCCCCCCcchhHHHHHHHHhcCc
Confidence 44445555555678899999999999988744321 12 44667888877642 355666666789999999999
Q ss_pred CCC-ceeecccccCCCCc----cccCCCCCCCCCCCceeEeCCCCCCCCcccccChhh
Q 004767 271 WPN-PVLLCAIEEGSLGL----QVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTST 323 (732)
Q Consensus 271 W~~-pV~l~~i~~G~l~~----~vWdP~~~~~dr~hlMpIiTP~~P~~Nsa~NVs~sT 323 (732)
|.. |.++.- .+| +.. +..+.-...+..+..|.|+||-+- .++...-+..+
T Consensus 882 W~~~PLIvd~-nn~-~~ed~~~e~~e~f~s~R~~lp~m~vit~yD~-~~~~~t~~~P~ 936 (1121)
T KOG2054|consen 882 WKFDPLIVDF-NNG-FPEDERSELEEKFISARKQLPPMVVITPYDH-LGSKFTRTSPN 936 (1121)
T ss_pred ccCCceEEEc-CCC-CcHHHHHHHHHHHhhhcccCCceEEeecccc-ccccccccCch
Confidence 986 666532 221 100 000000011122347999999554 44444444444
No 36
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=77.51 E-value=7.6 Score=47.60 Aligned_cols=56 Identities=23% Similarity=0.374 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCCCCCceEEeecCCCCC
Q 004767 55 GRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRHAT 114 (732)
Q Consensus 55 ~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~ 114 (732)
.....++..|+..+-...|+++ ..+.-|..+|.|.=|--.|.||||++++.|...+
T Consensus 42 ~~~~~~~d~~L~~lw~~~g~~~----~~~~aLvAVGGyGRgEL~P~SDiDlL~L~p~~~~ 97 (867)
T COG2844 42 ELRTDLVDQLLIRLWQEIGFAD----ASGLALVAVGGYGRGELHPLSDIDLLLLSPQKLT 97 (867)
T ss_pred HHHHHHHHHHHHHHHHHcCccc----ccceEEEEeccccccccCCCccceEEEecCCCCC
Confidence 3344555666666666677764 3568899999999999999999999999998766
No 37
>KOG3793 consensus Transcription factor NFAT, subunit NF45 [Transcription]
Probab=74.18 E-value=1.3e+02 Score=33.08 Aligned_cols=212 Identities=18% Similarity=0.250 Sum_probs=108.6
Q ss_pred HHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCCCCCc
Q 004767 24 DLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADI 103 (732)
Q Consensus 24 D~~~t~eL~~~L~~~~l~pS~eE~~~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDI 103 (732)
|-..+++|.+ ++.++-|+.+|..+=.....+++.++..-+ +.|+-+- .-..|.-.|||..|.-+-++|.
T Consensus 38 D~~f~~alLk--RnqdL~P~~~~q~~I~~~vtKV~~vLdn~~-----~~~L~~~----~ieevrqVGSF~k~T~~tg~~~ 106 (362)
T KOG3793|consen 38 DTSFSEALLK--RNQDLAPNSAEQASILSLVTKVNNVLDNLV-----APGLFEV----QIEEVRQVGSFKKGTMTTGHNV 106 (362)
T ss_pred chHHHHHHHh--hhccCCCCHHHHHHHHHHHHHHHHHHHhhc-----cCCceEe----ehhhhhhccceeccccccCCcc
Confidence 6677777665 345799999998776666666666665421 1233221 1245788999999999988876
Q ss_pred -eEEeecCCCCCch--hhHHHHHHHHHhcC-C-CceeeEeecCCcccEEEEE--e--cCeeeeEEeeeccccccCCCCCC
Q 004767 104 -DTLCVGPRHATRE--EDFFGELHQMLTEM-P-EVTELHPVPDAHVPVMKFK--F--SGVSIDLLYARLSLWVIPEDLDI 174 (732)
Q Consensus 104 -D~lcv~P~~v~r~--~dFf~~l~~~L~~~-~-~V~~l~~I~~ArVPIIKf~--~--~GI~iDLsfa~l~~~~ip~~ldl 174 (732)
|+|++-..-.+.+ ...-.++.+-|+.. + +|-. |-+.+-- + ..-.+-|+++.+ |+++.-
T Consensus 107 advVViLkTLPt~EaV~aLg~Kv~e~lka~d~~Evlt--------vl~~e~G~~I~s~~~~VRiLIt~i-----P~n~~K 173 (362)
T KOG3793|consen 107 ADLVVILKTLPTLEAVAALGNKVVESLRAQDPSEVLT--------VLTNETGFEISSSDATVRILITTV-----PPNLRK 173 (362)
T ss_pred cceEEEeecCCcHHHHHHHHHHHHHHhhhcChHHHHH--------HHhhccceeeecccceEEEEEeec-----Cchhcc
Confidence 5555543332321 01112233333321 1 2211 1111111 1 123344444443 544421
Q ss_pred Cchhhhccchhhh-hhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCcChHHHHH-HHHHHHHhC-C
Q 004767 175 SQDSILQNADEQT-VRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWAL-LVARICQLY-P 251 (732)
Q Consensus 175 ~~~~lL~~lde~s-vrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~LGG~swal-LVa~vcQly-P 251 (732)
. +.+-.+|.+- .-.|-.+|-+.++-+. ......+.++|++|---.+ +.||=-=-.|+| |++++|-+. |
T Consensus 174 L--EP~lHLD~K~M~~~l~a~RH~~WFee~-A~~s~~~~lir~LKDlr~r------~~~F~PLs~W~ldll~h~avmNnp 244 (362)
T KOG3793|consen 174 L--EPELHLDIKVMQSALAAIRHARWFEEN-ASQSTVKVLIRLLKDLRIR------FPGFEPLTPWILDLLGHYAVMNNP 244 (362)
T ss_pred c--ChhhhhhHHHHHHHHHHHhhhhhhhhh-hhHHHHHHHHHHHHHHHhh------cCCCCCchHHHHHHHHHHHHHcCC
Confidence 1 1122233221 1223344444433322 2234566788888875554 234422224544 567777553 4
Q ss_pred C---CCHHHHHHHHHHHhcc
Q 004767 252 N---AVPSMLVSRFFRVYTQ 268 (732)
Q Consensus 252 n---as~~~LL~~FF~~Ys~ 268 (732)
+ +.++.-..+||++.+.
T Consensus 245 ~RQ~l~ln~Afrr~~qilaA 264 (362)
T KOG3793|consen 245 TRQPLALNVAYRRCLQILAA 264 (362)
T ss_pred ccccchhhHHHHHHHHHHHh
Confidence 3 4678889999999874
No 38
>PF03445 DUF294: Putative nucleotidyltransferase DUF294; InterPro: IPR005105 This domain is found associated with an N-terminal cyclic nucleotide-binding domain (IPR000595 from INTERPRO) and two CBS domains (IPR000644 from INTERPRO). This domain, normally represents the C-terminal region, is uncharacterised; however, it seems to be similar to the nucleotidyltransferase domain (IPR002934 from INTERPRO), conserving the DXD motif, which strongly suggests that proteins containing this domain are also nucleotidyltransferases.; GO: 0008773 [protein-PII] uridylyltransferase activity
Probab=74.14 E-value=18 Score=34.92 Aligned_cols=48 Identities=17% Similarity=0.222 Sum_probs=36.7
Q ss_pred cCcEEEEeeeeecCCCCCCCCceEEeecCCCCCc-hhhHHHHHHHHHhc
Q 004767 82 ANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATR-EEDFFGELHQMLTE 129 (732)
Q Consensus 82 ~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~r-~~dFf~~l~~~L~~ 129 (732)
...-++.+||+.=+=.++.||+|..+|....... ...+|..|.+.+..
T Consensus 48 ~~~a~lalGS~GR~E~~~~sDqD~alv~~d~~~~~~~~~f~~~a~~~~~ 96 (138)
T PF03445_consen 48 VPFAWLALGSYGRREQTLYSDQDNALVFEDEESEEDRAYFEAFAERLVD 96 (138)
T ss_pred CCEEEEEECcccccCCCcCccccceeeecCccchhHHHHHHHHHHHHHH
Confidence 5678999999999999999999999988772221 13677776665553
No 39
>PRK05007 PII uridylyl-transferase; Provisional
Probab=69.40 E-value=16 Score=45.56 Aligned_cols=57 Identities=16% Similarity=0.327 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCCCCCceEEeecCCCC
Q 004767 53 VLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRHA 113 (732)
Q Consensus 53 VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v 113 (732)
++.....++.++++.+-...+++. ..+..|...|+|+=|=-.|.||||++++.+...
T Consensus 54 ~~~~~s~~~D~~l~~l~~~~~~~~----~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~ 110 (884)
T PRK05007 54 LVEARTEFIDQLLQRLWIEAGFDQ----IPDLALVAVGGYGRGELHPLSDIDLLILSRKKL 110 (884)
T ss_pred HHHHHHHHHHHHHHHHHHHccCCC----cCceEEEecCCCCCcccCCcccceEEEEeCCCC
Confidence 455555555555555444444432 246789999999999999999999999988443
No 40
>PF10620 MdcG: Phosphoribosyl-dephospho-CoA transferase MdcG; InterPro: IPR017557 Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A. Members of this protein family are the phosphoribosyl-dephospho-CoA transferase specific to the malonate decarboxylase system. This enzyme can also be designated holo-ACP synthase (2.7.7.61 from EC). The corresponding component of the citrate lyase system, CitX, shows little or no sequence similarity to this family.; GO: 0016779 nucleotidyltransferase activity
Probab=66.23 E-value=9.4 Score=39.71 Aligned_cols=40 Identities=20% Similarity=0.326 Sum_probs=27.9
Q ss_pred CcEEEEeeeee----cCCC--CCCCCceEEeecCCCCCchhhHHHHH
Q 004767 83 NAKIFTFGSYR----LGVH--GPGADIDTLCVGPRHATREEDFFGEL 123 (732)
Q Consensus 83 ~~kI~~FGSy~----lGv~--~p~SDID~lcv~P~~v~r~~dFf~~l 123 (732)
+...-+|||+. +|+. .++||||+++-.+..... ..+...+
T Consensus 116 ~~~~gv~GS~g~qlaTGl~~l~~~SDLDLli~~~~~~~~-~~l~~~L 161 (213)
T PF10620_consen 116 GLRWGVYGSLGFQLATGLPYLHADSDLDLLIRPPSPSQA-DALLALL 161 (213)
T ss_pred CCCEEEehhHHHHHHhCccccCCCCCceEEEeCCChhHH-HHHHHHH
Confidence 56799999985 4443 689999998888876543 1344444
No 41
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=64.76 E-value=16 Score=44.53 Aligned_cols=65 Identities=20% Similarity=0.144 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCCCCCceEEeecCCCCCchhhHHHHHHHHH
Q 004767 48 VSREEVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQML 127 (732)
Q Consensus 48 ~~R~~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~r~~dFf~~l~~~L 127 (732)
+.|+++-+.-..+++. .++++ +.-|...|+|+=|=-.|.||||++++.+.... +++.+.|-..|
T Consensus 6 ~~~~~~~~~~~~~~~~--------~~~~~------~~aLvAvGGYGR~EL~P~SDIDLLiL~~~~~~--~~~i~~~~~~L 69 (693)
T PRK00227 6 QLREDAEASALALLGS--------LQLPP------GTALAATGSLARREMTPYSDLDLILLHPPGAT--PDGVEDLWYPI 69 (693)
T ss_pred HHHHHHHHHHHHHHHh--------cCCCC------CeEEEEeccccccCcCCCcCceEEEEeCCccc--HHHHHHHHHHH
Confidence 4566666666666664 24542 45799999999999999999999999874333 24555544444
Q ss_pred h
Q 004767 128 T 128 (732)
Q Consensus 128 ~ 128 (732)
=
T Consensus 70 W 70 (693)
T PRK00227 70 W 70 (693)
T ss_pred H
Confidence 3
No 42
>PRK03059 PII uridylyl-transferase; Provisional
Probab=64.10 E-value=14 Score=45.86 Aligned_cols=54 Identities=28% Similarity=0.423 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCCCCCceEEeecCC
Q 004767 52 EVLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPR 111 (732)
Q Consensus 52 ~VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDID~lcv~P~ 111 (732)
+++..+..++.++++..-...+++ .+.-|...|+|+=|--.|.||||++++.+.
T Consensus 36 ~~~~~~s~l~d~~l~~~~~~~~~~------~~~alvAvGgyGR~EL~p~SDiDll~l~~~ 89 (856)
T PRK03059 36 ALLHALSRLVDQALRRLWQECGLP------AGAALVAVGGYGRGELFPYSDVDLLVLLPD 89 (856)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCC------CCeEEEEcCCCCCcccCCCCCCEEEEEecC
Confidence 356666666666665543332332 246799999999999999999999999864
No 43
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=61.65 E-value=32 Score=38.28 Aligned_cols=50 Identities=26% Similarity=0.379 Sum_probs=37.5
Q ss_pred ccCcEEEEeeeeecCCCCCCCCceEEeecCCCCCchhhHHHHHHHHHhcCC
Q 004767 81 EANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMP 131 (732)
Q Consensus 81 ~~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~r~~dFf~~l~~~L~~~~ 131 (732)
++++.+..-|||+=|- ..+.|||+|+-.|..-..+.-.+..+...|.+..
T Consensus 169 ~p~~~vt~~GsfRRGk-~~ggDvD~LithP~~~s~~~~~~~~l~~~le~~g 218 (353)
T KOG2534|consen 169 DPEAFVTVTGSFRRGK-KMGGDVDFLITHPGSTSTEAKLLQLLMILLEKKG 218 (353)
T ss_pred CCCcEEEEeccccCCc-ccCCCeeEEEeCCCCCchhhhHHHHHHHHHHhcC
Confidence 3568899999999984 5688999888888655433457778888887743
No 44
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=60.67 E-value=27 Score=43.41 Aligned_cols=56 Identities=14% Similarity=0.255 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCChhhhhccCcEEEEeeeeecCCCCCCCCceEEeecCCC
Q 004767 53 VLGRLDQIVKIWVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRH 112 (732)
Q Consensus 53 VL~~L~~ivk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~ 112 (732)
++.....++.++++..-.....+. ..+.-|...|+|+=|=-.|.||||++++.+..
T Consensus 30 ~~~~~~~~~D~~l~~l~~~~~~~~----~~~iaLvAvGGYGR~eL~P~SDIDlliL~~~~ 85 (854)
T PRK01759 30 LIENRSDFYDQLLIHLWQQFGLEE----QSDLALIAVGGYGRREMFPLSDLDILILTEQP 85 (854)
T ss_pred HHHHHHHHHHHHHHHHHHHccCCC----CCCeEEEEeCCcccccCCCcccceEEEEeCCC
Confidence 555555666666555443333221 13478999999999999999999999998743
No 45
>PRK08609 hypothetical protein; Provisional
Probab=59.12 E-value=59 Score=38.72 Aligned_cols=109 Identities=18% Similarity=0.254 Sum_probs=61.8
Q ss_pred cCcEEEEeeeeecCCCCCCCCceEEeecCCCCCchhhHHHHHHHHHhcCCCceeeEeecCCcccEEEEEe-cCeeeeEEe
Q 004767 82 ANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKF-SGVSIDLLY 160 (732)
Q Consensus 82 ~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~r~~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~-~GI~iDLsf 160 (732)
...++..-||||=|--+ ..|||+|+..+.. ..+.+.|.+.+.|+++..-...+.-+ .+.. .|+.|||-+
T Consensus 174 ~~~~v~~~GS~RR~~et-~gDiDili~~~~~--------~~~~~~l~~~~~v~~~~~~g~~~~~~-~~~~~~~~~vDl~~ 243 (570)
T PRK08609 174 EIIRFSRAGSLRRARET-VKDLDFIIATDEP--------EAVREQLLQLPNIVEVIAAGDTKVSV-ELEYEYTISVDFRL 243 (570)
T ss_pred CccEEEeccchhccccc-cCCeeEEEecCCH--------HHHHHHHHcCccHHHHHhcCCceEEE-EEecCCCeEEEEEE
Confidence 35689999999998765 4699988876542 12223344445444332222222211 2332 389999998
Q ss_pred eeccccccCCCCCCCchhhhccchhhhhhhcchhhhHHHHHHHcCChhhHHHHHHHHHHHHHHcCCCCCCCCCc
Q 004767 161 ARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFL 234 (732)
Q Consensus 161 a~l~~~~ip~~ldl~~~~lL~~lde~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RgIysn~~G~L 234 (732)
+....+ .-.++-..-. .. -.|-++.||++||..=|-.|..
T Consensus 244 v~~~~~------------------------------~~aL~yfTGS-~~---hn~~lr~~A~~~g~~l~e~gl~ 283 (570)
T PRK08609 244 VEPEAF------------------------------ATTLHHFTGS-KD---HNVRMRQLAKERGEKISEYGVE 283 (570)
T ss_pred eCHHHH------------------------------HHHHHHHhcc-HH---HHHHHHHHHHHcCCcccccccc
Confidence 764311 0011111111 22 2455689999999988887764
No 46
>PF03710 GlnE: Glutamate-ammonia ligase adenylyltransferase; InterPro: IPR005190 This is a conserved repeated domain found in GlnE proteins. These proteins adenylate and deadenylate glutamine synthases: ATP + {L-Glutamate:ammonia ligase (ADP-forming)} = Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase (ADP-forming)}. The domain is related to the nucleotidyltransferase domain IPR002934 from INTERPRO.; GO: 0008882 [glutamate-ammonia-ligase] adenylyltransferase activity; PDB: 1V4A_A 3K7D_A.
Probab=56.71 E-value=96 Score=32.84 Aligned_cols=47 Identities=21% Similarity=0.274 Sum_probs=28.4
Q ss_pred CcEEEEeeeeecCCCCCCCCceEEeecCCCCC------chhhHHHHHHHHHhc
Q 004767 83 NAKIFTFGSYRLGVHGPGADIDTLCVGPRHAT------REEDFFGELHQMLTE 129 (732)
Q Consensus 83 ~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~------r~~dFf~~l~~~L~~ 129 (732)
..-|.-.|-+.-+=-..+||||+++|.+.... ....||.++.+.|.+
T Consensus 127 ~~~ViamGKlGg~ELny~SDiDLifvy~~~~~~~~~~~~~~~~~~rl~~~~~~ 179 (247)
T PF03710_consen 127 GFAVIAMGKLGGRELNYSSDIDLIFVYDPDGETGRRSISNQEFFTRLAQRLIR 179 (247)
T ss_dssp SEEEEE-HHHHTT---TT--EEEEEEE---TT-SSS-SBHHHHHHHHHHHHHH
T ss_pred CeEEEEeccccccccCCccCCceEEEeccccccccChhhHHHHHHHHHHHHHH
Confidence 56788888888888889999999999764322 113689888877664
No 47
>PF10127 Nuc-transf: Predicted nucleotidyltransferase; InterPro: IPR018775 Proteins in this entry are predicted to catalyse the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms.
Probab=56.02 E-value=9.6 Score=39.93 Aligned_cols=26 Identities=27% Similarity=0.210 Sum_probs=21.9
Q ss_pred EEEEeeeeecCCCCCCCCceEEeecC
Q 004767 85 KIFTFGSYRLGVHGPGADIDTLCVGP 110 (732)
Q Consensus 85 kI~~FGSy~lGv~~p~SDID~lcv~P 110 (732)
-...+||.+-|+.+|+||.|+-+|.-
T Consensus 22 ~~~~sGS~a~G~~s~dSD~D~r~vy~ 47 (247)
T PF10127_consen 22 YACESGSRAYGFASPDSDYDVRGVYI 47 (247)
T ss_pred EEecccccccCCCCCCcCcccchhcc
Confidence 35678999999999999999876653
No 48
>PRK01293 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=55.96 E-value=27 Score=36.51 Aligned_cols=44 Identities=30% Similarity=0.312 Sum_probs=30.3
Q ss_pred CcEEEEeeeee----cCCC--CCCCCceEEeecCCCCCchhhHHHHHHHHHh
Q 004767 83 NAKIFTFGSYR----LGVH--GPGADIDTLCVGPRHATREEDFFGELHQMLT 128 (732)
Q Consensus 83 ~~kI~~FGSy~----lGv~--~p~SDID~lcv~P~~v~r~~dFf~~l~~~L~ 128 (732)
+...-+|||.. +|+. .++||||+++.+|....+ +-+..+.+.|.
T Consensus 109 ~~~wgv~GS~g~qlaTGl~~l~~~SDLDLlir~~~~l~~--~~~~~ll~~l~ 158 (207)
T PRK01293 109 GLAWGVTGSAGFELATGIPVLHADSDLDLLIRAPQPLAR--DQARELLQLLD 158 (207)
T ss_pred CCceeeehhHHHHHhhCCccccCCCCccEeecCCCcccH--HHHHHHHHHHh
Confidence 45688999975 4443 689999999988876665 33444544544
No 49
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=52.42 E-value=51 Score=33.43 Aligned_cols=76 Identities=21% Similarity=0.191 Sum_probs=44.1
Q ss_pred CcEEEEeeeeec----CCCCCCCCceEEeecCCCCCchhhHHHHHHHHHhcCCCceeeEeecCCcccEEEEEecCeeeeE
Q 004767 83 NAKIFTFGSYRL----GVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDL 158 (732)
Q Consensus 83 ~~kI~~FGSy~l----Gv~~p~SDID~lcv~P~~v~r~~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDL 158 (732)
+.+.+..|++++ |.-....|||+++..+.... +.++|..++....-.-+-+.+ ...-.++++...++.|||
T Consensus 16 gv~~~ivGG~av~l~~g~~r~T~DIDlfi~~~~~~~-~~~~~~~~a~~~g~~~~~~~~----~~~~~~~~~~~~~v~IDl 90 (181)
T PF09970_consen 16 GVEYVIVGGAAVNLAYGRRRTTKDIDLFIENPSPNL-EADALREVAEENGWDLGWTDF----GTPRYVVKVGGEDVRIDL 90 (181)
T ss_pred CCeEEEECHHHHHHHhCCCCCCCCeEEEeCCCchHH-HHHHHHHHHHHcCCCcCcccc----CCCceEEEeCCCCeEEEc
Confidence 457899999864 55567899997776654332 235555554322110111111 223455666667899999
Q ss_pred Eeeecc
Q 004767 159 LYARLS 164 (732)
Q Consensus 159 sfa~l~ 164 (732)
+.++.
T Consensus 91 -~~ni~ 95 (181)
T PF09970_consen 91 -LENIG 95 (181)
T ss_pred -hhccC
Confidence 55544
No 50
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=52.31 E-value=1.6e+02 Score=32.65 Aligned_cols=30 Identities=33% Similarity=0.526 Sum_probs=23.9
Q ss_pred cCcEEEEeeeeecCCCCCCCCceEEeecCCC
Q 004767 82 ANAKIFTFGSYRLGVHGPGADIDTLCVGPRH 112 (732)
Q Consensus 82 ~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~ 112 (732)
...++..-||||=|-.+ ..|||+|+..+..
T Consensus 163 ~~~~v~i~GSyRRgket-~gDIDili~~~~~ 192 (334)
T smart00483 163 PDAIVTLTGSFRRGKET-GHDVDFLITSPHP 192 (334)
T ss_pred CCcEEEEecccccCCCc-CCCeeEEEecCCc
Confidence 35789999999998765 4799988877653
No 51
>PRK03381 PII uridylyl-transferase; Provisional
Probab=47.77 E-value=55 Score=40.40 Aligned_cols=29 Identities=14% Similarity=0.150 Sum_probs=26.5
Q ss_pred CcEEEEeeeeecCCCCCCCCceEEeecCC
Q 004767 83 NAKIFTFGSYRLGVHGPGADIDTLCVGPR 111 (732)
Q Consensus 83 ~~kI~~FGSy~lGv~~p~SDID~lcv~P~ 111 (732)
..-|...|+|+-|--.|.||||++++.+.
T Consensus 57 ~~alvAvg~~gr~el~p~SD~Dll~l~~~ 85 (774)
T PRK03381 57 GVALVAVGGLGRRELLPYSDLDLVLLHDG 85 (774)
T ss_pred CeEEEEeCCcCCcCcCCCCCCeEEEEeCC
Confidence 46899999999999999999999999873
No 52
>PRK04374 PII uridylyl-transferase; Provisional
Probab=46.54 E-value=63 Score=40.47 Aligned_cols=29 Identities=28% Similarity=0.489 Sum_probs=26.4
Q ss_pred CcEEEEeeeeecCCCCCCCCceEEeecCC
Q 004767 83 NAKIFTFGSYRLGVHGPGADIDTLCVGPR 111 (732)
Q Consensus 83 ~~kI~~FGSy~lGv~~p~SDID~lcv~P~ 111 (732)
+.-|...|+|+=|=-.|.||||++++.+.
T Consensus 72 ~~alvAvGgYGR~EL~p~SDIDLliL~~~ 100 (869)
T PRK04374 72 GLSLHAVGGYGRGELFPRSDVDLLVLGET 100 (869)
T ss_pred CEEEEEcCCccccccCCcccceEEEEecC
Confidence 46899999999999999999999999874
No 53
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=46.54 E-value=67 Score=40.35 Aligned_cols=32 Identities=28% Similarity=0.367 Sum_probs=28.0
Q ss_pred cCcEEEEeeeeecCCCCCCCCceEEeecCCCC
Q 004767 82 ANAKIFTFGSYRLGVHGPGADIDTLCVGPRHA 113 (732)
Q Consensus 82 ~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v 113 (732)
.+..|...|.|+=|-=.|.||||++++.+...
T Consensus 77 ~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~ 108 (895)
T PRK00275 77 ADIALVAVGGYGRGELHPYSDIDLLILLDSAD 108 (895)
T ss_pred CCEEEEEcCCccccCcCCCCCceEEEEecCCC
Confidence 35789999999999999999999999987543
No 54
>PF03281 Mab-21: Mab-21 protein
Probab=45.92 E-value=4e+02 Score=28.38 Aligned_cols=97 Identities=19% Similarity=0.244 Sum_probs=65.2
Q ss_pred hhhHHHHHHHHHHHHHHcCCCCCCCCCcChHHHHHHHHHHHHhCCCC---CHHHHHHHHHHHhccCCCCCceeecccccC
Q 004767 207 IQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNA---VPSMLVSRFFRVYTQWRWPNPVLLCAIEEG 283 (732)
Q Consensus 207 ~~~FR~llr~IK~WAK~RgIysn~~G~LGG~swalLVa~vcQlyPna---s~~~LL~~FF~~Ys~wdW~~pV~l~~i~~G 283 (732)
....+.+++++|.-..... ...+.|++|++--++.+.|..+|.. ....|-.+|.++... +++.+++|
T Consensus 190 ~~~~~~~l~llk~l~~~~~---~~~~~l~syhLkt~ll~~~~~~p~~~~W~~~~l~~~l~~~l~~-------L~~~L~~~ 259 (292)
T PF03281_consen 190 NGCRKKCLRLLKALRDRHL---TNLSGLSSYHLKTVLLWLCEKHPSSSDWSEENLGERLLDLLDF-------LIKCLQEG 259 (292)
T ss_pred cccHHHHHHHHHHHHHhcc---ccCCCccHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHH-------HHHHHhcC
Confidence 4566889999999877766 5678899999999999999999875 234444444444321 12233334
Q ss_pred CCCccccCCCCCCCCCCCceeEeCCCCCCCCcccccChhhHHHHHHHHHH
Q 004767 284 SLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQR 333 (732)
Q Consensus 284 ~l~~~vWdP~~~~~dr~hlMpIiTP~~P~~Nsa~NVs~sTl~vI~~EF~R 333 (732)
.+. | -+.|.+|.=.+.+..++..+.+++.+
T Consensus 260 ~Lp--------------h------ff~~~~NLf~~~~~~~~~~~~~~~~~ 289 (292)
T PF03281_consen 260 RLP--------------H------FFIPNLNLFQHLSPEELDELARKLER 289 (292)
T ss_pred CCC--------------c------cCCCCcccCCCCCHHHHHHHHHHHHH
Confidence 321 1 13567888888888888777766654
No 55
>COG2413 Predicted nucleotidyltransferase [General function prediction only]
Probab=43.58 E-value=47 Score=34.92 Aligned_cols=27 Identities=30% Similarity=0.491 Sum_probs=22.7
Q ss_pred EEEEeeeeecCCCCCCCCceEEeecCC
Q 004767 85 KIFTFGSYRLGVHGPGADIDTLCVGPR 111 (732)
Q Consensus 85 kI~~FGSy~lGv~~p~SDID~lcv~P~ 111 (732)
.-+.+||.+.|=-.|+||+|+.+..|.
T Consensus 39 e~~v~gSvarGDV~p~SDvDV~I~~~v 65 (228)
T COG2413 39 EAVVYGSVARGDVRPGSDVDVAIPEPV 65 (228)
T ss_pred hhEEEeeeeccCcCCCCCceEEEecCC
Confidence 356789999998899999998887743
No 56
>PHA02603 nrdC.11 hypothetical protein; Provisional
Probab=42.46 E-value=15 Score=40.80 Aligned_cols=24 Identities=29% Similarity=0.285 Sum_probs=20.6
Q ss_pred EEEeeeeecCCCCCCCCceEEeec
Q 004767 86 IFTFGSYRLGVHGPGADIDTLCVG 109 (732)
Q Consensus 86 I~~FGSy~lGv~~p~SDID~lcv~ 109 (732)
+..+||...|+.+|+||+|.--|+
T Consensus 6 ~~~~GShaYG~~tp~SD~D~rGV~ 29 (330)
T PHA02603 6 KGLFGSHLYGTSTPESDVDYKGIF 29 (330)
T ss_pred EEecccceeCCCCCCcccccceee
Confidence 567999999999999999985444
No 57
>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase. This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.
Probab=42.44 E-value=79 Score=39.30 Aligned_cols=31 Identities=26% Similarity=0.411 Sum_probs=27.3
Q ss_pred cCcEEEEeeeeecCCCCCCCCceEEeecCCC
Q 004767 82 ANAKIFTFGSYRLGVHGPGADIDTLCVGPRH 112 (732)
Q Consensus 82 ~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~ 112 (732)
.+.-|...|||+=|=-.|.||||++++.+..
T Consensus 42 ~~~aliA~GgyGR~El~p~SDiDll~l~~~~ 72 (850)
T TIGR01693 42 SGIALVAVGGYGRGELAPYSDIDLLFLHDGK 72 (850)
T ss_pred CCeEEEEeCCccccCcCCCCCCeEEEEeCCC
Confidence 3577999999999999999999999998743
No 58
>PF12633 Adenyl_cycl_N: Adenylate cyclase NT domain; InterPro: IPR024685 Adenylate cyclase is the enzyme responsible for the synthesis of cAMP from ATP. On the basis of sequence similarity, it has been proposed that there are three different classes of adenylate cyclases [, ]. Class I cyclases are found in enterobacteria and related Gram-negative bacteria. This entry represents the N-terminal domain of class-I adenylate cyclases.
Probab=41.14 E-value=30 Score=36.10 Aligned_cols=30 Identities=17% Similarity=0.360 Sum_probs=24.1
Q ss_pred cEEEEeeeeecCCCCCCCCceE-EeecCCCCC
Q 004767 84 AKIFTFGSYRLGVHGPGADIDT-LCVGPRHAT 114 (732)
Q Consensus 84 ~kI~~FGSy~lGv~~p~SDID~-lcv~P~~v~ 114 (732)
--||+-||..+=-.++.||+|+ ||..+ ..+
T Consensus 98 ~GlY~MGS~gSi~Qs~~SDlDiWvCh~~-~L~ 128 (204)
T PF12633_consen 98 LGLYSMGSTGSIGQSSSSDLDIWVCHDS-DLS 128 (204)
T ss_pred EEEEecCCCccccCCCCCCCeEEEEcCC-CCC
Confidence 3489999999999999999999 55544 444
No 59
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=34.32 E-value=86 Score=39.90 Aligned_cols=48 Identities=17% Similarity=0.193 Sum_probs=36.5
Q ss_pred cCcEEEEeeeeecCCCCCCCCceEEeecCCCC--C--chhhHHHHHHHHHhc
Q 004767 82 ANAKIFTFGSYRLGVHGPGADIDTLCVGPRHA--T--REEDFFGELHQMLTE 129 (732)
Q Consensus 82 ~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v--~--r~~dFf~~l~~~L~~ 129 (732)
.+.-|..+|+|+-+=-.+.||||+++|..... . ....||..+.+.+..
T Consensus 722 ~~~avia~Gk~Gr~EL~~~SDlDl~fl~~~~~~~~~~~~~~~~~rlaq~l~~ 773 (1007)
T PRK14109 722 ARIAVIGMGRLGGRELGYGSDADVMFVHEPAPGADEAEAVRWATAVAEELRR 773 (1007)
T ss_pred CCEEEEEeccccccccCCCCCCcEEEEeCCCCCCCchhHHHHHHHHHHHHHH
Confidence 45789999999999999999999999986321 1 112688888777665
No 60
>COG3541 Predicted nucleotidyltransferase [General function prediction only]
Probab=32.60 E-value=21 Score=38.20 Aligned_cols=18 Identities=33% Similarity=0.425 Sum_probs=16.3
Q ss_pred eeeeecCCCCCCCCceEE
Q 004767 89 FGSYRLGVHGPGADIDTL 106 (732)
Q Consensus 89 FGSy~lGv~~p~SDID~l 106 (732)
-||+.-|+..|+||+|+=
T Consensus 16 sGS~~yGf~spdSDyDvR 33 (248)
T COG3541 16 SGSHLYGFPSPDSDYDVR 33 (248)
T ss_pred ccccccCCCCCCCcccee
Confidence 499999999999999973
No 61
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=31.97 E-value=76 Score=35.40 Aligned_cols=71 Identities=27% Similarity=0.313 Sum_probs=53.9
Q ss_pred cEEEEeeeeecCCCCCCCCceEEeecCCCCCchhhHHHHHHHHHhcCCCceeeEeecCCcccEEEEEecCeeeeEEeeec
Q 004767 84 AKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARL 163 (732)
Q Consensus 84 ~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~r~~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l 163 (732)
.++-.-||+|=|-.+ .+|||++|... +.. . +.+.|-+++++.++.+-.+.+|-++.--..|++||+-++..
T Consensus 181 ~~~~~aGs~RR~ret-v~DiD~~~s~~-~~~---~----v~~~~~~~~~~~~vi~~G~~k~s~~~~~~~~~svD~r~v~~ 251 (326)
T COG1796 181 IQASIAGSLRRGRET-VGDIDILISTS-HPE---S----VLEELLEMPNVQEVIAKGETKVSMLLILDEGTSVDFRVVPP 251 (326)
T ss_pred heeeeccchhhcccc-ccceeeEeccC-CcH---H----HHHHHhcCCCcceeeecCCceeeEEEEecCCCeeEEEEcCH
Confidence 456667899887765 57999766543 321 1 44556678999999999999999999889999999987653
No 62
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=31.76 E-value=37 Score=25.81 Aligned_cols=31 Identities=16% Similarity=0.317 Sum_probs=24.3
Q ss_pred hHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 004767 28 TRKLEKYLRDVNLYESQEEAVSREEVLGRLDQ 59 (732)
Q Consensus 28 t~eL~~~L~~~~l~pS~eE~~~R~~VL~~L~~ 59 (732)
+.+|.++|...|+..++.. ..|+++|+.+++
T Consensus 6 ~~~L~~wL~~~gi~~~~~~-~~rd~Ll~~~k~ 36 (38)
T PF10281_consen 6 DSDLKSWLKSHGIPVPKSA-KTRDELLKLAKK 36 (38)
T ss_pred HHHHHHHHHHcCCCCCCCC-CCHHHHHHHHHH
Confidence 4689999999998766554 788888887664
No 63
>PF07357 DRAT: Dinitrogenase reductase ADP-ribosyltransferase (DRAT); InterPro: IPR009953 This family consists of several bacterial dinitrogenase reductase ADP-ribosyltransferase (DRAT) proteins. Members of this family seem to be specific to Rhodospirillum, Rhodobacter and Azospirillum species. Dinitrogenase reductase ADP-ribosyl transferase (DRAT) carries out the transfer of the ADP-ribose from NAD to the Arg-101 residue of one subunit of the dinitrogenase reductase homodimer, resulting in inactivation of that enzyme. Dinitrogenase reductase-activating glycohydrolase (DRAG) removes the ADP-ribose group attached to dinitrogenase reductase, thus restoring nitrogenase activity. The DRAT-DRAG system negatively regulates nitrogenase activity in response to exogenous NH4+ or energy limitation in the form of a shift to darkness or to anaerobic conditions [].
Probab=31.52 E-value=19 Score=38.77 Aligned_cols=21 Identities=43% Similarity=0.639 Sum_probs=17.3
Q ss_pred ecChhhhhhhhhHHHHHHHHH
Q 004767 373 AENADDLRNWKGWVESRLRQL 393 (732)
Q Consensus 373 a~~~e~~~~w~GwVESRlR~L 393 (732)
-+|.-+...++||||||+-.+
T Consensus 95 DSn~~EGAVLKGWVESRFGL~ 115 (262)
T PF07357_consen 95 DSNSPEGAVLKGWVESRFGLL 115 (262)
T ss_pred CCCChhhhhhhhhhhhccCcC
Confidence 346778899999999999765
No 64
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=29.42 E-value=1.6e+02 Score=37.51 Aligned_cols=48 Identities=13% Similarity=0.084 Sum_probs=35.9
Q ss_pred cCcEEEEeeeeecCCCCCCCCceEEeecCCCCCc----hhhHHHHHHHHHhc
Q 004767 82 ANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATR----EEDFFGELHQMLTE 129 (732)
Q Consensus 82 ~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~v~r----~~dFf~~l~~~L~~ 129 (732)
.+.-|..+|+|+-+=-.+.||||++++.+..... ...||..+.+.|.+
T Consensus 214 ~~~aviamGklG~~EL~~~SDiDLi~ly~~~~~~~~~~~~~~~~rl~q~l~~ 265 (1007)
T PRK14109 214 VRLAVIAMGKCGARELNYVSDVDVIFVAEPAEGVDEAAALAVATRLASELMR 265 (1007)
T ss_pred CCeEEEEeccccccccCCccCCCEEEEeCCCCCcccccHHHHHHHHHHHHHH
Confidence 3568999999999999999999999998633211 12577777776665
No 65
>COG1391 GlnE Glutamine synthetase adenylyltransferase [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms]
Probab=26.36 E-value=4e+02 Score=33.91 Aligned_cols=45 Identities=29% Similarity=0.488 Sum_probs=28.2
Q ss_pred EEEEeeeeecCCC--CCCCCceEEeecCCCCCc------hhhHHHHHHHHHhc
Q 004767 85 KIFTFGSYRLGVH--GPGADIDTLCVGPRHATR------EEDFFGELHQMLTE 129 (732)
Q Consensus 85 kI~~FGSy~lGv~--~p~SDID~lcv~P~~v~r------~~dFf~~l~~~L~~ 129 (732)
.++..|=--+|-. .=.||||++.+.|..-.. ..+||..+.+.|-+
T Consensus 173 ~l~VlgMGKlGa~ELNysSDIDlIf~y~~~~~t~g~~~dn~~fFtRl~qrLIr 225 (963)
T COG1391 173 GLLVLGMGKLGARELNYSSDIDLIFVYPESGPTQGGELDNAEFFTRLGQRLIR 225 (963)
T ss_pred ceEEEeccccCccccccccccceEEEeCCCCCccCCccchHHHHHHHHHHHHH
Confidence 3444444444444 346999999998765432 23599988777655
No 66
>PRK05092 PII uridylyl-transferase; Provisional
Probab=24.56 E-value=2.1e+02 Score=36.20 Aligned_cols=29 Identities=34% Similarity=0.612 Sum_probs=26.6
Q ss_pred CcEEEEeeeeecCCCCCCCCceEEeecCC
Q 004767 83 NAKIFTFGSYRLGVHGPGADIDTLCVGPR 111 (732)
Q Consensus 83 ~~kI~~FGSy~lGv~~p~SDID~lcv~P~ 111 (732)
...|...|.|+-|--.|.||||++++.+.
T Consensus 105 ~~alvA~GgyGr~EL~p~SDiDLl~l~~~ 133 (931)
T PRK05092 105 RLAVLAVGGYGRGELAPGSDIDLLFLLPY 133 (931)
T ss_pred ceEEEEecCcCCcccCCCCCceEEEEeCC
Confidence 46899999999999999999999999874
No 67
>PRK11072 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed
Probab=24.22 E-value=2e+02 Score=36.58 Aligned_cols=48 Identities=27% Similarity=0.335 Sum_probs=34.9
Q ss_pred cCcEEEEeeeeecCCCCCCCCceEEeecCCC-CC-------chhhHHHHHHHHHhc
Q 004767 82 ANAKIFTFGSYRLGVHGPGADIDTLCVGPRH-AT-------REEDFFGELHQMLTE 129 (732)
Q Consensus 82 ~~~kI~~FGSy~lGv~~p~SDID~lcv~P~~-v~-------r~~dFf~~l~~~L~~ 129 (732)
....|...|-|.-+==.+.||||++++.+.. .+ ....||.++.+.|-+
T Consensus 153 ~~~aViamGKlG~~ELn~~SDIDLifly~~~~~~~~~~~~~~~~~~f~rl~q~li~ 208 (943)
T PRK11072 153 QPLLILGMGKLGGRELNFSSDIDLIFTYPEHGETQGGRRSIDNQQFFTRLGQRLIK 208 (943)
T ss_pred CCEEEEEeccccCccCCCccCCceEEEeCCCCCCCCCcccchHHHHHHHHHHHHHH
Confidence 4567888888888888999999999998632 11 113688888776654
No 68
>PF04439 Adenyl_transf: Streptomycin adenylyltransferase; InterPro: IPR007530 Also known as aminoglycoside 6-adenylyltransferase (2.7.7 from EC), this protein confers resistance to aminoglycoside antibiotics.; PDB: 2PBE_A.
Probab=23.74 E-value=53 Score=35.68 Aligned_cols=79 Identities=20% Similarity=0.210 Sum_probs=28.7
Q ss_pred EEEeeeeecCCCC--CCCCceEEeecCCCC--CchhhHHHHHHHHH-hcCCCceeeEeecCCcccEEEEEe-cCeeeeEE
Q 004767 86 IFTFGSYRLGVHG--PGADIDTLCVGPRHA--TREEDFFGELHQML-TEMPEVTELHPVPDAHVPVMKFKF-SGVSIDLL 159 (732)
Q Consensus 86 I~~FGSy~lGv~~--p~SDID~lcv~P~~v--~r~~dFf~~l~~~L-~~~~~V~~l~~I~~ArVPIIKf~~-~GI~iDLs 159 (732)
|+.-||.+.--.. .-+|.|++.++.... ..+..+...|-+.| .+.|+=.+..+......+..-+.| +|..|||.
T Consensus 24 V~l~GSR~n~~~~~D~fqDyDIv~~v~d~~~f~~d~~Wi~~FG~~li~q~pe~~~~~~~~~~~~~~~L~~f~dg~rIDlt 103 (282)
T PF04439_consen 24 VILNGSRANPNAPKDEFQDYDIVYVVTDIESFIKDDSWIDQFGERLIMQKPEDMDLFPPDLGNWFSYLMLFEDGNRIDLT 103 (282)
T ss_dssp EEE----------------EEEEEEES-HHHHHT-SGGGGGG--EEEEE-TTS-SSS---STT-EEEEEEETTS-EEEEE
T ss_pred EEEecCCCCCCCCccccccccEEEEecchhhhhhcchHHHHhChHHhEecccccccCCcccCCCeeEEEEecCCcEEEEE
Confidence 6677999877655 458999999885310 00012222333222 112221111122123344455556 69999999
Q ss_pred eeecc
Q 004767 160 YARLS 164 (732)
Q Consensus 160 fa~l~ 164 (732)
+..+.
T Consensus 104 l~~~~ 108 (282)
T PF04439_consen 104 LIPLE 108 (282)
T ss_dssp EEEGG
T ss_pred EecHH
Confidence 98875
No 69
>PRK11072 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed
Probab=23.52 E-value=2e+02 Score=36.53 Aligned_cols=59 Identities=17% Similarity=0.235 Sum_probs=38.4
Q ss_pred hhcCCChhh-hhccCcEEEEeeeeecCCCCCCCCceEEeecCC----------CCCchhhHHHHHHHHHhc
Q 004767 70 RAKGLNDQL-LQEANAKIFTFGSYRLGVHGPGADIDTLCVGPR----------HATREEDFFGELHQMLTE 129 (732)
Q Consensus 70 ~~~g~~~~~-~~~~~~kI~~FGSy~lGv~~p~SDID~lcv~P~----------~v~r~~dFf~~l~~~L~~ 129 (732)
..+|.+... ....+.-|.-+|-+.-+=-+-+||||++.|... ... ...||..+.+.|.+
T Consensus 667 ~~~G~p~~~~~~~~~~aViamGKlGg~EL~y~SDlDlifvy~~~~~~~t~g~~~~~-~~~~~~rl~qrli~ 736 (943)
T PRK11072 667 KRHGEPPHLEGRERGFAVIGYGKLGGKELGYASDLDLVFLHDCPEDAMTDGDKSID-GRQFYLRLAQRIIH 736 (943)
T ss_pred HHhCCCCCccCCCCCEEEEeecCccCCccCCcccceEEEEeecCccccCCCCCccc-HHHHHHHHHHHHHH
Confidence 345665321 112345788888877777788999999998851 111 13689988887765
Done!