Query 005394
Match_columns 698
No_of_seqs 258 out of 769
Neff 4.9
Searched_HMMs 46136
Date Thu Mar 28 22:45:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005394.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005394hhsearch_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 1E-142 3E-147 1153.1 41.7 491 1-500 1-501 (562)
2 PTZ00418 Poly(A) polymerase; P 100.0 4E-135 8E-140 1131.7 53.1 485 10-498 46-541 (593)
3 COG5186 PAP1 Poly(A) polymeras 100.0 2E-122 4E-127 965.0 33.7 478 13-495 4-525 (552)
4 PF04928 PAP_central: Poly(A) 100.0 9.2E-74 2E-78 589.6 21.2 254 13-362 1-254 (254)
5 COG5260 TRF4 DNA polymerase si 100.0 4.1E-31 8.9E-36 288.4 24.6 266 29-347 52-342 (482)
6 PF04926 PAP_RNA-bind: Poly(A) 100.0 7.2E-32 1.6E-36 259.3 9.1 135 363-498 1-156 (157)
7 KOG1906 DNA polymerase sigma [ 100.0 2.5E-28 5.3E-33 271.5 24.8 270 28-348 57-342 (514)
8 cd05402 NT_PAP_TUTase Nucleoti 99.8 6.3E-19 1.4E-23 159.8 13.3 110 56-210 1-113 (114)
9 KOG2277 S-M checkpoint control 99.8 4.9E-17 1.1E-21 185.0 22.7 253 47-348 125-431 (596)
10 TIGR03671 cca_archaeal CCA-add 99.6 1.1E-12 2.5E-17 143.8 34.5 343 39-461 3-364 (408)
11 PRK13300 tRNA CCA-pyrophosphor 99.6 1E-12 2.2E-17 146.0 31.2 346 38-461 3-367 (447)
12 COG1746 CCA1 tRNA nucleotidylt 99.2 7.9E-09 1.7E-13 113.3 28.7 345 36-461 5-368 (443)
13 PF03813 Nrap: Nrap protein; 99.2 5.7E-09 1.2E-13 126.4 28.1 341 98-460 1-425 (972)
14 KOG2054 Nucleolar RNA-associat 98.3 1.5E-05 3.3E-10 94.7 17.7 291 91-392 148-479 (1121)
15 smart00572 DZF domain in DSRM 98.2 7.9E-05 1.7E-09 77.7 17.5 213 93-346 5-230 (246)
16 cd05400 NT_2-5OAS_ClassI-CCAas 97.8 0.00021 4.4E-09 67.4 11.2 77 90-169 27-110 (143)
17 PF03828 PAP_assoc: Cid1 famil 97.6 4.1E-05 8.9E-10 62.4 2.4 56 261-319 1-59 (60)
18 cd05397 NT_Pol-beta-like Nucle 97.5 0.00013 2.7E-09 58.1 4.8 26 90-115 17-42 (49)
19 PF09249 tRNA_NucTransf2: tRNA 97.5 0.00038 8.2E-09 64.9 7.5 93 221-335 3-97 (114)
20 PF01909 NTP_transf_2: Nucleot 97.4 0.00023 4.9E-09 61.8 4.8 32 90-121 14-45 (93)
21 PF03813 Nrap: Nrap protein; 97.3 0.0021 4.6E-08 78.8 13.6 156 200-361 668-839 (972)
22 cd05403 NT_KNTase_like Nucleot 96.9 0.0012 2.5E-08 56.7 4.7 32 90-121 18-49 (93)
23 PF14091 DUF4269: Domain of un 96.1 0.054 1.2E-06 53.2 10.9 117 93-236 18-144 (152)
24 PF07528 DZF: DZF domain; Int 95.3 0.67 1.5E-05 49.0 15.8 208 96-345 2-231 (248)
25 COG1669 Predicted nucleotidylt 95.2 0.087 1.9E-06 48.2 7.8 29 91-119 25-53 (97)
26 COG1708 Predicted nucleotidylt 94.6 0.18 3.9E-06 45.5 8.4 29 90-118 26-54 (128)
27 PRK13746 aminoglycoside resist 94.2 0.089 1.9E-06 55.9 6.3 32 91-122 29-60 (262)
28 PF10421 OAS1_C: 2'-5'-oligoad 94.2 0.079 1.7E-06 53.8 5.4 48 214-261 41-89 (190)
29 cd00141 NT_POLXc Nucleotidyltr 93.0 1.3 2.9E-05 47.9 12.7 113 89-241 159-277 (307)
30 PRK02098 phosphoribosyl-dephos 91.6 0.35 7.5E-06 50.3 6.0 33 90-122 120-158 (221)
31 TIGR03135 malonate_mdcG holo-A 90.9 0.42 9.1E-06 49.0 5.7 33 90-122 108-146 (202)
32 PF14792 DNA_pol_B_palm: DNA p 89.5 1.6 3.5E-05 40.5 7.8 53 89-142 23-78 (112)
33 cd05401 NT_GlnE_GlnD_like Nucl 86.7 3.4 7.3E-05 40.4 8.5 48 89-136 54-101 (172)
34 COG1665 Predicted nucleotidylt 83.9 0.2 4.3E-06 53.5 -1.6 26 94-119 125-150 (315)
35 KOG2054 Nucleolar RNA-associat 83.4 5.5 0.00012 49.3 9.8 122 202-330 806-936 (1121)
36 PF03445 DUF294: Putative nucl 81.2 12 0.00025 36.0 9.5 49 88-136 47-96 (138)
37 KOG3793 Transcription factor N 78.7 36 0.00079 36.8 12.7 212 31-275 38-264 (362)
38 COG2844 GlnD UTP:GlnB (protein 73.5 12 0.00026 45.7 8.5 58 61-122 41-98 (867)
39 PF10620 MdcG: Phosphoribosyl- 70.5 7.2 0.00016 40.3 5.2 32 90-121 116-153 (213)
40 PRK05007 PII uridylyl-transfer 69.3 18 0.00039 44.9 9.0 57 59-119 53-109 (884)
41 smart00483 POLXc DNA polymeras 68.4 67 0.0015 35.4 12.4 30 89-119 163-192 (334)
42 PRK08609 hypothetical protein; 67.8 25 0.00054 41.5 9.5 109 89-241 174-283 (570)
43 PF03281 Mab-21: Mab-21 protei 63.9 2E+02 0.0044 30.4 14.7 96 214-339 190-288 (292)
44 PRK01759 glnD PII uridylyl-tra 62.0 29 0.00062 43.0 8.9 56 60-119 30-85 (854)
45 KOG2534 DNA polymerase IV (fam 59.1 36 0.00079 37.6 7.9 49 88-137 169-217 (353)
46 PF03710 GlnE: Glutamate-ammon 58.1 30 0.00064 36.4 7.0 62 75-136 111-179 (247)
47 PRK01293 phosphoribosyl-dephos 57.3 19 0.00041 37.3 5.3 44 90-135 109-158 (207)
48 PF10127 Nuc-transf: Predicted 57.2 9.5 0.0002 39.7 3.2 26 91-116 21-46 (247)
49 PF09970 DUF2204: Nucleotidyl 57.1 33 0.00071 34.6 6.9 80 90-176 16-100 (181)
50 PRK00227 glnD PII uridylyl-tra 56.6 34 0.00074 41.5 8.0 51 55-119 6-56 (693)
51 PRK03059 PII uridylyl-transfer 51.5 48 0.001 41.1 8.3 54 59-118 36-89 (856)
52 PRK00275 glnD PII uridylyl-tra 49.1 63 0.0014 40.3 8.9 56 60-119 52-107 (895)
53 PRK04374 PII uridylyl-transfer 47.5 65 0.0014 40.1 8.6 54 60-118 47-100 (869)
54 PF12633 Adenyl_cycl_N: Adenyl 46.0 26 0.00055 36.4 4.1 46 91-136 98-144 (204)
55 TIGR01693 UTase_glnD [Protein- 45.5 71 0.0015 39.4 8.6 31 89-119 42-72 (850)
56 COG2413 Predicted nucleotidylt 45.3 40 0.00087 35.2 5.3 28 91-118 38-65 (228)
57 PRK03381 PII uridylyl-transfer 45.1 52 0.0011 40.4 7.2 29 89-117 56-84 (774)
58 PF03296 Pox_polyA_pol: Poxvir 43.0 35 0.00075 33.6 4.2 78 38-135 9-92 (149)
59 PRK14109 bifunctional glutamin 37.9 79 0.0017 40.0 7.4 48 89-136 722-773 (1007)
60 PRK14109 bifunctional glutamin 36.1 1.3E+02 0.0027 38.3 8.8 48 89-136 214-265 (1007)
61 COG3541 Predicted nucleotidylt 36.0 17 0.00038 38.6 1.2 20 95-114 15-34 (248)
62 COG1796 POL4 DNA polymerase IV 34.1 87 0.0019 34.7 6.1 70 91-169 181-250 (326)
63 KOG2708 Predicted metalloprote 33.1 6.6E+02 0.014 27.2 12.7 104 45-181 38-155 (336)
64 PF10281 Ish1: Putative stress 31.7 38 0.00083 25.6 2.1 31 35-66 6-36 (38)
65 PHA02603 nrdC.11 hypothetical 29.0 31 0.00066 38.3 1.7 25 92-116 5-29 (330)
66 PF07357 DRAT: Dinitrogenase r 28.1 25 0.00054 37.7 0.8 21 378-398 95-115 (262)
67 PRK11072 bifunctional glutamin 26.7 2E+02 0.0042 36.4 8.1 48 89-136 153-208 (943)
68 PRK05092 PII uridylyl-transfer 26.1 1.3E+02 0.0029 37.7 6.6 30 89-118 104-133 (931)
69 PRK11072 bifunctional glutamin 25.7 2.1E+02 0.0045 36.2 8.2 60 76-136 666-736 (943)
70 COG1391 GlnE Glutamine synthet 22.7 6.4E+02 0.014 32.1 11.1 47 90-136 173-225 (963)
71 PRK14108 bifunctional glutamin 20.2 5E+02 0.011 33.1 9.9 48 89-136 185-238 (986)
No 1
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=100.00 E-value=1.5e-142 Score=1153.11 Aligned_cols=491 Identities=54% Similarity=0.943 Sum_probs=465.4
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 005394 1 MSSSERMSSPPPPKQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRG 80 (698)
Q Consensus 1 ~~~~~~~~s~~~~~~~Gvt~Pis~~~Pt~~d~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g 80 (698)
|.+.. +...+..+.||||+|||+++||++|+++|.+|+++|+++|+||++||..+|++||++|++||++|++++++++|
T Consensus 1 m~~~~-~~~~~~~~~~Gvt~PiS~a~p~~~d~~lt~~L~~~L~~~g~fEs~eEt~~R~~VL~~L~~iVk~wVk~vs~~k~ 79 (562)
T KOG2245|consen 1 MVSVQ-NPMSPSTKSYGVTQPISTAGPTEADIALTQELIKTLKNEGLFESKEETQRREEVLGKLNQIVKEWVKKVSEQKG 79 (562)
T ss_pred CCCcc-cCcCCccccccccCCcccCCCcHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 44444 33333469999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccccCCeEEEEeeeecccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEecC
Q 005394 81 YSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDG 160 (698)
Q Consensus 81 ~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~~Ff~~l~~~L~~~~~V~el~~I~~ArVPIIKf~~~G 160 (698)
+++++..+++++|+||||||||||+||||||+|||+|+|++|+ |||..|.++|+++++|++|++|++|+||||||+|+|
T Consensus 80 ~p~~~~~~aggkIftfGSYRLGVhg~GADIDtLcV~Prhv~R~-DFF~sf~~mL~~~~eVteL~~V~dAfVPiikfKf~G 158 (562)
T KOG2245|consen 80 LPDGMIENAGGKIFTFGSYRLGVHGPGADIDTLCVGPRHVSRS-DFFTSFYDMLKERPEVTELHAVEDAFVPIIKFKFDG 158 (562)
T ss_pred CChhhhhhcCceEEeccceeecccCCCCCcceeeeccccccHH-HHHHHHHHHHhcCccccccccccccccceEEEEecC
Confidence 9999999999999999999999999999999999999999996 999999999999999999999999999999999999
Q ss_pred eeeeEEeeeccccccccccccccccccCCCCcccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCc
Q 005394 161 LSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGF 240 (698)
Q Consensus 161 I~iDLsfa~l~~~~vp~~l~i~~d~~L~~lDe~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~ 240 (698)
|+|||+||+++.+.+|++|||.||++|+||||+|+||||||||||+||+|||+.+.||.+|||||+|||+||||+|.+||
T Consensus 159 I~IDllfArL~l~~VP~dldl~ddslLknlDe~~vrSLNGcRVtdqiL~LVPn~~~F~~tLRaiKlWAKrrgVYsN~~GF 238 (562)
T KOG2245|consen 159 IEIDLLFARLALPVVPEDLDLSDDSLLKNLDERCVRSLNGCRVTDQILKLVPNQENFRITLRAIKLWAKRRGVYSNVMGF 238 (562)
T ss_pred eeeeeeehhcccccCCCcccccchHhhhcccHHHHHHhcCcCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchHHHHHHHHHHHhhCCCCChHHHHHHHHHHhhcCCCCCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCCCC
Q 005394 241 LGGVNWALLVARVCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCM 320 (698)
Q Consensus 241 LGG~swaLLVa~vcQlyPnas~~~LL~~FF~~Ys~wdW~~pV~L~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~ 320 (698)
|||++|||||||+|||||||+++.||.+||.+|++|+||+||+|++++++.|++++|||+.|++||+|+||||||+||+|
T Consensus 239 ~GGV~wA~LVARiCQLYPNA~~s~Lv~kfF~ifs~W~WP~PVlL~~ie~~~L~~~VWdPr~n~~DryHlMPIITPAyP~~ 318 (562)
T KOG2245|consen 239 LGGVAWAMLVARICQLYPNASPSTLVAKFFRVFSQWNWPNPVLLKPIEEGNLNLPVWDPRVNPSDRYHLMPIITPAYPQM 318 (562)
T ss_pred cchHHHHHHHHHHHccCCCcchHHHHHHHHHHHhhccCCCceEeccccccccCccccCCCCCCCCcceecccccCCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccCccCHhHHHHHHHHHHHHHHHHHHhhhcCccccccccccchhhhcccEEEEEEEeCChhhhhhhhhhhHhhHHHHHH
Q 005394 321 NSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTL 400 (698)
Q Consensus 321 Nsa~nVs~sTlrvI~~EF~Ra~~Il~~i~~~~~~W~~Lf~p~~Ff~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~ 400 (698)
|++||||+||+++|.+||+||++||++|+.++.+|++|||+++||.+|||||+|+++|.++|++.+|.||||||+|+|+.
T Consensus 319 nsthNVS~ST~~Vi~~Ef~~g~~I~~~i~~~k~~W~~LFE~~~FF~rYk~yl~i~~~A~~~ed~l~w~G~vESriR~Lv~ 398 (562)
T KOG2245|consen 319 NSTHNVSRSTLKVITEEFKRGLEICDDIELNKLDWSDLFELYNFFSRYKHYLQITASAATEEDLLKWVGWVESRIRQLVL 398 (562)
T ss_pred cccccccHHHHHHHHHHHHHHHHHHHHHHhccccHHHHhhhhHHHHHHhhHheeeeeccChHHHhhhhhHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcccCceeeccCCCCCCCCCC----CCceeEEEEeeeeCCCCccCCCceecchHHHHHHHHHHh----hccccCCc-
Q 005394 401 MIERDTYGKLQCHPYPHEYVDTSK----PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSIN----MYMFWKPG- 471 (698)
Q Consensus 401 ~LE~~~~~~l~ahp~P~~f~~~~~----~~~~~~ffIGL~~~~~~~~~~~~~~dl~~~v~eF~~~i~----~~~~~~~~- 471 (698)
+||+.. .++.|||+|+.|.++.. ..+...|||||.+.++ .++||+..+++|...++ ..+.+.+|
T Consensus 399 klE~~~-~i~~ahp~P~~f~~~~~~~~~~~~~~~~~igl~~~e~------~~~Dlt~~iq~f~~~v~~q~~~~~~~~~g~ 471 (562)
T KOG2245|consen 399 KLERNQ-VILIAHPNPKKFKDTYNCPLEEDPESLWFIGLEFDEN------VKIDLTKDIQSFKKNVERQAVNLTLIKAGC 471 (562)
T ss_pred HHHhhc-ceEEecCCcccccccccCCcccchhHhhhhccccccc------ccchhhhhHHHhhhhhhhcceeeeeeeccc
Confidence 999954 66889999999987653 2346689999987654 34999999999999887 45677899
Q ss_pred -eEEEEEeeccCCCCCCcCCCCccccCCCc
Q 005394 472 -MEICVSHIRRKQIPPYVFPEGYKRTRHPR 500 (698)
Q Consensus 472 -m~i~v~~vkr~~LP~~v~~~g~~~~~~~~ 500 (698)
|.+.+.|+||++|+.+++++++++.|.-+
T Consensus 472 ~~~~~~~~~krr~l~~~~~~~~l~~~k~~~ 501 (562)
T KOG2245|consen 472 DVEIDFGHVKRRSLIQTITKEFLRLCKQYK 501 (562)
T ss_pred ccccccccccccccccccCHHHhhHHHhhc
Confidence 77888899999999999999887765543
No 2
>PTZ00418 Poly(A) polymerase; Provisional
Probab=100.00 E-value=3.6e-135 Score=1131.70 Aligned_cols=485 Identities=42% Similarity=0.786 Sum_probs=459.9
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccC
Q 005394 10 PPPPKQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDA 89 (698)
Q Consensus 10 ~~~~~~~Gvt~Pis~~~Pt~~d~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~ 89 (698)
..+++.||||+|||+++||++|++.+.+|+++|+++|+|||+||.++|++||++|++||++|+++++.++|++++++.++
T Consensus 46 ~~~~~~~Gvt~Pis~~~Pt~~d~~~s~~L~~~L~~~~~fes~ee~~kR~~vL~~L~~iv~~wv~~vs~~k~~~~~~~~~~ 125 (593)
T PTZ00418 46 IECALSYGVTDPISLNGPTEEDLKLSNELINLLKSYNLYETEEGKKKRERVLGSLNKLVREFVVEASIEQGINEEEASQI 125 (593)
T ss_pred cCcccccCCCCCccCCCCChHHHhhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhHHhcC
Confidence 34678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEEeeeecccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEecCeeeeEEeee
Q 005394 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYAS 169 (698)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~~Ff~~l~~~L~~~~~V~el~~I~~ArVPIIKf~~~GI~iDLsfa~ 169 (698)
+++|+|||||+||||+|+||||+|||+|.|++|+ +||..|+++|++.++|++|++|++|+||||||+++||+|||+||+
T Consensus 126 ~g~I~tfGSYrLGV~~pgSDID~L~V~P~~vtre-dFF~~f~~~L~~~~~V~eL~~V~~A~VPiIk~~~~GI~iDL~fa~ 204 (593)
T PTZ00418 126 SGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRE-SFFSDFYAKLQQDPNITKLQPVPDAYTPVIKFVYDGIDIDLLFAN 204 (593)
T ss_pred CeEEEEeccccccCCCCCCcccEEEECCCCCCHH-HHHHHHHHHHhcCCCcceeeccCccccCeEEEEECCEEEeeeecc
Confidence 9999999999999999999999999999999996 999999999999999999999999999999999999999999999
Q ss_pred cccccccccccccccc-ccCCCCcccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHH
Q 005394 170 ISRLVVREDLDISDMS-VLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWAL 248 (698)
Q Consensus 170 l~~~~vp~~l~i~~d~-~L~~lDe~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaL 248 (698)
++...+|+++++.+|+ +|++||++++||||||||+|+|+++||+.+.||.+|||||+|||+||||+|++||||||+|||
T Consensus 205 l~~~~vp~~~~~l~d~~lL~nlde~s~rSLNG~Rvtd~Il~lVPn~~~Fr~aLR~IKlWAkrRGIYsNv~GflGGV~wAI 284 (593)
T PTZ00418 205 LPLPTIPDCLNSLDDDYILRNVDEKTVRSLNGCRVADLILASVPNKDYFRTTLRFIKLWAKRRGIYSNVLGYLGGVSWAI 284 (593)
T ss_pred cCCCCCCccccccCchhhhhcCCHHHhhhhccHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccccccccccchHHHHH
Confidence 9999999999988886 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhCCCCChHHHHHHHHHHhhcCCCCCceeeccccc-----ccCCcccccCCCCCCCCCCceEEeCCCCCCCCcc
Q 005394 249 LVARVCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDE-----AELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSS 323 (698)
Q Consensus 249 LVa~vcQlyPnas~~~LL~~FF~~Ys~wdW~~pV~L~~i~~-----g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa 323 (698)
||||+||+|||+++++||.+||.+|++|+||+||+|+++++ |.+++++|||+.|++|++|+||||||+||+||+|
T Consensus 285 LvARVCQLyPna~~s~Lv~~FF~iys~W~Wp~PV~L~~i~~~~~~~g~~~~~VWdPr~~~~dr~h~MPIITPayP~mNst 364 (593)
T PTZ00418 285 LTARICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKEVPNIPGLMNFKVWDPRVNPQDRAHLMPIITPAFPSMNST 364 (593)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCCCeEcccccccccCCcccCCcccCCCCCcccccccCCeecCCCCCcccc
Confidence 99999999999999999999999999999999999998875 5688999999999999999999999999999999
Q ss_pred CccCHhHHHHHHHHHHHHHHHHHHhhh-cCccccccccccchhhhcccEEEEEEEeCChhhhhhhhhhhHhhHHHHHHHh
Q 005394 324 YNVSTSTLRVMMDQFQYGNTICEEVEL-NKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMI 402 (698)
Q Consensus 324 ~nVs~sTlrvI~~EF~Ra~~Il~~i~~-~~~~W~~Lf~p~~Ff~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~L 402 (698)
||||.+|+++|++||+||++|++++.. ++.+|++||+|++||.+|++||+|++.+.+++++..|.||||||||.|+.+|
T Consensus 365 ~nVt~sT~~vI~~Ef~Ra~~i~~~i~~~~~~~W~~Lfep~~Ff~~Yk~yl~V~v~a~~~~~~~~w~G~VESRlR~Lv~~L 444 (593)
T PTZ00418 365 HNVTYTTKRVITEEFKRAHEIIKYIEKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKKL 444 (593)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHcCCcchhhhcceEEEEEEEECCHHHhhhhhhHHHHHHHHHHHHh
Confidence 999999999999999999999999988 8899999999999999999999999999999999999999999999999999
Q ss_pred hhcccCceeeccCCCCCCCCCC-CCceeEEEEeeeeCCCCccCCCceecchHHHHHHHHHHhhcc---ccCCceEEEEEe
Q 005394 403 ERDTYGKLQCHPYPHEYVDTSK-PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSINMYM---FWKPGMEICVSH 478 (698)
Q Consensus 403 E~~~~~~l~ahp~P~~f~~~~~-~~~~~~ffIGL~~~~~~~~~~~~~~dl~~~v~eF~~~i~~~~---~~~~~m~i~v~~ 478 (698)
|+. +.+.+||||++|.+... ..|.++|||||.++.+.. .+..++||+.++++|.+.|++|. .|.++|||+|+|
T Consensus 445 E~~--~~i~~~p~P~~f~~~~~~~~~~~~ffIGL~~~~~~~-~~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~~i~v~~ 521 (593)
T PTZ00418 445 ETL--NNLKIRPYPKFFKYQDDGWDYASSFFIGLVFFSKNV-YNNSTFDLRYAIRDFVDIINNWPEMEKYPDQIDINIKY 521 (593)
T ss_pred hcc--CCceEeecCcccccCCCCceeEEEEEEeEeeccCCC-CCCceEecHHHHHHHHHHHHhhhhcccCCCCceEEEEE
Confidence 974 34678999999988653 356789999999876543 23358999999999999999886 367889999999
Q ss_pred eccCCCCCCcCCCCccccCC
Q 005394 479 IRRKQIPPYVFPEGYKRTRH 498 (698)
Q Consensus 479 vkr~~LP~~v~~~g~~~~~~ 498 (698)
||+++||++||++|++|+..
T Consensus 522 Vk~~~Lp~~v~~~~~~~~~~ 541 (593)
T PTZ00418 522 LKKSQLPAFVLSQTPEEPVK 541 (593)
T ss_pred eehHhCCHhhccCCCcCCCc
Confidence 99999999999999877443
No 3
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=100.00 E-value=1.8e-122 Score=965.03 Aligned_cols=478 Identities=42% Similarity=0.755 Sum_probs=457.1
Q ss_pred CCCCCCCCCCCCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeE
Q 005394 13 PKQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANAL 92 (698)
Q Consensus 13 ~~~~Gvt~Pis~~~Pt~~d~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~ 92 (698)
.++||||+|||+.+.|+++.+++.+|+++|+..|+|+++.|.+.|.+||++|+.++++|+.++++.+|+.+.|+.++|++
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 EEEeeeecccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEecCeeeeEEeeeccc
Q 005394 93 IFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISR 172 (698)
Q Consensus 93 I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~~Ff~~l~~~L~~~~~V~el~~I~~ArVPIIKf~~~GI~iDLsfa~l~~ 172 (698)
||+|||||||||+||||||++||.|.|++|+ +||+.|..+|++.++++++.+|++|+||||||+|.||+|||.||++..
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 9999999999999999999999999999996 999999999999999999999999999999999999999999999999
Q ss_pred cccccccccccccccCCCCcccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHH
Q 005394 173 LVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVAR 252 (698)
Q Consensus 173 ~~vp~~l~i~~d~~L~~lDe~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~ 252 (698)
+.+|..|.++|+++|++|||+|++||||.||||+||++||+...|+.+||+||+||++|.||.|.+||.||++|+|||||
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 HHhhCCCCChHHHHHHHHHHhhcCCCCCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHH
Q 005394 253 VCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLR 332 (698)
Q Consensus 253 vcQlyPnas~~~LL~~FF~~Ys~wdW~~pV~L~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~sTlr 332 (698)
+||||||++...++.+||.++++|+||+||+|+||++|+++.++|||+.|+.|+.|.||||||+||+||.|||||.||..
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 HHHHHHHHHHHHHHHhhhcCccccccccccchhhhcccEEEEEEEeCChhhhhhhhhhhHhhHHHHHHHhhhcccCceee
Q 005394 333 VMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQC 412 (698)
Q Consensus 333 vI~~EF~Ra~~Il~~i~~~~~~W~~Lf~p~~Ff~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~a 412 (698)
+|..||-||++|+++|+.+..+|..||+..|||.+||+||.|++.+.++|++.+|.|+||||+|.|+.+||... +++.|
T Consensus 323 vIl~EfvRa~~I~~di~~n~~~w~~lFek~DFF~RYk~yleitA~s~~~E~~lKW~GlvESKiR~Lv~klE~vd-~i~~A 401 (552)
T COG5186 323 VILMEFVRAHKILSDIERNALDWRRLFEKSDFFSRYKLYLEITAMSSCEEDFLKWEGLVESKIRILVSKLEAVD-DILYA 401 (552)
T ss_pred hHHHHHHHHHHhhhhHhhccccHHHHHHhhhHHHHHhHhhhhhhhhcchhhhhhhhhHHHHHHHHHHHHHHHhh-hhhhc
Confidence 99999999999999999998999999999999999999999999999999999999999999999999999754 56889
Q ss_pred ccCCCCCCCCC----------------------------------C---------CCceeEEEEeeeeCCCCccCCCcee
Q 005394 413 HPYPHEYVDTS----------------------------------K---------PCAHCAFFMGLQRKPGEVVQEGQQF 449 (698)
Q Consensus 413 hp~P~~f~~~~----------------------------------~---------~~~~~~ffIGL~~~~~~~~~~~~~~ 449 (698)
||||+.|...- . ..|-+.|||||+.... ..++++
T Consensus 402 hPF~K~F~~~y~c~~Ee~~e~i~~~~~~~~a~~s~d~~kl~~d~~~eees~~d~~k~y~tt~yIgld~~~~---~~~kkv 478 (552)
T COG5186 402 HPFPKAFRKVYNCVAEESIEKIGSGVTLEVAYESTDHEKLANDTVPEEESMEDGMKVYCTTFYIGLDVIPV---KPGKKV 478 (552)
T ss_pred CcCChhhhhhcCCccHHHHHHHhcccceeehhhccchhhhccccCchhhhhccccceeeeEEEEEEEeeec---CCCcee
Confidence 99999995110 0 1245689999998653 235689
Q ss_pred cchHHHHHHHHHHhhcccc-CCceEEEEEeeccCCCCCCcCCCCccc
Q 005394 450 DIRGSVEEFKLSINMYMFW-KPGMEICVSHIRRKQIPPYVFPEGYKR 495 (698)
Q Consensus 450 dl~~~v~eF~~~i~~~~~~-~~~m~i~v~~vkr~~LP~~v~~~g~~~ 495 (698)
||..+++||.+.++.|+++ ..+|.|.|+.+|+++||+-||.+|+.|
T Consensus 479 di~~p~~EF~elcr~~d~gd~~~mni~v~~~K~~dlpdeVF~~geer 525 (552)
T COG5186 479 DIEQPVKEFIELCREYDEGDASGMNIEVNSLKRKDLPDEVFYPGEER 525 (552)
T ss_pred eeeccHHHHHHHHHHhhccccceeeeehhhccccCCchhhcCCCccC
Confidence 9999999999999999654 578999999999999999999988766
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=9.2e-74 Score=589.55 Aligned_cols=254 Identities=59% Similarity=1.048 Sum_probs=204.1
Q ss_pred CCCCCCCCCCCCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeE
Q 005394 13 PKQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANAL 92 (698)
Q Consensus 13 ~~~~Gvt~Pis~~~Pt~~d~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~ 92 (698)
.++||||+|||+++||+.|++.+++|+++|++.+++||+||.++|++||++|+++|++|+++
T Consensus 1 ~~~~Gvt~PIS~~~Pt~~Dl~~s~~L~~~l~~~~~~es~ee~~~R~~vl~~L~~iv~~wv~~------------------ 62 (254)
T PF04928_consen 1 QKQYGVTKPISLAPPTEKDLKRSASLEEFLKDYGLFESEEEEQKREEVLRKLQQIVKEWVKQ------------------ 62 (254)
T ss_dssp -GGGSTT--S------HHHHHHHHHHHHHHHHCT-S--HHHHHHHHHHHHHHHHHHHHHHHH------------------
T ss_pred CCccCCCCCccCCCCChhhHHhHHHHHHHHHHcCCCCChHHHhHHHHHHHHHHHHHHHHHHh------------------
Confidence 37999999999999999999999999999999999999999999999999999999999863
Q ss_pred EEEeeeecccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEecCeeeeEEeeeccc
Q 005394 93 IFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISR 172 (698)
Q Consensus 93 I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~~Ff~~l~~~L~~~~~V~el~~I~~ArVPIIKf~~~GI~iDLsfa~l~~ 172 (698)
..
T Consensus 63 ------------------------------------------------------------------------------~~ 64 (254)
T PF04928_consen 63 ------------------------------------------------------------------------------AL 64 (254)
T ss_dssp ------------------------------------------------------------------------------SS
T ss_pred ------------------------------------------------------------------------------hh
Confidence 45
Q ss_pred cccccccccccccccCCCCcccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHH
Q 005394 173 LVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVAR 252 (698)
Q Consensus 173 ~~vp~~l~i~~d~~L~~lDe~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~ 252 (698)
..+|+++++.++++|++||++|++||||+||+++|+++||+.+.||.++|+||+|||+||||+|++||||||+||||||+
T Consensus 65 ~~~p~~l~~~~~~~l~~ld~~s~~sLnG~Rv~~~il~~Vp~~~~Fr~~lR~IK~WAk~RGIYsn~~GylGGI~waILvAr 144 (254)
T PF04928_consen 65 PRVPEDLDLLDDDPLRNLDEASVRSLNGVRVTDYILRLVPNQETFRTALRFIKLWAKRRGIYSNVFGYLGGIHWAILVAR 144 (254)
T ss_dssp SSB-TT--TT-GGGGTT--HHHHHHHHHHHHHHHHHCTSS-HHHHHHHHHHHHHHHHHTT-B-CCCTSB-HHHHHHHHHH
T ss_pred cCCCcccccCCchhhhCCCHhhccCcccccHHHHHHHHCCCHHHHHHHHHHHHHHHHHccccchhhccchHHHHHHHHHH
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCChHHHHHHHHHHhhcCCCCCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHH
Q 005394 253 VCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLR 332 (698)
Q Consensus 253 vcQlyPnas~~~LL~~FF~~Ys~wdW~~pV~L~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~sTlr 332 (698)
+||+|||+++++||.+||.+|++|+|++||+|+++.++.+++++|+|+.|++|++|+||||||+||+||+|+|||.+|++
T Consensus 145 vcql~Pn~~~~~ll~~FF~~ys~W~W~~PV~l~~~~~~~~~~~~w~p~~~~~~~~~~MpIiTP~yP~~Nst~nVt~st~~ 224 (254)
T PF04928_consen 145 VCQLYPNASPSTLLSRFFQIYSQWDWPNPVVLDPIEDGPLGFKVWNPRLYPRDRRHLMPIITPAYPSMNSTYNVTRSTLR 224 (254)
T ss_dssp HHHHSTT--HHHHHHHHHHHHHCS-TTS-EESS-----SSSCGS--TTT-HHHHC-SS-EE-SSSS--BTTTT--HHHHH
T ss_pred HHHHCccccccchHHHHHHHhcCCCCCCceeecccccCcccccCCCCCCCCCCcccceeEccCCCCccccccccCHHHHH
Confidence 99999999999999999999999999999999999888899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcCcccccccccc
Q 005394 333 VMMDQFQYGNTICEEVELNKAQWSALFEPY 362 (698)
Q Consensus 333 vI~~EF~Ra~~Il~~i~~~~~~W~~Lf~p~ 362 (698)
+|++||+||+++++++..++.+|++||+|+
T Consensus 225 ~i~~Ef~ra~~i~~~~~~~~~~W~~L~e~~ 254 (254)
T PF04928_consen 225 IIREEFQRAHEILSEILKGGASWSDLFEPH 254 (254)
T ss_dssp HHHHHHHHHHHHHHHHHTTSS-HHHCT---
T ss_pred HHHHHHHHHHHHHHHHHcCCCCHHHHcCCC
Confidence 999999999999999998899999999985
No 5
>COG5260 TRF4 DNA polymerase sigma [DNA replication, recombination, and repair]
Probab=99.98 E-value=4.1e-31 Score=288.39 Aligned_cols=266 Identities=22% Similarity=0.265 Sum_probs=213.5
Q ss_pred HHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCCC
Q 005394 29 EADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGA 108 (698)
Q Consensus 29 ~~d~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~S 108 (698)
+....++.+|.+++. .+.|+.+|.++|.+.|++|++++++- ++ .+.+++|||+.+|+++|+|
T Consensus 52 ~~~~~lt~el~~~y~--~I~ps~eEl~~R~~~leklr~~lk~~--------------~p--da~l~vFGS~~t~L~l~~S 113 (482)
T COG5260 52 EESDELTSELLEFYD--YIAPSDEELKRRKALLEKLRTLLKKE--------------FP--DADLKVFGSTETGLALPKS 113 (482)
T ss_pred hhHHHHHHHHHHHHH--hhCCCHHHHHHHHHHHHHHHHHHHHh--------------CC--ccceeEecccccccccCcc
Confidence 344567777877776 48899999999999999999999853 23 4699999999999999999
Q ss_pred CeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEe--cCeeeeEEeeeccccccccccccccccc
Q 005394 109 DIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKF--DGLSIDLLYASISRLVVREDLDISDMSV 186 (698)
Q Consensus 109 DID~l~v~P~~v~re~~Ff~~l~~~L~~~~~V~el~~I~~ArVPIIKf~~--~GI~iDLsfa~l~~~~vp~~l~i~~d~~ 186 (698)
|||++++.+.....+..-...++..|.......++.+|.+|+||||||.. .|+.|||+|++.
T Consensus 114 DiDl~I~s~~~~~~et~~~~~l~~~l~~~~~~~~~~~v~tarVPIIKl~d~~s~l~~Disfn~~---------------- 177 (482)
T COG5260 114 DIDLCIISDPRGYKETRNAGSLASHLFKKNLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNT---------------- 177 (482)
T ss_pred cccEEEecCCccccccccHHHHHHHHHHhccCeeeEEEEecccceEEEecCccceEEEeecCch----------------
Confidence 99999999776665422222455555555667889999999999999998 599999999973
Q ss_pred cCCCCcccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHHHHhhCCC-------
Q 005394 187 LNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPN------- 259 (698)
Q Consensus 187 L~~lDe~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~vcQlyPn------- 259 (698)
+|++.|..++.++-.++++|+|+.+||+||++|.+++..+|+|+||++++||..++|++|.
T Consensus 178 ------------~~~~~akl~~~~~~~~P~lrpLvliIKhwl~~R~ln~~~~GtL~sy~i~cmV~sfLq~~~~~~~~~~~ 245 (482)
T COG5260 178 ------------NGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPFLFFDNG 245 (482)
T ss_pred ------------hHHHHHHHHHHHHhcCcccchHHHHHHHHHHHHhhcccccCcchhhhhHHHHHHHHHhCCcccccccc
Confidence 6889999999999999999999999999999999999999999999999999999999971
Q ss_pred -----------CChHHHHHHHHHHhh-cCCCCCceeeccccccc-C--CcccccCCCCCCCCCCceEEeCCC-CCCCCcc
Q 005394 260 -----------AVPSMLVSRFFRVYT-MWRWPNPVMLCAIDEAE-L--GFSVWDPRKNRRDKTHHMPIITPA-YPCMNSS 323 (698)
Q Consensus 260 -----------as~~~LL~~FF~~Ys-~wdW~~pV~L~~i~~g~-l--g~~~W~p~~~~~dr~~~MpIiTP~-~P~~Nsa 323 (698)
..++.|+..||++|+ .|+|..-++...-. +. + ..+.|--... ...++|++|. .+ |..
T Consensus 246 ~~~~l~~~~~~~~lgvLf~dFf~~yG~~f~Y~~~~~si~~g-~~~~~K~e~g~~~~~~----p~~LsiqdP~td~--n~~ 318 (482)
T COG5260 246 LLSPLKYNKNIDNLGVLFDDFFELYGKSFNYSLVVLSINSG-DFYLPKYEKGWLKPSK----PNSLSIQDPGTDR--NND 318 (482)
T ss_pred ccchhhccccccccchHHHHHHHHhccccChhheEEEecCC-ceeeehhhcccccccC----CCcEeecCCCCCc--ccc
Confidence 248999999999999 59998755543322 11 1 1134432111 2689999999 55 333
Q ss_pred CccCHhHHHHHHHHHHHHHHHHHH
Q 005394 324 YNVSTSTLRVMMDQFQYGNTICEE 347 (698)
Q Consensus 324 ~nVs~sTlrvI~~EF~Ra~~Il~~ 347 (698)
-.....+.+.|+.+|.+|.+++.+
T Consensus 319 ~~a~s~~ik~i~~~F~~aF~lls~ 342 (482)
T COG5260 319 ISAVSFNIKDIKAAFIRAFELLSN 342 (482)
T ss_pred cccccchHHHHHHHHHHHHHHHhh
Confidence 334445799999999999999987
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=7.2e-32 Score=259.33 Aligned_cols=135 Identities=36% Similarity=0.714 Sum_probs=104.8
Q ss_pred chhhhcccEEEEEEEeCChhhhhhhhhhhHhhHHHHHHHhhhcccCceeeccCCCCCC------------------CCCC
Q 005394 363 LFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYV------------------DTSK 424 (698)
Q Consensus 363 ~Ff~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~------------------~~~~ 424 (698)
+||.+|||||+|+|++.+++++.+|.||||||||.||.+||+.. .+..|||||++|. +...
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 69999999999999999999999999999999999999999865 4677999999998 1122
Q ss_pred CCceeEEEEeeeeCCCCccCCCceecchHHHHHHHHHHhhccc---cCCceEEEEEeeccCCCCCCcCCCCccccCC
Q 005394 425 PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSINMYMF---WKPGMEICVSHIRRKQIPPYVFPEGYKRTRH 498 (698)
Q Consensus 425 ~~~~~~ffIGL~~~~~~~~~~~~~~dl~~~v~eF~~~i~~~~~---~~~~m~i~v~~vkr~~LP~~v~~~g~~~~~~ 498 (698)
..+.++|||||.+........++++||+.++++|++.|++|.. +.++|+|+|+||||++||++||++|.+|+++
T Consensus 80 ~~~~~~~fIGL~~~~~~~~~~~~~~dL~~~i~~F~~~v~~~~~~~~~~~~m~i~i~~vk~~~Lp~~v~~~~~~r~~k 156 (157)
T PF04926_consen 80 NEYTSSFFIGLEFDSKESNEGSKKLDLTYAIQEFKDLVRNWEKYYYDEEGMDISISHVKRSQLPDFVFEEGEKRPKK 156 (157)
T ss_dssp EEEEEEEEEEEEE--SSSS---S-EE-HHHHHHHHHHHHCCCCTTC-TTTEEEEEEEEEHHHHGGGGS-TTS-----
T ss_pred ceeEEEEEEEEEECCCCccccceEEehHHHHHHHHHHHHhhhccccCCCccEEEEEEechHHCChhhhcccCcCCCC
Confidence 3578899999999876543334679999999999999999754 6788999999999999999999999988665
No 7
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=99.96 E-value=2.5e-28 Score=271.50 Aligned_cols=270 Identities=21% Similarity=0.301 Sum_probs=212.3
Q ss_pred CHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCC
Q 005394 28 TEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPG 107 (698)
Q Consensus 28 t~~d~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~ 107 (698)
.+.-..++++++.+++ .+.||.+|.+.|.++++++++.|++- + ..+.|++||||.+|+++|+
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 5555667788888887 48899999999999999999988721 2 3699999999999999999
Q ss_pred CCeeEEeecCCccCchhhHHHHHHHHHHh--ccCCceEEEeccCccceEEEEe--cCeeeeEEeeecccccccccccccc
Q 005394 108 ADIDALCVGPSYVSREEDFFFILHNILAE--MEEVTELQPVLDAHVPVMKFKF--DGLSIDLLYASISRLVVREDLDISD 183 (698)
Q Consensus 108 SDID~l~v~P~~v~re~~Ff~~l~~~L~~--~~~V~el~~I~~ArVPIIKf~~--~GI~iDLsfa~l~~~~vp~~l~i~~ 183 (698)
||||+++..+....++ +.+..+.-++.. ...-..+..|..|+||||||+. .+|.|||+|++
T Consensus 119 sDIDl~v~~~~~~~~e-~~~~~~~l~~~~e~~~~~~~v~~v~karvpiik~~d~~s~i~vDISFn~-------------- 183 (514)
T KOG1906|consen 119 SDIDLVVLSKFLNDKE-DRAVKLELALELEEDNSAFHVKVVQKARVPIIKFKDPVSNIHVDISFNQ-------------- 183 (514)
T ss_pred cceEEEEecccccCch-hhHHHHHHHHhhhhccccceEEEeeeeeeeeEEeecCccceEEEeeecc--------------
Confidence 9999999999776664 555555444443 2233468889999999999997 79999999997
Q ss_pred ccccCCCCcccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHHHHhhCCCC---
Q 005394 184 MSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPNA--- 260 (698)
Q Consensus 184 d~~L~~lDe~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~vcQlyPna--- 260 (698)
.|||+.++.|..++-+.+.+|.++.++|+|...|++++...|+++||++++||+.++|++|..
T Consensus 184 --------------~~G~~aa~~i~~~~~~~p~~~~lvlvlk~fl~~r~ln~v~tGgisSyal~~Lv~~fl~l~~~~~s~ 249 (514)
T KOG1906|consen 184 --------------TNGVKAAKFIKDFLRDHPFLRSLVLVLKQFLYERRLNGVHTGGISSYALELLVLSFLQLHPRSKSG 249 (514)
T ss_pred --------------cCchhHHHHHHHHHhcCccchhHHHHHHHHHHhhcccccccccchHHHHHHHHHHHHhhcccccCC
Confidence 478999999999999999999999999999999999999999999999999999999999864
Q ss_pred ------ChHHHHHHHHHHhh-cCCCCC-ceeecccccccC-CcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHH
Q 005394 261 ------VPSMLVSRFFRVYT-MWRWPN-PVMLCAIDEAEL-GFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTL 331 (698)
Q Consensus 261 ------s~~~LL~~FF~~Ys-~wdW~~-pV~L~~i~~g~l-g~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~sTl 331 (698)
.++.||.+||++|+ +|++.. -|.+....+... ....|- .+...+...+.|+||..|..+.++. ..++
T Consensus 250 ~~~~~~~~~vll~~f~e~yG~~f~~~k~~i~~~~~g~~~~~~~~~~~--~~~~~~~~~LsieDP~~P~ndigr~--s~~~ 325 (514)
T KOG1906|consen 250 RLAVLKNLGVLLIKFFELYGRNFGYDKLGISLSLGGEYVSKELTGFF--NNSLERPGSLSIEDPVDPTNDIGRS--SFNF 325 (514)
T ss_pred ccchhcccchHHHHHHHHhccccCchhhceeccCCcccccHHhhhhh--cccccCCCccccCCCCCcccccccc--cccH
Confidence 36789999999999 576664 233322111100 011121 1222355679999999996655422 2358
Q ss_pred HHHHHHHHHHHHHHHHh
Q 005394 332 RVMMDQFQYGNTICEEV 348 (698)
Q Consensus 332 rvI~~EF~Ra~~Il~~i 348 (698)
..|+.+|..|+.++...
T Consensus 326 ~~v~~~F~~af~~l~~~ 342 (514)
T KOG1906|consen 326 SQVKGAFAYAFKVLTNA 342 (514)
T ss_pred HHHHHHHHHHHHHHhhh
Confidence 88999999999888653
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=99.80 E-value=6.3e-19 Score=159.85 Aligned_cols=110 Identities=39% Similarity=0.751 Sum_probs=97.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCCCCeeEEeecCCc-cCchhhHHHHHHHHH
Q 005394 56 KREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY-VSREEDFFFILHNIL 134 (698)
Q Consensus 56 ~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~-v~re~~Ff~~l~~~L 134 (698)
.|++++++|++++++|. .++++++|||+++|+++|+||||+++..|.. ... ..++..+.+.|
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 38899999999999873 3689999999999999999999999999986 333 48999999999
Q ss_pred HhccCCceEEEeccCccceEEEEec--CeeeeEEeeeccccccccccccccccccCCCCcccccccchhhhHHHHHHh
Q 005394 135 AEMEEVTELQPVLDAHVPVMKFKFD--GLSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKL 210 (698)
Q Consensus 135 ~~~~~V~el~~I~~ArVPIIKf~~~--GI~iDLsfa~l~~~~vp~~l~i~~d~~L~~lDe~svrSLNG~Rvtd~Il~l 210 (698)
++...+.++..|.+|+||||||.+. |++|||+|++ .+|++++++|..+
T Consensus 64 ~~~~~~~~~~~i~~ArVPiik~~~~~~~i~~Dis~~~----------------------------~~g~~~s~li~~y 113 (114)
T cd05402 64 KKSGEVVEVEPIINARVPIIKFVDKPTGIEVDISFNN----------------------------LNGIRNTKLLRAY 113 (114)
T ss_pred HhCCCceeeEEeccCCCCEEEEEEcCCCeEEEEEccc----------------------------chHHHHHHHHHHh
Confidence 9988888999999999999999997 9999999987 4788888887765
No 9
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=99.76 E-value=4.9e-17 Score=185.04 Aligned_cols=253 Identities=22% Similarity=0.295 Sum_probs=191.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCCCCeeEEeecCCc-cCc---
Q 005394 47 LYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY-VSR--- 122 (698)
Q Consensus 47 l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~-v~r--- 122 (698)
..+...+...|...+..++.++..-+ +.....+..|||..+|+....+|+|+++..... ..-
T Consensus 125 ~~~~~~~~~~~~~~~~~l~~~~~~~~--------------p~~~~~~~~~gs~~~~~~~~~~d~d~~~~~~~~~~~~~~~ 190 (596)
T KOG2277|consen 125 FKLPHSDVKTRKLILDKLRALASLLF--------------PDSILSLYLFGSSDLGLGERSSDLDLCVDFTSSFLSFEKI 190 (596)
T ss_pred cCCCccccchHHHHHHHHHHHHHHhc--------------CCCcceeeccCcccccccccccCcceeecccccccccchh
Confidence 33455666777777777777776432 222334789999999999999999943333222 110
Q ss_pred -hhhHHHHHHHHHHhccC--CceEEEeccCccceEEEEe--cCeeeeEEeeeccccccccccccccccccCCCCcccccc
Q 005394 123 -EEDFFFILHNILAEMEE--VTELQPVLDAHVPVMKFKF--DGLSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRS 197 (698)
Q Consensus 123 -e~~Ff~~l~~~L~~~~~--V~el~~I~~ArVPIIKf~~--~GI~iDLsfa~l~~~~vp~~l~i~~d~~L~~lDe~svrS 197 (698)
...++..+.+.|....+ +..++.|..|+|||||+.+ .++++|+++.+..
T Consensus 191 ~~~~~~~l~~~~~~~~~~~~~~~~~~i~~A~vPiik~~~~~~~~~~d~s~~n~~-------------------------- 244 (596)
T KOG2277|consen 191 KGLEILKLLAKCLASLLEEGVREVQQILSARVPIIKFNDSGSGLECDLSVNNSD-------------------------- 244 (596)
T ss_pred hhHHHHHHHHHHHHhccccccceeeeeeecCCCEEEecCCCCCCceeeeeccch--------------------------
Confidence 13456667777777543 7889999999999999965 5899999988632
Q ss_pred cchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccc-hHHHHHHHHHHHhhCCCC----------------
Q 005394 198 LNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLG-GVNWALLVARVCQLYPNA---------------- 260 (698)
Q Consensus 198 LNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LG-G~swaLLVa~vcQlyPna---------------- 260 (698)
|.+++..+..+...+.+|++|...||+||+++++++...|.+. +|++.+||++++|.++..
T Consensus 245 --~~~nS~ll~~~~~~d~r~~~L~~~vk~wa~~~~~~d~~~g~~~s~ysl~lmvi~fLq~~~~~ilp~l~~l~~~~~~~~ 322 (596)
T KOG2277|consen 245 --AILNSQLLRNYSEIDPRVRPLVLLVKHWAKEKGLNDAKPGGLNSSYSLTLMVIHFLQTLSPPILPPLSKLLPESDSND 322 (596)
T ss_pred --hhhhhHHHHHhHhcCCCcchHhHHHHHHHHhccCCCCCCCceeccccHHHHHHHHHHhcCCcCCCchhhhchhccccc
Confidence 3455666777777778999999999999999999999999998 699999999999986310
Q ss_pred ---------------------------ChHHHHHHHHHHhh-cCCCCCceeecccccccCCcccccCCCCCCCCCCceEE
Q 005394 261 ---------------------------VPSMLVSRFFRVYT-MWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPI 312 (698)
Q Consensus 261 ---------------------------s~~~LL~~FF~~Ys-~wdW~~pV~L~~i~~g~lg~~~W~p~~~~~dr~~~MpI 312 (698)
+++.|+..||.||+ .|+|++-++-...... +... |. ......+.|
T Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~f~~yy~~~Fdf~~~~I~~r~~~~-l~~~-~~-----~~~~~~l~i 395 (596)
T KOG2277|consen 323 KPVVKKKVLCSFLRVFQRNPSNSQNTGSLGELLLGFFSYYASLFDFRKNAISIRRGRA-LKRA-KK-----IKSKKFLCI 395 (596)
T ss_pred ccchhhhhhhccccccccccccccccchHHHHHHHHHHHHhhhcccccceeeeeeccc-cccc-ch-----hhhccceee
Confidence 25689999999999 7999987554332111 1100 11 112356999
Q ss_pred eCCCCCCCCccCccCHhHHHHHHHHHHHHHHHHHHh
Q 005394 313 ITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEV 348 (698)
Q Consensus 313 iTP~~P~~Nsa~nVs~sTlrvI~~EF~Ra~~Il~~i 348 (698)
.+|+....|.+..++...+..|+.+|+....++...
T Consensus 396 ~dp~~~~~n~~~~~~~~~~~~i~~~~~~~~~~~~~~ 431 (596)
T KOG2277|consen 396 EDPFEVSHNADAGVTLKVLLLIQDEFQESRRVFKDV 431 (596)
T ss_pred ccccccccCccccchHHHHHHHHHHHHHHHHHhhhh
Confidence 999999999999999999999999999999998875
No 10
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=99.62 E-value=1.1e-12 Score=143.82 Aligned_cols=343 Identities=20% Similarity=0.245 Sum_probs=209.7
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCC-CCCeeEEeecC
Q 005394 39 EKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGP-GADIDALCVGP 117 (698)
Q Consensus 39 ~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p-~SDID~l~v~P 117 (698)
.+.|+ .+-||+||.++-+.+.++|...+++++++. ...++++.|||++=|.|++ +||||++++.|
T Consensus 3 ~~vl~--~i~Ps~eE~~~~~~~~~~l~~~l~~~~~e~------------~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~ 68 (408)
T TIGR03671 3 EEVLE--RIKPTEEEREKLKKVADELIARLEEIIEEL------------GVDAEVVLVGSYARGTWLKGDRDIDIFILFP 68 (408)
T ss_pred HHHhh--hcCCCHHHHHHHHHHHHHHHHHHHHHHHhc------------CCcceEEEEeeEecCCccCCCCceeEEEEeC
Confidence 34444 377999999999999999999988876532 1247999999999999999 99999999999
Q ss_pred CccCchhhHH---HHHHHHHHhc-cCCceEEEeccCccceEEEEecCeeeeEEeeecccccccccccccccc-ccCCCCc
Q 005394 118 SYVSREEDFF---FILHNILAEM-EEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDMS-VLNDVDE 192 (698)
Q Consensus 118 ~~v~re~~Ff---~~l~~~L~~~-~~V~el~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~~vp~~l~i~~d~-~L~~lDe 192 (698)
....++ ++= ..+...+.+. +... ..-|--|-++..+.|+++||.=|- ++.+.+ +...+|-
T Consensus 69 ~~~~~e-~l~~~gl~i~~~~~~~~~~~~----~~yaeHpYv~~~~~G~~VDiVPcy----------~v~~g~~~~taVDR 133 (408)
T TIGR03671 69 KDTSRE-ELEEYGLEIGHEVLKRGGNYE----ERYAEHPYVSGEIEGFEVDVVPCY----------KVESGEEIISAVDR 133 (408)
T ss_pred CCCCHH-HHHHHHHHHHHHHHhhCCCHh----heeccCceEEEEEccEEEEEEeeE----------EccCcCeeeccccC
Confidence 887764 332 1222222221 1111 357778999999999999998442 222221 1222221
Q ss_pred ccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCC--ccCccchHHHHHHHHHHHhhCCCCChHHHHHHHH
Q 005394 193 PTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSN--VTGFLGGVNWALLVARVCQLYPNAVPSMLVSRFF 270 (698)
Q Consensus 193 ~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn--~~G~LGG~swaLLVa~vcQlyPnas~~~LL~~FF 270 (698)
. ..-+++++.-.. +.|+..+|++|.|+|.-|+|++ +.++++||.+-||++++ -+-..++..+
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 1 122466665543 3488999999999999999955 57889999999999995 2223333222
Q ss_pred HHhhcCCCCCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHHHHHHHHHHHHHHhhh
Q 005394 271 RVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVEL 350 (698)
Q Consensus 271 ~~Ys~wdW~~pV~L~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~sTlrvI~~EF~Ra~~Il~~i~~ 350 (698)
+ +|..++.+.....+ .. .-.+++.|+||.+|..|+|.++|..++..+...-+++. .+
T Consensus 198 ---~--~wk~~~~id~~~~~--------~~----~f~~PlvViDPvDp~RNVAaalS~~~~~~fv~aar~fl---~~--- 254 (408)
T TIGR03671 198 ---S--KWKPGVVIDIEEHG--------TK----KFDDPLVVIDPVDPKRNVAAALSLENLARFILAARMFL---KN--- 254 (408)
T ss_pred ---H--hcCCCeEEecCccc--------cc----cCCCCEEEeCCCCCcchHHHHcCHHHHHHHHHHHHHHH---HC---
Confidence 3 34556666322111 11 11468999999999999999999988877765443332 22
Q ss_pred cCcccccccccc-----ch---hhh-cccEEEEEEEeCChhhhhhhhhhhHhhHHHHHHHhhhcccCceeeccCCCCCCC
Q 005394 351 NKAQWSALFEPY-----LF---FES-YRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYVD 421 (698)
Q Consensus 351 ~~~~W~~Lf~p~-----~F---f~~-Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~~ 421 (698)
+=..+|.|. ++ +.+ -.+.+.|..-.++.-+= ..-|-++--.+.|...||+.....+....|- +
T Consensus 255 ---Ps~~fF~p~~~~~~~~~~~l~~r~t~~~~~~f~~p~~v~D-il~pQl~r~~~~i~~~L~~~gF~v~r~~~~~----~ 326 (408)
T TIGR03671 255 ---PSLEFFFPPEIEPEEFLERLERRGTTLLAIVFRTPDVVDD-ILYPQLERSGRSLVKLLEREGFEVLRYGVWA----D 326 (408)
T ss_pred ---CCHHHcCCCCCChHHHHHHHhhcCcEEEEEEeCCCCCCcc-chhHHHHHHHHHHHHHHHHCCCEEEEeeeec----C
Confidence 112344332 11 122 22344444444442222 3446666667777777887655444444442 2
Q ss_pred CCCCCceeEEEEeeeeCCCC--ccCCCceecchHHHHHHHHH
Q 005394 422 TSKPCAHCAFFMGLQRKPGE--VVQEGQQFDIRGSVEEFKLS 461 (698)
Q Consensus 422 ~~~~~~~~~ffIGL~~~~~~--~~~~~~~~dl~~~v~eF~~~ 461 (698)
. -.|..++=|....-. ....|.++.-+.-...|.+.
T Consensus 327 ~----~~~~l~~el~~~~lp~~~~h~GPpv~~~~~a~~F~~k 364 (408)
T TIGR03671 327 E----NTCYLLLELESAELPRVKLHVGPPVWVRDHAEKFIEK 364 (408)
T ss_pred C----CeEEEEEEeeccccCCceeeeCCCccchhHHHHHHHH
Confidence 1 124445555432211 11234445555667788864
No 11
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=99.60 E-value=1e-12 Score=146.01 Aligned_cols=346 Identities=20% Similarity=0.241 Sum_probs=207.3
Q ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCC-CCCeeEEeec
Q 005394 38 LEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGP-GADIDALCVG 116 (698)
Q Consensus 38 L~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p-~SDID~l~v~ 116 (698)
+.+.|+. +.||++|.++-.++.+.|...+++++++ .+ ..++++.+|||+-|.|++ +||||++++.
T Consensus 3 ~~evl~~--i~Ps~eE~~~l~~~~~~l~~~L~~~~~~----~~--------~~~~V~l~GS~ArgT~L~GdsDIDIFv~f 68 (447)
T PRK13300 3 LEEVLER--IKPTEEEREKLKKVAEELIERLEEAIKE----LG--------LDAEVELVGSTARGTWLSGDRDIDIFVLF 68 (447)
T ss_pred HHHHHHh--cCCCHHHHHHHHHHHHHHHHHHHHHHHh----cC--------CceEEEEEeeecCCcccCCCCceeEEEEe
Confidence 3444543 7799999999999999998888887643 22 138999999999999999 7899999999
Q ss_pred CCccCchhhH----HHHHHHHHHhccCCceEEEeccCccceEEEEecCeeeeEEeeeccccccccccccccc-cccCCCC
Q 005394 117 PSYVSREEDF----FFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDM-SVLNDVD 191 (698)
Q Consensus 117 P~~v~re~~F----f~~l~~~L~~~~~V~el~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~~vp~~l~i~~d-~~L~~lD 191 (698)
|....++ ++ ......+++..-.-.+++ -|--|-++..+.|+++||.=|- ++.+. .+...+|
T Consensus 69 p~~~~~e-~L~~~gl~i~~~~~~~~~~~~~~~---yaeHpyv~~~~~G~~VDiVPcy----------~v~~~~~~~saVD 134 (447)
T PRK13300 69 PKDTSRE-ELEEKGLEIGKEVAKELLGDYEER---YAEHPYVTGEIDGFEVDIVPCY----------KVESGEEIISAVD 134 (447)
T ss_pred CCCCCHH-HHHHHHHHHHHHHHHhhCCcceee---eccCceEEEEECCEEEEEEeeE----------EccCcCccccccc
Confidence 9887764 22 122223333311112333 4888999999999999998552 22222 1222222
Q ss_pred cccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCC--ccCccchHHHHHHHHHHHhhCCCCChHHHHHHH
Q 005394 192 EPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSN--VTGFLGGVNWALLVARVCQLYPNAVPSMLVSRF 269 (698)
Q Consensus 192 e~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn--~~G~LGG~swaLLVa~vcQlyPnas~~~LL~~F 269 (698)
-. ..=+++|+.-.- +.++..+|++|.|+|.-|+|++ +.++++||..-||++++ -+-..+|..+
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-------PFHTKYVKERLK--GKLEDEVRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHY------GSFENVLKAA 199 (447)
T ss_pred Cc-------hHHHHHHHHhhh--hhHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHh------CCHHHHHHHH
Confidence 11 122567765543 3488999999999999999955 57899999999999995 2333333332
Q ss_pred HHHhhcCCCCCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHHHHHHHHHHHHHHhh
Q 005394 270 FRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVE 349 (698)
Q Consensus 270 F~~Ys~wdW~~pV~L~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~sTlrvI~~EF~Ra~~Il~~i~ 349 (698)
++| .-++.+.....+ .. .....++.|+||.+|..|+|.++|..++..+...- ..-+.+
T Consensus 200 ----~~w--~~~~~I~~~~~~--------~~---~~f~~PlvViDPvDp~RNVAaa~S~~~~~~fv~aa---r~fL~~-- 257 (447)
T PRK13300 200 ----SKW--KPPVKIDLEKHG--------KE---YKFDDPLVVIDPVDPNRNVAAALSLENLATFILAA---REFLKN-- 257 (447)
T ss_pred ----HhC--CCCceEeccccC--------cc---ccCCCCEEEeCCCCCcchHHHHcCHHHHHHHHHHH---HHHHhC--
Confidence 334 434554321111 00 01246899999999999999999988877665322 222332
Q ss_pred hcCccccccccccc-----h---hh-hcccEEEEEEEeCChhhhhhhhhhhHhhHHHHHHHhhhcccCceeeccCCCCCC
Q 005394 350 LNKAQWSALFEPYL-----F---FE-SYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYV 420 (698)
Q Consensus 350 ~~~~~W~~Lf~p~~-----F---f~-~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~ 420 (698)
+=..+|.|.+ + +. +=.+.+.|..-.++.-+= ..-|-++--.+.|...||+.....+....| .
T Consensus 258 ----Ps~~fF~~~~~~~~~~~~~l~~R~t~~~~v~f~~p~~v~D-il~pQl~r~~~~i~~~L~~~gF~v~~~~~~----~ 328 (447)
T PRK13300 258 ----PSLEFFFPSDLSPEEILEELERRGTTVLALEFPRPDIVED-ILYPQLERSLRSIVKLLEREGFEVLRSGAW----A 328 (447)
T ss_pred ----CCHHhcCCCCCChHHHHHHHhhcCceEEEEEeCCCCCCcc-chhHHHHHHHHHHHHHHHHCCCEEEEeeee----c
Confidence 1223333333 1 11 122455555544442222 334666666777777788765444433222 2
Q ss_pred CCCCCCceeEEEEeeeeCC--CCccCCCceecchHHHHHHHHH
Q 005394 421 DTSKPCAHCAFFMGLQRKP--GEVVQEGQQFDIRGSVEEFKLS 461 (698)
Q Consensus 421 ~~~~~~~~~~ffIGL~~~~--~~~~~~~~~~dl~~~v~eF~~~ 461 (698)
+ . -.|..++=|.... .-....|.++.-..-...|.+.
T Consensus 329 d-~---~~~~l~~el~~~~lp~~~~h~GPpv~~~~~a~~F~~k 367 (447)
T PRK13300 329 D-E---DRAYLLLELEVAELPNVKLHIGPPVWVREHAENFIEK 367 (447)
T ss_pred C-C---CeEEEEEEeecccCCCeeeeeCCCcCchhhHHHHHHH
Confidence 2 1 1344444444221 1111223345444447788763
No 12
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=99.22 E-value=7.9e-09 Score=113.29 Aligned_cols=345 Identities=19% Similarity=0.202 Sum_probs=204.0
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCC-CCCeeEEe
Q 005394 36 RELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGP-GADIDALC 114 (698)
Q Consensus 36 ~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p-~SDID~l~ 114 (698)
..|.+.|+. +.||+||.++=+.+.+.|...+++.+ .+.|+ .+.+..+||++=|.|++ +.|||+.|
T Consensus 5 ~~l~evl~~--i~P~~eE~~~~~~~~e~l~~~~~~~~----~e~~~--------~aev~lVGS~AkgTwL~gd~DIDvFi 70 (443)
T COG1746 5 EVLEEVLKR--IKPTEEERKKLKEVAEELRERINEII----EELGI--------DAEVVLVGSYAKGTWLRGDHDIDVFI 70 (443)
T ss_pred HHHHHHHHH--cCCCHHHHHHHHHHHHHHHHHHHHHH----HhcCC--------cceEEEEeecccCcccCCCcceeEEE
Confidence 345566654 67999999988888888877777654 34443 58899999999999999 67999999
Q ss_pred ecCCccCchhhH----HHHHHHHHHhccCCceEEEeccCccceEEEEecCeeeeEEeeecccccccccccccccc-ccCC
Q 005394 115 VGPSYVSREEDF----FFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDMS-VLND 189 (698)
Q Consensus 115 v~P~~v~re~~F----f~~l~~~L~~~~~V~el~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~~vp~~l~i~~d~-~L~~ 189 (698)
..|....++ .. +......|.+. --.+.-|-=|-+.-.++|+++|+.=|-. +.+.. +...
T Consensus 71 ~Fp~d~~~e-el~~~GL~ig~~~l~~~-----~~~~~YAeHPYV~g~v~G~eVDvVPCy~----------v~~~~~~~sA 134 (443)
T COG1746 71 AFPKDTSEE-ELEEKGLEIGREVLKRG-----NYEERYAEHPYVTGEVDGYEVDVVPCYK----------VEDGEKIISA 134 (443)
T ss_pred ECCCCCCHH-HHHHHHHHHHHHHhcCC-----chhhhhccCCeeEEEEccEEEEEEeccc----------ccCccccccc
Confidence 999987764 22 12223333320 1124577779999999999999986542 11111 2222
Q ss_pred CCcccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCc--cCccchHHHHHHHHHHHhhCCCCChHHHHH
Q 005394 190 VDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNV--TGFLGGVNWALLVARVCQLYPNAVPSMLVS 267 (698)
Q Consensus 190 lDe~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~--~G~LGG~swaLLVa~vcQlyPnas~~~LL~ 267 (698)
+| |+. -=+.++..-+-... +.=+|++|.+.|.=|+|++- .++++||.--||+++|=
T Consensus 135 VD----RTp---lHt~yv~e~L~~~~--~deVrLLK~FlK~iGvYGaE~rt~GFSGYL~ELLII~yG------------- 192 (443)
T COG1746 135 VD----RTP---LHTRYVEEHLKGRQ--KDEVRLLKQFLKGIGVYGAELRTQGFSGYLCELLIIHYG------------- 192 (443)
T ss_pred cc----Ccc---hhHHHHHHHhcccc--hhHHHHHHHHHhccCccceeeeeccchHHHHHHHHhhhc-------------
Confidence 22 111 11345554443221 13478999999999999975 78999999999999872
Q ss_pred HHHHHhhcC-CCCCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHHHHHHHHHHHHH
Q 005394 268 RFFRVYTMW-RWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICE 346 (698)
Q Consensus 268 ~FF~~Ys~w-dW~~pV~L~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~sTlrvI~~EF~Ra~~Il~ 346 (698)
.|-.+--.. +|.-+++|..- .|..... ...+|.|+||.+|..|+|.+||..++..++ -|.+..-
T Consensus 193 sFe~vl~~a~~wrp~~~ID~~--------~~~~e~f---~d~PliVvDPVDP~RNVAAalSl~~la~f~----~aar~FL 257 (443)
T COG1746 193 SFENVLKAASRWRPGKIIDLE--------GHKRERF---EDEPLIVVDPVDPKRNVAAALSLENLARFV----HAAREFL 257 (443)
T ss_pred cHHHHHHHHhccCCCeEEecc--------chhhhcc---CCCCeEecCCCCCccchhhhcCHHHHHHHH----HHHHHHh
Confidence 233333322 38877776541 2211221 123899999999999999999988766554 2322221
Q ss_pred HhhhcCcccccccccc---c-----hhhhcccEEEEEEEeCChhhhhhhhhhhHhhHHHHHHHhhhcccCceeeccCCCC
Q 005394 347 EVELNKAQWSALFEPY---L-----FFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHE 418 (698)
Q Consensus 347 ~i~~~~~~W~~Lf~p~---~-----Ff~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~ 418 (698)
+ .+=...|.|. . ...+=.+-+.|.+-.++.-+ ...-|-++---+.|...||......+..+.|
T Consensus 258 ~-----~PS~efF~p~~~~~~~~~~~~~rgt~v~~l~~~~pd~vd-DilypQl~r~~~~l~r~Le~~gF~vl~~~~~--- 328 (443)
T COG1746 258 K-----NPSPEFFFPRKPKPLLLSKLRRRGTHVLALVFPKPDLVD-DILYPQLERTARSLFRALEEEGFRVLRSGVW--- 328 (443)
T ss_pred c-----CCChhhcCCCCcCcccccchhhcCceEEEEEeCCCCCCc-chhhHHHHHHHHHHHHHHHHcCCEEeeeeee---
Confidence 1 1222233221 1 11122233334333444322 2344777777788888888765544444433
Q ss_pred CCCCCCCCceeEEEEeeeeCCCC--ccCCCceecchHHHHHHHHH
Q 005394 419 YVDTSKPCAHCAFFMGLQRKPGE--VVQEGQQFDIRGSVEEFKLS 461 (698)
Q Consensus 419 f~~~~~~~~~~~ffIGL~~~~~~--~~~~~~~~dl~~~v~eF~~~ 461 (698)
.|... +|.-|+=+....-. ....+.++.-+.+++ |.+.
T Consensus 329 -~D~~~---~~~v~~E~~~~~l~~i~~r~GPp~~~e~a~r-F~~k 368 (443)
T COG1746 329 -SDESE---RIYVLLELESKELPRIELRVGPPVWTEHAVR-FIEK 368 (443)
T ss_pred -ecCCc---ceEEEEEEecccccceeeecCCCccchhHHH-HHHh
Confidence 22221 34445555432211 011233344466666 7763
No 13
>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=99.19 E-value=5.7e-09 Score=126.42 Aligned_cols=341 Identities=15% Similarity=0.222 Sum_probs=206.9
Q ss_pred eecccCcC---CCCCeeEEeecCCccCchhhH------------HHHHHHHH--HhccCCceEEEe---ccCccceEEEE
Q 005394 98 SYRLGVHG---PGADIDALCVGPSYVSREEDF------------FFILHNIL--AEMEEVTELQPV---LDAHVPVMKFK 157 (698)
Q Consensus 98 Sy~lGv~~---p~SDID~l~v~P~~v~re~~F------------f~~l~~~L--~~~~~V~el~~I---~~ArVPIIKf~ 157 (698)
||.++... ++-.||+.+.-|..+-.++|| ...++..| ++...+.++... .+.+-|||.+.
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 467999999999866555443 23456667 223333344332 57788999998
Q ss_pred ec-----C------eeeeEEeeeccccccccc-c-----------------------ccccccccCCCCcccccccchhh
Q 005394 158 FD-----G------LSIDLLYASISRLVVRED-L-----------------------DISDMSVLNDVDEPTVRSLNGCR 202 (698)
Q Consensus 158 ~~-----G------I~iDLsfa~l~~~~vp~~-l-----------------------~i~~d~~L~~lDe~svrSLNG~R 202 (698)
-. + +.|-|..+.... .+|.. + ...|..+|.++- -..
T Consensus 81 p~~~~~~~~~~~~~~~iRi~~~~~~~-~F~~~rl~P~rnnvR~~~~~~~~~~~~~pTP~YNssIL~D~~--------~~~ 151 (972)
T PF03813_consen 81 PKGKKDSDDFSKTKFRIRIIPSIPSD-TFPLSRLAPSRNNVRPSWFDEEDSSSLPPTPHYNSSILEDML--------MEE 151 (972)
T ss_pred ECCccccccccCCcEEEEEEecCCcc-cCCHHhcCCCCCccCcCcccccccCCCCCCCcchHHHHHHHh--------HHH
Confidence 42 2 445555443211 11110 0 011222222110 011
Q ss_pred hHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCc-cCccchHHHHHHHHHHHhh---------CCCCChHHHHHHHHHH
Q 005394 203 VADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNV-TGFLGGVNWALLVARVCQL---------YPNAVPSMLVSRFFRV 272 (698)
Q Consensus 203 vtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~-~G~LGG~swaLLVa~vcQl---------yPnas~~~LL~~FF~~ 272 (698)
-..++.+.....+.|+.+++++|.||++||+.+.. .|++||+-|+||+++.+|- .+..+.-+|+..+..+
T Consensus 152 ~l~~l~~~~~~~p~f~dA~iLlkvWl~QRg~~~~~~~~Gf~~f~~s~lla~Ll~~g~~~~~~~l~~~mSsyQlFr~~l~f 231 (972)
T PF03813_consen 152 HLKYLHEASKSSPAFRDACILLKVWLRQRGFGSGISQGGFGGFEWSMLLAYLLQGGGRNGKKKLSKSMSSYQLFRAVLQF 231 (972)
T ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHhcCCCCcccCCCCcchHHHHHHHHHHHcCCCccCCcccCCCCCHHHHHHHHHHH
Confidence 23344455566799999999999999999998765 5899999999999999976 3556788999999999
Q ss_pred hhcCCC-CCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHHHHHHHHHHHHHHhhhc
Q 005394 273 YTMWRW-PNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELN 351 (698)
Q Consensus 273 Ys~wdW-~~pV~L~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~sTlrvI~~EF~Ra~~Il~~i~~~ 351 (698)
.+..|| .+|+.++...+.......| .+.+....+||. -.+|.+++++.++++.++.|-+++.+++++..
T Consensus 232 LA~~d~~~~~l~~~~~~~~~~~~~~~-------~~~~~~vf~D~s-g~~Nl~~~ms~~s~~~L~~eA~~tl~lL~~~~-- 301 (972)
T PF03813_consen 232 LATTDLSKKPLFFKSSSDSTESLEEF-------HSAFDPVFVDPS-GGLNLLAKMSPSSYEELQHEAKLTLELLDDSS-- 301 (972)
T ss_pred HhccccccCceEEecCCCccchhhhh-------hccCCeEEEeCC-CCEEEEEcCCHHHHHHHHHHHHHHHHHhcccc--
Confidence 999999 6689887644211111111 123456666664 56899999999999999999999999998632
Q ss_pred Ccccccccc-c-cchhhhcccEEEEE---EEe----CChhhhhhhhhhhHhhHHHHHH-HhhhcccCceeeccC---CCC
Q 005394 352 KAQWSALFE-P-YLFFESYRNYLQVD---IVA----ANADDLLAWKGWVESRLRQLTL-MIERDTYGKLQCHPY---PHE 418 (698)
Q Consensus 352 ~~~W~~Lf~-p-~~Ff~~Yk~yl~I~---v~a----~~~e~~~~w~GwVESRlR~Lv~-~LE~~~~~~l~ahp~---P~~ 418 (698)
......+|- + ..+..+|.+++.|. ... ....+...|...+..++-.|+. .|..... .++++ +.+
T Consensus 302 ~d~F~~lFl~~~~~~~~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lL~raLgdR~~---~i~v~~~~~~~ 378 (972)
T PF03813_consen 302 DDGFDSLFLTKVDPPALRFDHVLRISPDSLLSSFSPDESLDFLSFSNYLLRKIYRLLKRALGDRAK---LIRVLRPSQPP 378 (972)
T ss_pred ccchhhhhcccCCcccccCCEEEEEcchhhcccccccccccccchhHHHHHHHHHHHHHHHHHHHH---eEEEeCCCCCC
Confidence 346777774 4 46678999999991 111 1123333444456667766664 3543221 12333 122
Q ss_pred CCCCCC--CCceeEEEEeeeeCCCCc---cCCCceecchHHHHHHHH
Q 005394 419 YVDTSK--PCAHCAFFMGLQRKPGEV---VQEGQQFDIRGSVEEFKL 460 (698)
Q Consensus 419 f~~~~~--~~~~~~ffIGL~~~~~~~---~~~~~~~dl~~~v~eF~~ 460 (698)
+.-... ........|||..+.... ..-|-..|-.....+|++
T Consensus 379 w~i~~~~~~~~~~~l~vGl~ln~~~~~r~vd~GP~a~d~~ea~~FR~ 425 (972)
T PF03813_consen 379 WSISSKPPKSKPKTLTVGLILNPENAFRLVDRGPSAEDKEEAAAFRE 425 (972)
T ss_pred cccCCCCCCCCCceEEEEEEEchhhceeeeeeCcCCcCcHHHHHHHH
Confidence 211111 111226789998875211 111112233456677876
No 14
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=98.32 E-value=1.5e-05 Score=94.74 Aligned_cols=291 Identities=17% Similarity=0.204 Sum_probs=171.7
Q ss_pred eEEE-EeeeecccCc-CCCCCeeEEeecCCccCchhhH------------HHHHHHHHHhccCCceEEEe---ccCccce
Q 005394 91 ALIF-TFGSYRLGVH-GPGADIDALCVGPSYVSREEDF------------FFILHNILAEMEEVTELQPV---LDAHVPV 153 (698)
Q Consensus 91 ~~I~-~FGSy~lGv~-~p~SDID~l~v~P~~v~re~~F------------f~~l~~~L~~~~~V~el~~I---~~ArVPI 153 (698)
+++. ..||+.+|.. .|+.-+|+++..|+..-...|+ +..+...|.+.+....+... -+-.-||
T Consensus 148 ~~v~~vv~sal~~~~~~P~i~vDvll~mP~e~~~~kd~ln~Ryf~kra~yla~~~~hl~e~l~~~~~~f~~~n~d~~~pi 227 (1121)
T KOG2054|consen 148 AQVTKVVGSALLGTCLRPDISVDVLLTMPREILQQKDGLNQRYFRKRALYLAYLAHHLLEDLLFGSLEFSYTNGDHLKPI 227 (1121)
T ss_pred cccceeeeecccCcccCCcchhhhhhhhhHHhhcCcccccccccchHHHHHHHHHHHHHhccccceeeecccCCccccch
Confidence 4555 5566666544 6889999999998754332232 33344444444433333332 2345588
Q ss_pred EEEEecCeeeeEEeeecccccccccccc-ccccccCCCC----------cccccccchh--------hhHHHHHHhCCCh
Q 005394 154 MKFKFDGLSIDLLYASISRLVVREDLDI-SDMSVLNDVD----------EPTVRSLNGC--------RVADQILKLVPNV 214 (698)
Q Consensus 154 IKf~~~GI~iDLsfa~l~~~~vp~~l~i-~~d~~L~~lD----------e~svrSLNG~--------Rvtd~Il~lVP~~ 214 (698)
+.+.-.|-..|++-.+.+..-+|-.+.+ .++.+|-+.- +..---.|-. -..+++.+....-
T Consensus 228 l~i~~~~~~~~~~~~~~~~~li~~~~~~f~~~kllp~~~~ir~~~e~~e~ppTP~yN~svL~~~~le~~~q~L~K~~s~~ 307 (1121)
T KOG2054|consen 228 LLIRPRGKDERLVTVRPPDFLIPCRLLPFKNNKLLPWYNGIRPAGEGSEEPPTPRYNTSVLEDQVLEEYLQLLSKTLSSA 307 (1121)
T ss_pred hhccccCCccccccccCccccccccccccccccccchhcccCccccCCCCCCCCccchhHHHHHHHHHHHHHHHHHHhhh
Confidence 8888766555554333221112211111 1111111000 0000001110 1122334445566
Q ss_pred hhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHHHHh---hCCCCChHHHHHHHHHHhhcCCCCC-ceeecccccc
Q 005394 215 EHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQ---LYPNAVPSMLVSRFFRVYTMWRWPN-PVMLCAIDEA 290 (698)
Q Consensus 215 ~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~vcQ---lyPnas~~~LL~~FF~~Ys~wdW~~-pV~L~~i~~g 290 (698)
+.|+.++.+.|.|+++|.. +-..|++||+-|++++++... ++.+.+..+++..-|++.+.|||.. -+-+++-. .
T Consensus 308 ~~f~da~~Llk~WlrqRs~-~~~~~gfg~f~~s~lvv~L~s~~ki~~~~S~yqvfR~vl~flat~dlt~~~~~l~~~~-~ 385 (1121)
T KOG2054|consen 308 KGFKDALALLKVWLRQRSL-DIGQGGFGGFLLSALVVYLVSTRKIHTTLSAYQVFRSVLQFLATTDLTVNGISLVPSS-P 385 (1121)
T ss_pred hhHHHHHHHHHHHHHhhhh-hcccCcchHHHHHHHHHHHHhcCchhhcchHHHHHHHHHHHHhhhhhhccceEeccCC-C
Confidence 8999999999999999922 224689999999999998774 4567788999999999999999986 45554411 0
Q ss_pred cCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHHHHHHHHHHHHHHhhhcCccccccc-cccchhhhcc
Q 005394 291 ELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALF-EPYLFFESYR 369 (698)
Q Consensus 291 ~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~sTlrvI~~EF~Ra~~Il~~i~~~~~~W~~Lf-~p~~Ff~~Yk 369 (698)
.+ |....-+..+....++ ..-..|...|++.++++.+++|.+-+..++.+.. ...++.+| ++.+.|..|.
T Consensus 386 s~------~~~~~f~e~~~~~f~D-~s~~~NLc~~mt~s~y~~~q~ea~ltl~lL~~~~--~~~F~~IFmtkip~~~~yD 456 (1121)
T KOG2054|consen 386 SL------PALADFHEGQLVTFID-SSGHLNLCANMTASTYEQVQEEARLTLMLLDSRA--DDGFSLIFMTKIPVFRAYD 456 (1121)
T ss_pred Cc------hhhhhhhhcceeeEec-cCCcchhhhhccHHHHHHHHHHHHHHHHHHhhhh--hcCcceeeeecCCchhhhh
Confidence 00 0000000113333333 2346799999999999999999999999999765 35678777 7889999999
Q ss_pred cEEEEEEEeCChhhhhhhhhhhH
Q 005394 370 NYLQVDIVAANADDLLAWKGWVE 392 (698)
Q Consensus 370 ~yl~I~v~a~~~e~~~~w~GwVE 392 (698)
|-+.+.--..-+.....-.||.|
T Consensus 457 h~l~l~~~~~l~~~~~~~~~~~~ 479 (1121)
T KOG2054|consen 457 HVLHLSPLSRLQAAEHLLSGFCE 479 (1121)
T ss_pred eeeeccccchhhhHHhhcccchh
Confidence 98887654333333334444433
No 15
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=98.19 E-value=7.9e-05 Score=77.72 Aligned_cols=213 Identities=16% Similarity=0.147 Sum_probs=146.7
Q ss_pred EEEeeeecccCcCCCC-CeeEEeecCCccCchhhHHHHH----HHHHHhccCCceEEEeccCccceEEEEec----Ceee
Q 005394 93 IFTFGSYRLGVHGPGA-DIDALCVGPSYVSREEDFFFIL----HNILAEMEEVTELQPVLDAHVPVMKFKFD----GLSI 163 (698)
Q Consensus 93 I~~FGSy~lGv~~p~S-DID~l~v~P~~v~re~~Ff~~l----~~~L~~~~~V~el~~I~~ArVPIIKf~~~----GI~i 163 (698)
|.-.||+.-|+.+.|. +.|+++++....+.+ ....+ .+-|+...+=.....|..+.+|.++..+. -...
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 VMRVGSFAKGTLLKGDNVAELVLLCKEKPTSE--LVARLARKLPEQLKAVTEDEALIIVTSTKEPTMEVGILITSPLARV 82 (246)
T ss_pred eEEeeeeccCceecCCCceeEEEEecCCCcHH--HHHHHHHHHHHHHhhcCcccceeeeeccCCCceeEEEEEecccccc
Confidence 5678999999999876 789999998777753 44443 44444322111223456777788887762 2223
Q ss_pred eEEeeeccccccccccccccccccCCCC-cccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccc
Q 005394 164 DLLYASISRLVVREDLDISDMSVLNDVD-EPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLG 242 (698)
Q Consensus 164 DLsfa~l~~~~vp~~l~i~~d~~L~~lD-e~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LG 242 (698)
+...+ ..|+++.-.+ .-.-+| ..|+.+|-.+|-+.+..+.......|+.++|++|-|.++.-... -|.
T Consensus 83 ~~~~~-----~~~~~~~~~~--p~~~ld~~~cl~aLAalRhakWFq~~a~~l~s~~iviRilKd~~~R~~~~~----pL~ 151 (246)
T smart00572 83 ELLIT-----TVPENLRKLD--PEDHLDRKKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQ----PLS 151 (246)
T ss_pred ccccc-----ccCcccccCC--ccccCCHHHHHHHHHHHHHhHHHHHhccCCcchhhHHHHHHHHHHhccccc----ccc
Confidence 33322 2333332111 112234 35888899999999999988888899999999999999876544 389
Q ss_pred hHHHHHHHHHHHhhCC-CCChHHHHHHHHHHhhc-CCCCCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCC-C
Q 005394 243 GVNWALLVARVCQLYP-NAVPSMLVSRFFRVYTM-WRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYP-C 319 (698)
Q Consensus 243 G~swaLLVa~vcQlyP-nas~~~LL~~FF~~Ys~-wdW~~pV~L~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P-~ 319 (698)
++.+-|++++.+-... ..+++.-+.+||++.++ .=+|.. --|+||+.+ .
T Consensus 152 ~w~iELl~~~~i~~~~~~l~~~~a~RR~fe~lAsG~l~p~~----------------------------~gI~DPce~~~ 203 (246)
T smart00572 152 GWPLELLVEKAIGSARQPLGLGDAFRRVFECLASGILLPGS----------------------------PGLTDPCEKDN 203 (246)
T ss_pred cccHHHHHHHHhccCCCCCCHHHHHHHHHHHHHhccCcCCC----------------------------CCCcCCCCCCc
Confidence 9999999999885332 23689999999999985 212210 137788886 7
Q ss_pred CCccCccCHhHHHHHHHHHHHHHHHHH
Q 005394 320 MNSSYNVSTSTLRVMMDQFQYGNTICE 346 (698)
Q Consensus 320 ~Nsa~nVs~sTlrvI~~EF~Ra~~Il~ 346 (698)
.|++...|......|...-+.+.+++.
T Consensus 204 ~nv~~~lT~qqrd~It~sAQ~alRl~A 230 (246)
T smart00572 204 TDALTALTLQQREDVTASAQTALRLLA 230 (246)
T ss_pred ccHHHhcCHHHHHHHHHHHHHHHHHHH
Confidence 888888888888888888887777764
No 16
>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=97.80 E-value=0.00021 Score=67.45 Aligned_cols=77 Identities=29% Similarity=0.324 Sum_probs=56.1
Q ss_pred CeEEEEeeeecccCcCC-CCCeeEEeecCCccC----chhhHHHHHHHHHHhccCCceEEEeccCccceEEEEec--Cee
Q 005394 90 NALIFTFGSYRLGVHGP-GADIDALCVGPSYVS----REEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFD--GLS 162 (698)
Q Consensus 90 ~~~I~~FGSy~lGv~~p-~SDID~l~v~P~~v~----re~~Ff~~l~~~L~~~~~V~el~~I~~ArVPIIKf~~~--GI~ 162 (698)
...++.||||+.|...+ .||||++++.+.... ...+++..+.+.|.+...- -..+ ...-|.|.+.+. |++
T Consensus 27 ~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~~~~~~~~~~~~l~~~L~~~~~~--~~~~-~~~~~~v~v~~~~~~~~ 103 (143)
T cd05400 27 VAEVFLQGSYARGTALRGDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEYYGA--NEEV-KAQHRSVTVKFKGQGFH 103 (143)
T ss_pred ccEEEEEcceeCCCCCCCCCceeEEEEEcCcccccccCHHHHHHHHHHHHHHhcCc--cccc-ccCceEEEEEEcCCCeE
Confidence 47899999999999987 899999999876543 1235667777777764321 1112 455578888886 899
Q ss_pred eeEEeee
Q 005394 163 IDLLYAS 169 (698)
Q Consensus 163 iDLsfa~ 169 (698)
|||+-+.
T Consensus 104 vDvvP~~ 110 (143)
T cd05400 104 VDVVPAF 110 (143)
T ss_pred EEEEEEe
Confidence 9997665
No 17
>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=97.57 E-value=4.1e-05 Score=62.39 Aligned_cols=56 Identities=20% Similarity=0.322 Sum_probs=36.5
Q ss_pred ChHHHHHHHHHHhh-cCCCCCceeecccccccC--CcccccCCCCCCCCCCceEEeCCCCCC
Q 005394 261 VPSMLVSRFFRVYT-MWRWPNPVMLCAIDEAEL--GFSVWDPRKNRRDKTHHMPIITPAYPC 319 (698)
Q Consensus 261 s~~~LL~~FF~~Ys-~wdW~~pV~L~~i~~g~l--g~~~W~p~~~~~dr~~~MpIiTP~~P~ 319 (698)
++++||..||+||+ .|||.+-|+.... .+.+ ....|.. ....+...|+|++|+.|.
T Consensus 1 slg~Ll~~Ff~~Y~~~Fd~~~~~Isi~~-g~~~~k~~~~~~~--~~~~~~~~l~IeDP~~~~ 59 (60)
T PF03828_consen 1 SLGELLLGFFEYYGRKFDYENNVISIRN-GGYFPKEEKNWSK--SRNQRKKRLCIEDPFDPS 59 (60)
T ss_dssp -HHHHHHHHHHHHHHTS-TTTEEEESSS-SSEEEHHHHTGCH--CCCCECSSSEBBESSSTT
T ss_pred CHHHHHHHHHHHhCCcCCCCceEEEecC-CceEEhhhccccc--cccCCCCeEEEECCCCCC
Confidence 47899999999999 8999997665432 1111 1234441 112245789999999885
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=97.54 E-value=0.00013 Score=58.15 Aligned_cols=26 Identities=35% Similarity=0.532 Sum_probs=24.4
Q ss_pred CeEEEEeeeecccCcCCCCCeeEEee
Q 005394 90 NALIFTFGSYRLGVHGPGADIDALCV 115 (698)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v 115 (698)
..+++.||||+.|.+.+.||||++|+
T Consensus 17 ~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 17 GYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred CcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 57899999999999999999999887
No 19
>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=97.47 E-value=0.00038 Score=64.87 Aligned_cols=93 Identities=24% Similarity=0.335 Sum_probs=60.1
Q ss_pred HHHHHHHHHHhCCCCCc--cCccchHHHHHHHHHHHhhCCCCChHHHHHHHHHHhhcCCCCCceeecccccccCCccccc
Q 005394 221 LRCLKFWAKRRGVYSNV--TGFLGGVNWALLVARVCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWD 298 (698)
Q Consensus 221 lr~IK~WAK~RGIysn~--~G~LGG~swaLLVa~vcQlyPnas~~~LL~~FF~~Ys~wdW~~pV~L~~i~~g~lg~~~W~ 298 (698)
+|++|.++|.-|+|++- .++++||..-|||++|=- +....+.-+ +|..|+.|..-..+... +
T Consensus 3 VrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~yGs----------F~~~l~~a~--~W~~~~~Id~~~~~~~~-~--- 66 (114)
T PF09249_consen 3 VRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHYGS----------FENVLEAAA--KWKPPVVIDLEDHGEPS-K--- 66 (114)
T ss_dssp HHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHHHSS----------HHHHHHHHT--T--TTEEEETT-TTE---E---
T ss_pred hHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHHHCC----------HHHHHHHHH--hcCCCeEEccCccchhh-h---
Confidence 58999999999999875 789999999999998731 233333334 77778887653211100 1
Q ss_pred CCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHH
Q 005394 299 PRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMM 335 (698)
Q Consensus 299 p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~sTlrvI~ 335 (698)
.-..++.|+||.+|.+|+|.+||..++..+.
T Consensus 67 ------~f~~PlvviDPvDp~RNVAAalS~~~~~~fv 97 (114)
T PF09249_consen 67 ------KFDDPLVVIDPVDPNRNVAAALSLENLAEFV 97 (114)
T ss_dssp ------EE-SS-EEEETTEEEEETTTTS-HHHHHHHH
T ss_pred ------hcCCCeEEcCCCCCCchHhHhcCHHHHHHHH
Confidence 1136899999999999999999988766554
No 20
>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=97.38 E-value=0.00023 Score=61.76 Aligned_cols=32 Identities=34% Similarity=0.464 Sum_probs=29.5
Q ss_pred CeEEEEeeeecccCcCCCCCeeEEeecCCccC
Q 005394 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVS 121 (698)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~ 121 (698)
...|+.||||+.|.+.|+||||++++.+....
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 58999999999999999999999999988764
No 21
>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=97.31 E-value=0.0021 Score=78.84 Aligned_cols=156 Identities=23% Similarity=0.359 Sum_probs=108.6
Q ss_pred hhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHHHH-hhCC---CCChHHHHHHHHHHhhc
Q 005394 200 GCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVC-QLYP---NAVPSMLVSRFFRVYTM 275 (698)
Q Consensus 200 G~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~vc-QlyP---nas~~~LL~~FF~~Ys~ 275 (698)
..+-+..|..+.-.++.|.+++|++|.|...+-+ .|++.--.+=||||++. +-+| ..++..=+.+|.++-++
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 3444566666666788999999999999999977 46788889999999977 3344 34566667788888899
Q ss_pred CCCCC-ceeeccccccc--------CCcccccCCCCCCCCCCceEEeCCCCCCCCccC---ccCHhHHHHHHHHHHHHHH
Q 005394 276 WRWPN-PVMLCAIDEAE--------LGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSY---NVSTSTLRVMMDQFQYGNT 343 (698)
Q Consensus 276 wdW~~-pV~L~~i~~g~--------lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~---nVs~sTlrvI~~EF~Ra~~ 343 (698)
|||.+ |+++...++-. ..|..|.. ..+......|.|.||.+|.-. .. .-+..-+++|+.--+.+.+
T Consensus 744 ~dW~~~PLiVd~~~~l~~~~~~~i~~~f~~~R~-~dp~~~~p~~~IaT~~D~~g~-~wT~~~Ps~~v~~Rl~~LAk~sl~ 821 (972)
T PF03813_consen 744 WDWREEPLIVDFNNELTEEDRAEIETNFDAWRK-IDPAMNLPAMFIATPYDPEGS-LWTRNGPSKVVAKRLTALAKASLK 821 (972)
T ss_pred CCCCcCCEEEECCCCCCHHHHHHHHHHHHHhhc-cCccccCCcEEEEeCCCCCCC-EeECCCCCHHHHHHHHHHHHHHHH
Confidence 99995 88775432110 12334432 344445678999999998532 23 3444557777777677788
Q ss_pred HHHHhhhcCccccccccc
Q 005394 344 ICEEVELNKAQWSALFEP 361 (698)
Q Consensus 344 Il~~i~~~~~~W~~Lf~p 361 (698)
+++.-..+..+|..||.|
T Consensus 822 ~l~~~~~~~~~~~~lF~~ 839 (972)
T PF03813_consen 822 LLEEQGLSDLDWKSLFRP 839 (972)
T ss_pred HHHhcCCCCCCHHHhcCC
Confidence 887433346799999976
No 22
>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=96.93 E-value=0.0012 Score=56.69 Aligned_cols=32 Identities=31% Similarity=0.492 Sum_probs=28.7
Q ss_pred CeEEEEeeeecccCcCCCCCeeEEeecCCccC
Q 005394 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVS 121 (698)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~ 121 (698)
-..++.|||++.|-+.++||||++++++....
T Consensus 18 i~~i~LfGS~arg~~~~~SDiDl~vi~~~~~~ 49 (93)
T cd05403 18 VEKVYLFGSYARGDARPDSDIDLLVIFDDPLD 49 (93)
T ss_pred ccEEEEEeeeecCCCCCCCCeeEEEEeCCCCC
Confidence 37899999999999999999999999987654
No 23
>PF14091 DUF4269: Domain of unknown function (DUF4269)
Probab=96.13 E-value=0.054 Score=53.22 Aligned_cols=117 Identities=23% Similarity=0.376 Sum_probs=74.5
Q ss_pred EEEeeeecccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceE-EEeccCccceEEEEecCeeeeEEeeecc
Q 005394 93 IFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTEL-QPVLDAHVPVMKFKFDGLSIDLLYASIS 171 (698)
Q Consensus 93 I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~~Ff~~l~~~L~~~~~V~el-~~I~~ArVPIIKf~~~GI~iDLsfa~l~ 171 (698)
-...|.+.+|+..++||||++|.++.. ..|-..+.+...+.++.+-- ..|..-..=+..|.+.|..|-|---..
T Consensus 18 PiL~GTiPi~Idi~~SDLDIic~~~d~----~~F~~~l~~~f~~~~~f~~~~~~i~~~~~~~~~F~~~~~~~EiF~Q~~- 92 (152)
T PF14091_consen 18 PILVGTIPIGIDIPGSDLDIICEVPDP----EAFEQLLQSLFGQFEGFTIKEKTIRGEPSIVANFRYEGFPFEIFGQPI- 92 (152)
T ss_pred CEEecccccccCCCCCCccEEEEeCCH----HHHHHHHHHHhccCCCceeeeceeCCceeEEEEEEECCceEEEeecCC-
Confidence 456799999999999999999999753 13433444444444443221 233444555677888899888753222
Q ss_pred ccccccccccccccccCCCCcccccccchhhhHHHHHHhCCCh-hhHHHHHHHHH--------HHHHHhCCCCC
Q 005394 172 RLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNV-EHFCTTLRCLK--------FWAKRRGVYSN 236 (698)
Q Consensus 172 ~~~vp~~l~i~~d~~L~~lDe~svrSLNG~Rvtd~Il~lVP~~-~~FR~llr~IK--------~WAK~RGIysn 236 (698)
.+..-||+|=-..-.+++-.. +.||.-+|-+| +||+--||-++
T Consensus 93 ----------------------Pv~~QnayrHm~iE~rLL~~~g~~~r~~Ii~LK~~GlKTEPAFa~lLgL~GD 144 (152)
T PF14091_consen 93 ----------------------PVEEQNAYRHMLIEHRLLELHGPSFREEIIELKESGLKTEPAFAKLLGLEGD 144 (152)
T ss_pred ----------------------ChhhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHcCCcchHHHHHHhCCCCC
Confidence 234568888543333444444 78999998888 46666666554
No 24
>PF07528 DZF: DZF domain; InterPro: IPR006561 This domain is found in proteins containing the double-stranded RNA-binding motif, DSRM (IPR001159 from INTERPRO), or the zinc finger domain C2H2 (IPR007087 from INTERPRO). This domain is found exclusively in the metazoa.
Probab=95.28 E-value=0.67 Score=48.99 Aligned_cols=208 Identities=13% Similarity=0.162 Sum_probs=131.8
Q ss_pred eeeecccCcCCCC-CeeEEeecCCccCchhhHHHHHHHHHH----hc-cCCceEEEe------ccCccceEEEEe--c--
Q 005394 96 FGSYRLGVHGPGA-DIDALCVGPSYVSREEDFFFILHNILA----EM-EEVTELQPV------LDAHVPVMKFKF--D-- 159 (698)
Q Consensus 96 FGSy~lGv~~p~S-DID~l~v~P~~v~re~~Ff~~l~~~L~----~~-~~V~el~~I------~~ArVPIIKf~~--~-- 159 (698)
.||+.-|+.+.|. ++|+++++..-.+. +.+..+.+.|. .. +. +-...+ ...+.|.+...+ .
T Consensus 2 VG~~aKGllL~Gd~~~eLVVlck~kPT~--~lL~~v~~~L~~~L~~~~~~-ev~~~~e~~~~~~~~~~~~~~~~~~lts~ 78 (248)
T PF07528_consen 2 VGSFAKGLLLKGDNDVELVVLCKEKPTK--ELLNRVAEKLPEQLKKVTPE-EVTNSVEAAIIIDSCKEPKLEVGIDLTSP 78 (248)
T ss_pred cceecCCceecCCceEeEEEEcCCCCcH--HHHHHHHHHHHHHHhhhCcc-ccccchhhhhhhcccccccceeeEEecCC
Confidence 5999999999877 89999999887775 46655554443 32 22 111122 222335555543 2
Q ss_pred CeeeeEEeeeccccccccccccccccccCCCCc-ccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCcc
Q 005394 160 GLSIDLLYASISRLVVREDLDISDMSVLNDVDE-PTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVT 238 (698)
Q Consensus 160 GI~iDLsfa~l~~~~vp~~l~i~~d~~L~~lDe-~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~ 238 (698)
.+.+.+.... .+++..- .+.-..||. .|..+|-.+|-|.++.+........+.++|++|-...+--- +
T Consensus 79 ~~r~~~~~~~-----~~~~~~~--~dp~~~Ld~~~cl~aLaalRhakWFq~~a~~l~s~~~viRIlrDl~~R~p~----w 147 (248)
T PF07528_consen 79 VMRVRVLITT-----IPENLSK--LDPEDHLDRKKCLSALAALRHAKWFQARANGLQSCVIVIRILRDLRQRVPT----W 147 (248)
T ss_pred ceEEEEeccc-----cCccccc--cChhhcCCHHHHHHHHHHHHHhHHHHHHhccCCCcceehhhHHHHHHhCCC----C
Confidence 2333333222 2222211 112223454 58888888999999998888888889999999999877533 5
Q ss_pred CccchHHHHHHHHHHHhhCCC---CChHHHHHHHHHHhhc-CCCCCceeecccccccCCcccccCCCCCCCCCCceEEeC
Q 005394 239 GFLGGVNWALLVARVCQLYPN---AVPSMLVSRFFRVYTM-WRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIIT 314 (698)
Q Consensus 239 G~LGG~swaLLVa~vcQlyPn---as~~~LL~~FF~~Ys~-wdW~~pV~L~~i~~g~lg~~~W~p~~~~~dr~~~MpIiT 314 (698)
+-|+++.+-+|+-+..---|+ .++++-+.+||+..|. +=.|.-. -|.|
T Consensus 148 ~~L~~W~leLL~~~~i~~~~~~~~l~~g~a~RRvle~lasGillp~~~----------------------------gl~D 199 (248)
T PF07528_consen 148 QPLSSWALELLVEKAISNNSSRQPLSPGDAFRRVLECLASGILLPGSP----------------------------GLRD 199 (248)
T ss_pred CCCChhHHHHHHHHHeeeCCCCCCCChHHHHHHHHHHHhCceecCCCC----------------------------CCcC
Confidence 668888888887776653332 4689999999999884 3222100 1335
Q ss_pred CCC-CCCCccCccCHhHHHHHHHHHHHHHHHH
Q 005394 315 PAY-PCMNSSYNVSTSTLRVMMDQFQYGNTIC 345 (698)
Q Consensus 315 P~~-P~~Nsa~nVs~sTlrvI~~EF~Ra~~Il 345 (698)
|+. ...+...+.|......|..--|.+.+++
T Consensus 200 PcE~~~~~~~~~lt~qq~e~it~sAQ~~LRll 231 (248)
T PF07528_consen 200 PCEKDPVDVLDTLTLQQREDITSSAQTALRLL 231 (248)
T ss_pred CCCCCCceeeccCCHHHHHHHHHHHHHHHHHH
Confidence 555 4566777778777777777666666555
No 25
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=95.20 E-value=0.087 Score=48.23 Aligned_cols=29 Identities=34% Similarity=0.438 Sum_probs=25.4
Q ss_pred eEEEEeeeecccCcCCCCCeeEEeecCCc
Q 005394 91 ALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (698)
Q Consensus 91 ~~I~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (698)
..+-.||||+=|=..|+||||+++-....
T Consensus 25 ~~~~vFGS~aRgE~~~~SDIDILVef~~~ 53 (97)
T COG1669 25 KRVAVFGSYARGEQKPDSDIDILVEFEPG 53 (97)
T ss_pred ceEEEeeeeecCCCCCCCCceeEEeecCC
Confidence 67999999999999999999999866443
No 26
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=94.61 E-value=0.18 Score=45.47 Aligned_cols=29 Identities=41% Similarity=0.614 Sum_probs=26.5
Q ss_pred CeEEEEeeeecccCcCCCCCeeEEeecCC
Q 005394 90 NALIFTFGSYRLGVHGPGADIDALCVGPS 118 (698)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v~P~ 118 (698)
...++.|||++-|=+.+.||||++++++.
T Consensus 26 ~~~v~LfGS~arG~~~~~SDiDv~vv~~~ 54 (128)
T COG1708 26 DLLIYLFGSYARGDFVKESDIDLLVVSDD 54 (128)
T ss_pred CeEEEEEccCcccccccCCCeeEEEEcCC
Confidence 58999999999999999999999999833
No 27
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=94.23 E-value=0.089 Score=55.91 Aligned_cols=32 Identities=28% Similarity=0.265 Sum_probs=28.3
Q ss_pred eEEEEeeeecccCcCCCCCeeEEeecCCccCc
Q 005394 91 ALIFTFGSYRLGVHGPGADIDALCVGPSYVSR 122 (698)
Q Consensus 91 ~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~r 122 (698)
.-|+.|||+..|-..|.||||++++.....+.
T Consensus 29 ~~vyLfGS~~~G~~~p~SDIDllvvv~~~l~~ 60 (262)
T PRK13746 29 LAIHLYGSAVDGGLKPHSDIDLLVTVAVPLDE 60 (262)
T ss_pred EEEEEECCcccCCCCCCCceeEEEEeCCCCCH
Confidence 46899999999999999999999999877653
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=94.15 E-value=0.079 Score=53.80 Aligned_cols=48 Identities=13% Similarity=0.037 Sum_probs=33.5
Q ss_pred hhhHHHHHHHHHHHHHHhCCCCCc-cCccchHHHHHHHHHHHhhCCCCC
Q 005394 214 VEHFCTTLRCLKFWAKRRGVYSNV-TGFLGGVNWALLVARVCQLYPNAV 261 (698)
Q Consensus 214 ~~~FR~llr~IK~WAK~RGIysn~-~G~LGG~swaLLVa~vcQlyPnas 261 (698)
....+.|+|+||+|-+...-.... -+.+.+|++-||+++.-..-.+..
T Consensus 41 P~klK~LIrLVKhWy~~~~~~~~~~~~lPpsYaLELLtIyAWE~g~~~~ 89 (190)
T PF10421_consen 41 PTKLKNLIRLVKHWYQQCKKKKCGGGSLPPSYALELLTIYAWEQGCGAE 89 (190)
T ss_dssp -HHHHHHHHHHHHHHHHHHCC--HTT-S--HHHHHHHHHHHHHHHT-SS
T ss_pred CHHHHHHHHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHhcCCCc
Confidence 368889999999999987655333 345679999999999987655443
No 29
>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=92.95 E-value=1.3 Score=47.89 Aligned_cols=113 Identities=24% Similarity=0.251 Sum_probs=71.1
Q ss_pred CCeEEEEeeeecccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEe------cCee
Q 005394 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKF------DGLS 162 (698)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~~Ff~~l~~~L~~~~~V~el~~I~~ArVPIIKf~~------~GI~ 162 (698)
...++.+-||||=|-.+ .+|||+|+..+.... ..++..+...|.+.+.+..+. ..-..-....+ .|+.
T Consensus 159 ~~~~v~i~GS~RRg~et-~gDiDilv~~~~~~~--~~~~~~v~~~l~~~~~~~~~~---~~g~~k~~~~~~~~~~~~~~r 232 (307)
T cd00141 159 PVLQVEIAGSYRRGKET-VGDIDILVTHPDATS--RGLLEKVVDALVELGFVTEVL---SKGDTKASGILKLPGGWKGRR 232 (307)
T ss_pred CceEEEEcccccCCCCc-cCCEEEEEecCCccc--cccHHHHHHHHHhCCCeehhh---hCCCceEEEEEecCCCCCceE
Confidence 46899999999998776 579999988876544 256777888888877664321 11111112222 2899
Q ss_pred eeEEeeeccccccccccccccccccCCCCcccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCcc
Q 005394 163 IDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFL 241 (698)
Q Consensus 163 iDLsfa~l~~~~vp~~l~i~~d~~L~~lDe~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~L 241 (698)
|||.++.... . .-.++-+-.+. . -.|-++.||++||..=+.+|..
T Consensus 233 VDl~~~p~~~------~------------------------~~all~fTGs~-~---~nr~lR~~A~~~G~~L~~~GL~ 277 (307)
T cd00141 233 VDLRVVPPEE------F------------------------GAALLYFTGSK-Q---FNRALRRLAKEKGLKLNEYGLF 277 (307)
T ss_pred EEEEEeCHHH------H------------------------HHHHHHhhCCH-H---HHHHHHHHHHHcCCeeeccccc
Confidence 9999876321 0 11222222222 2 2466699999999877766664
No 30
>PRK02098 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=91.62 E-value=0.35 Score=50.31 Aligned_cols=33 Identities=24% Similarity=0.274 Sum_probs=27.9
Q ss_pred CeEEEEeeeec----ccC--cCCCCCeeEEeecCCccCc
Q 005394 90 NALIFTFGSYR----LGV--HGPGADIDALCVGPSYVSR 122 (698)
Q Consensus 90 ~~~I~~FGSy~----lGv--~~p~SDID~l~v~P~~v~r 122 (698)
+..+.+|||+. +|+ -.++||||+++-.|.....
T Consensus 120 g~~~gv~GS~a~qlaTG~~~l~~~SDLDLLi~~~~~~~~ 158 (221)
T PRK02098 120 GVDCRVFGSLAWQALTGLPYLSASSDLDLLWPLPAAAQI 158 (221)
T ss_pred CCcEEEeeehHHHHhhCCcccCCCCCeeEEEecCChhhH
Confidence 56899999999 999 7899999999988765443
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=90.88 E-value=0.42 Score=49.01 Aligned_cols=33 Identities=27% Similarity=0.272 Sum_probs=28.0
Q ss_pred CeEEEEeeee----cccC--cCCCCCeeEEeecCCccCc
Q 005394 90 NALIFTFGSY----RLGV--HGPGADIDALCVGPSYVSR 122 (698)
Q Consensus 90 ~~~I~~FGSy----~lGv--~~p~SDID~l~v~P~~v~r 122 (698)
+..+.+|||+ .+|+ -.++||||+++-.|.....
T Consensus 108 ~~~~gv~GS~~~qlaTg~~~~~~~SDLDLLi~~~~~~~~ 146 (202)
T TIGR03135 108 GVPWGVYGSAGWQLLTGLPYLHASSDLDLLLRAPSPLSL 146 (202)
T ss_pred CCcEEEecchHHHHhcCCcccCCCCCeeEEEcCCChhhH
Confidence 5789999999 8999 7899999999988865544
No 32
>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=89.48 E-value=1.6 Score=40.54 Aligned_cols=53 Identities=32% Similarity=0.330 Sum_probs=39.6
Q ss_pred CCeEEEEeeeecccCcCCCCCeeEEeecCCccCc---hhhHHHHHHHHHHhccCCce
Q 005394 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSR---EEDFFFILHNILAEMEEVTE 142 (698)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~r---e~~Ff~~l~~~L~~~~~V~e 142 (698)
++..+..-||||=|-...+ |||+++..|..... ...++..+.+.|.+..-++.
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 4699999999999988765 99999998876552 13688889999987554443
No 33
>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=86.69 E-value=3.4 Score=40.36 Aligned_cols=48 Identities=23% Similarity=0.275 Sum_probs=36.6
Q ss_pred CCeEEEEeeeecccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHh
Q 005394 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAE 136 (698)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~~Ff~~l~~~L~~ 136 (698)
...-++.+|||.-|=-.+.||||++++.+........+|..+.+.+.+
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 468999999999999999999999998865432123567666655554
No 34
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=83.93 E-value=0.2 Score=53.45 Aligned_cols=26 Identities=31% Similarity=0.395 Sum_probs=22.4
Q ss_pred EEeeeecccCcCCCCCeeEEeecCCc
Q 005394 94 FTFGSYRLGVHGPGADIDALCVGPSY 119 (698)
Q Consensus 94 ~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (698)
=.-||..+|++..+||||+++-|+.+
T Consensus 125 GVTGSiL~gl~~~nSDIDfVVYG~~~ 150 (315)
T COG1665 125 GVTGSILLGLYDENSDIDFVVYGQMW 150 (315)
T ss_pred cccccccccccCCCCCceEEEEcHHH
Confidence 34599999999999999999999543
No 35
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=83.41 E-value=5.5 Score=49.29 Aligned_cols=122 Identities=18% Similarity=0.269 Sum_probs=72.9
Q ss_pred hhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHHHHhh-C---CCCChHHHHHHHHHHhhcCC
Q 005394 202 RVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQL-Y---PNAVPSMLVSRFFRVYTMWR 277 (698)
Q Consensus 202 Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~vcQl-y---Pnas~~~LL~~FF~~Ys~wd 277 (698)
|.+-.|-.+...++.|-.++|+-|.|...+=+-+ |.+ ==++-||||...+. + |..++-.=+.+|..+-|+||
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 LHTLALQSLSQSHPFYSSVVRLAKRWLGSHLLSG---HHL-DEAIELLVAALFLKPGPLVPPSSPENGFLRFLSLLSTWD 881 (1121)
T ss_pred HHHHHHHHHhhcccchhHHHHHHHHHHHHHhhcc---chH-HHHHHHHHHHHhcCccCCCCCCCcchhHHHHHHHHhcCc
Confidence 4445555555567889999999999988775443 222 45567888876643 3 34566666888899999999
Q ss_pred CCC-ceeecccccccCCc----ccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhH
Q 005394 278 WPN-PVMLCAIDEAELGF----SVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTST 330 (698)
Q Consensus 278 W~~-pV~L~~i~~g~lg~----~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~sT 330 (698)
|.. |.+++- .++ +.. ..-+.-...|.....|.|+||-+- .++.+.=+..+
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 666643 211 000 000000112223458999999654 34444444444
No 36
>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=81.24 E-value=12 Score=35.96 Aligned_cols=49 Identities=20% Similarity=0.148 Sum_probs=37.5
Q ss_pred cCCeEEEEeeeecccCcCCCCCeeEEeecCCccCch-hhHHHHHHHHHHh
Q 005394 88 DANALIFTFGSYRLGVHGPGADIDALCVGPSYVSRE-EDFFFILHNILAE 136 (698)
Q Consensus 88 ~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re-~~Ff~~l~~~L~~ 136 (698)
....-++.+||+.=+=.++.||+|..+|.......+ ..+|..|.+.+..
T Consensus 47 p~~~a~lalGS~GR~E~~~~sDqD~alv~~d~~~~~~~~~f~~~a~~~~~ 96 (138)
T PF03445_consen 47 PVPFAWLALGSYGRREQTLYSDQDNALVFEDEESEEDRAYFEAFAERLVD 96 (138)
T ss_pred CCCEEEEEECcccccCCCcCccccceeeecCccchhHHHHHHHHHHHHHH
Confidence 357899999999999999999999999887722221 3677766665553
No 37
>KOG3793 consensus Transcription factor NFAT, subunit NF45 [Transcription]
Probab=78.70 E-value=36 Score=36.84 Aligned_cols=212 Identities=17% Similarity=0.199 Sum_probs=109.6
Q ss_pred HHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCCCCe
Q 005394 31 DMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADI 110 (698)
Q Consensus 31 d~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDI 110 (698)
|-..+++|.+- +.++.|+.+|...=...+.+++.++.+.+ ..|+- .-.-..|--.|||..|..+-++|.
T Consensus 38 D~~f~~alLkR--nqdL~P~~~~q~~I~~~vtKV~~vLdn~~-----~~~L~----~~~ieevrqVGSF~k~T~~tg~~~ 106 (362)
T KOG3793|consen 38 DTSFSEALLKR--NQDLAPNSAEQASILSLVTKVNNVLDNLV-----APGLF----EVQIEEVRQVGSFKKGTMTTGHNV 106 (362)
T ss_pred chHHHHHHHhh--hccCCCCHHHHHHHHHHHHHHHHHHHhhc-----cCCce----EeehhhhhhccceeccccccCCcc
Confidence 66677666553 35799999988776666666666665542 12222 111256778999999999988876
Q ss_pred -eEEeecCCccCch--hhHHHHHHHHHHhc-c-CCceEEEeccCccceEEEEe----cCeeeeEEeeecccccccccccc
Q 005394 111 -DALCVGPSYVSRE--EDFFFILHNILAEM-E-EVTELQPVLDAHVPVMKFKF----DGLSIDLLYASISRLVVREDLDI 181 (698)
Q Consensus 111 -D~l~v~P~~v~re--~~Ff~~l~~~L~~~-~-~V~el~~I~~ArVPIIKf~~----~GI~iDLsfa~l~~~~vp~~l~i 181 (698)
|++++-.--.+.| ...-.++.+-|+.. + ++-. |=+.+--+ ..-.+-|+++. +|+++.
T Consensus 107 advVViLkTLPt~EaV~aLg~Kv~e~lka~d~~Evlt--------vl~~e~G~~I~s~~~~VRiLIt~-----iP~n~~- 172 (362)
T KOG3793|consen 107 ADLVVILKTLPTLEAVAALGNKVVESLRAQDPSEVLT--------VLTNETGFEISSSDATVRILITT-----VPPNLR- 172 (362)
T ss_pred cceEEEeecCCcHHHHHHHHHHHHHHhhhcChHHHHH--------HHhhccceeeecccceEEEEEee-----cCchhc-
Confidence 6666554333332 01112233333321 1 1111 11111111 12233344433 344332
Q ss_pred ccccccCCCCccc-ccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHH-HHHHHHhhC-C
Q 005394 182 SDMSVLNDVDEPT-VRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWAL-LVARVCQLY-P 258 (698)
Q Consensus 182 ~~d~~L~~lDe~s-vrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaL-LVa~vcQly-P 258 (698)
.-.++-.||-+- ...+-.+|-+.++-+. ......+.++|++|---.+ +.||--=-.|+| |++++|-+. |
T Consensus 173 -KLEP~lHLD~K~M~~~l~a~RH~~WFee~-A~~s~~~~lir~LKDlr~r------~~~F~PLs~W~ldll~h~avmNnp 244 (362)
T KOG3793|consen 173 -KLEPELHLDIKVMQSALAAIRHARWFEEN-ASQSTVKVLIRLLKDLRIR------FPGFEPLTPWILDLLGHYAVMNNP 244 (362)
T ss_pred -ccChhhhhhHHHHHHHHHHHhhhhhhhhh-hhHHHHHHHHHHHHHHHhh------cCCCCCchHHHHHHHHHHHHHcCC
Confidence 112223334321 1223334444333322 2234567788888865443 235533334665 778888653 4
Q ss_pred C---CChHHHHHHHHHHhhc
Q 005394 259 N---AVPSMLVSRFFRVYTM 275 (698)
Q Consensus 259 n---as~~~LL~~FF~~Ys~ 275 (698)
+ +.++.-..+||++.+.
T Consensus 245 ~RQ~l~ln~Afrr~~qilaA 264 (362)
T KOG3793|consen 245 TRQPLALNVAYRRCLQILAA 264 (362)
T ss_pred ccccchhhHHHHHHHHHHHh
Confidence 4 3577889999999985
No 38
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=73.50 E-value=12 Score=45.69 Aligned_cols=58 Identities=21% Similarity=0.354 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCCCCeeEEeecCCccCc
Q 005394 61 LGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSR 122 (698)
Q Consensus 61 L~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~r 122 (698)
++....++..|...+-...|+++ ..+.-|...|.|.=|--.|.||||++++.|.-.+.
T Consensus 41 ~~~~~~~~d~~L~~lw~~~g~~~----~~~~aLvAVGGyGRgEL~P~SDiDlL~L~p~~~~~ 98 (867)
T COG2844 41 IELRTDLVDQLLIRLWQEIGFAD----ASGLALVAVGGYGRGELHPLSDIDLLLLSPQKLTD 98 (867)
T ss_pred HHHHHHHHHHHHHHHHHHcCccc----ccceEEEEeccccccccCCCccceEEEecCCCCCh
Confidence 34445555666666666777764 35789999999999999999999999999987653
No 39
>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=70.50 E-value=7.2 Score=40.32 Aligned_cols=32 Identities=25% Similarity=0.298 Sum_probs=25.1
Q ss_pred CeEEEEeeeecc----cCc--CCCCCeeEEeecCCccC
Q 005394 90 NALIFTFGSYRL----GVH--GPGADIDALCVGPSYVS 121 (698)
Q Consensus 90 ~~~I~~FGSy~l----Gv~--~p~SDID~l~v~P~~v~ 121 (698)
+...-+|||+.. |+. .++||||+++-.+....
T Consensus 116 ~~~~gv~GS~g~qlaTGl~~l~~~SDLDLli~~~~~~~ 153 (213)
T PF10620_consen 116 GLRWGVYGSLGFQLATGLPYLHADSDLDLLIRPPSPSQ 153 (213)
T ss_pred CCCEEEehhHHHHHHhCccccCCCCCceEEEeCCChhH
Confidence 678999999854 433 58999999988887653
No 40
>PRK05007 PII uridylyl-transferase; Provisional
Probab=69.31 E-value=18 Score=44.90 Aligned_cols=57 Identities=19% Similarity=0.282 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCCCCeeEEeecCCc
Q 005394 59 QVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (698)
Q Consensus 59 ~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (698)
+++..+..++.++++.+-...+++. ..+.-|...|+|+=|=-.|.||||++++.+..
T Consensus 53 ~~~~~~s~~~D~~l~~l~~~~~~~~----~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~ 109 (884)
T PRK05007 53 QLVEARTEFIDQLLQRLWIEAGFDQ----IPDLALVAVGGYGRGELHPLSDIDLLILSRKK 109 (884)
T ss_pred HHHHHHHHHHHHHHHHHHHHccCCC----cCceEEEecCCCCCcccCCcccceEEEEeCCC
Confidence 3555666666666665554555432 24689999999999999999999999998743
No 41
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=68.41 E-value=67 Score=35.38 Aligned_cols=30 Identities=33% Similarity=0.548 Sum_probs=24.7
Q ss_pred CCeEEEEeeeecccCcCCCCCeeEEeecCCc
Q 005394 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (698)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (698)
....+.+-||||=|-.+ ..|||+|+..+..
T Consensus 163 ~~~~v~i~GSyRRgket-~gDIDili~~~~~ 192 (334)
T smart00483 163 PDAIVTLTGSFRRGKET-GHDVDFLITSPHP 192 (334)
T ss_pred CCcEEEEecccccCCCc-CCCeeEEEecCCc
Confidence 36789999999998766 5799999887764
No 42
>PRK08609 hypothetical protein; Provisional
Probab=67.79 E-value=25 Score=41.48 Aligned_cols=109 Identities=17% Similarity=0.174 Sum_probs=61.5
Q ss_pred CCeEEEEeeeecccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEe-cCeeeeEEe
Q 005394 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKF-DGLSIDLLY 167 (698)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~~Ff~~l~~~L~~~~~V~el~~I~~ArVPIIKf~~-~GI~iDLsf 167 (698)
...++..-||||=|--+ ..|||+|+..+... .+.+.|.+.+.+.++..-...+.-+ .+.. .|+.|||-+
T Consensus 174 ~~~~v~~~GS~RR~~et-~gDiDili~~~~~~--------~~~~~l~~~~~v~~~~~~g~~~~~~-~~~~~~~~~vDl~~ 243 (570)
T PRK08609 174 EIIRFSRAGSLRRARET-VKDLDFIIATDEPE--------AVREQLLQLPNIVEVIAAGDTKVSV-ELEYEYTISVDFRL 243 (570)
T ss_pred CccEEEeccchhccccc-cCCeeEEEecCCHH--------HHHHHHHcCccHHHHHhcCCceEEE-EEecCCCeEEEEEE
Confidence 35789999999998776 56999998775421 1223334444443321111111111 2332 499999998
Q ss_pred eeccccccccccccccccccCCCCcccccccchhhhHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCcc
Q 005394 168 ASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFL 241 (698)
Q Consensus 168 a~l~~~~vp~~l~i~~d~~L~~lDe~svrSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~L 241 (698)
+.... + .-.++-+-.. ..| .|-++.||+++|+.=|-+|..
T Consensus 244 v~~~~------~------------------------~~aL~yfTGS-~~h---n~~lr~~A~~~g~~l~e~gl~ 283 (570)
T PRK08609 244 VEPEA------F------------------------ATTLHHFTGS-KDH---NVRMRQLAKERGEKISEYGVE 283 (570)
T ss_pred eCHHH------H------------------------HHHHHHHhcc-HHH---HHHHHHHHHHcCCcccccccc
Confidence 76311 1 0112212222 222 355689999999988887774
No 43
>PF03281 Mab-21: Mab-21 protein
Probab=63.88 E-value=2e+02 Score=30.42 Aligned_cols=96 Identities=17% Similarity=0.177 Sum_probs=62.8
Q ss_pred hhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHHHHhhCCCC---ChHHHHHHHHHHhhcCCCCCceeecccccc
Q 005394 214 VEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPNA---VPSMLVSRFFRVYTMWRWPNPVMLCAIDEA 290 (698)
Q Consensus 214 ~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~vcQlyPna---s~~~LL~~FF~~Ys~wdW~~pV~L~~i~~g 290 (698)
....+.+++++|.-..... ...+.|++|++-.++.+.|..+|.. ....|-.+|.++.... ++-..++
T Consensus 190 ~~~~~~~l~llk~l~~~~~---~~~~~l~syhLkt~ll~~~~~~p~~~~W~~~~l~~~l~~~l~~L-------~~~L~~~ 259 (292)
T PF03281_consen 190 NGCRKKCLRLLKALRDRHL---TNLSGLSSYHLKTVLLWLCEKHPSSSDWSEENLGERLLDLLDFL-------IKCLQEG 259 (292)
T ss_pred cccHHHHHHHHHHHHHhcc---ccCCCccHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHHH-------HHHHhcC
Confidence 4567889999999977766 5678899999999999999999876 2334444444332211 1111111
Q ss_pred cCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHHHHHH
Q 005394 291 ELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQ 339 (698)
Q Consensus 291 ~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~sTlrvI~~EF~ 339 (698)
.+ + .-+.|.+|.=.+.+..++..+..++.
T Consensus 260 ~L----------p----------hff~~~~NLf~~~~~~~~~~~~~~~~ 288 (292)
T PF03281_consen 260 RL----------P----------HFFIPNLNLFQHLSPEELDELARKLE 288 (292)
T ss_pred CC----------C----------ccCCCCcccCCCCCHHHHHHHHHHHH
Confidence 11 0 12567888888888877777766554
No 44
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=62.03 E-value=29 Score=42.95 Aligned_cols=56 Identities=14% Similarity=0.199 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCCCCeeEEeecCCc
Q 005394 60 VLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (698)
Q Consensus 60 VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (698)
++.....++..+++.+-...+.+. ..+.-|...|+|+=|=-.|.||||++++.+..
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 666666677776665544333321 13588999999999999999999999998743
No 45
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=59.13 E-value=36 Score=37.62 Aligned_cols=49 Identities=31% Similarity=0.482 Sum_probs=38.3
Q ss_pred cCCeEEEEeeeecccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhc
Q 005394 88 DANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEM 137 (698)
Q Consensus 88 ~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~~Ff~~l~~~L~~~ 137 (698)
++++.+..-|||+=| ...+.|||+|+-.|..-+.+...+..+...|.+.
T Consensus 169 ~p~~~vt~~GsfRRG-k~~ggDvD~LithP~~~s~~~~~~~~l~~~le~~ 217 (353)
T KOG2534|consen 169 DPEAFVTVTGSFRRG-KKMGGDVDFLITHPGSTSTEAKLLQLLMILLEKK 217 (353)
T ss_pred CCCcEEEEeccccCC-cccCCCeeEEEeCCCCCchhhhHHHHHHHHHHhc
Confidence 457899999999998 4568899999988876553446777788888764
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=58.09 E-value=30 Score=36.39 Aligned_cols=62 Identities=21% Similarity=0.168 Sum_probs=34.7
Q ss_pred HHhhcCCCccc-cccCCeEEEEeeeecccCcCCCCCeeEEeecCCccCc------hhhHHHHHHHHHHh
Q 005394 75 LTRLRGYSDQM-VEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSR------EEDFFFILHNILAE 136 (698)
Q Consensus 75 v~~~~g~~~~~-~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~r------e~~Ff~~l~~~L~~ 136 (698)
+....|.+... ....+.-|.-.|-+.-+=-..+||||++++.+..-.. ...||..+.+.|.+
T Consensus 111 ~~~~~G~p~~~~~~~~~~~ViamGKlGg~ELny~SDiDLifvy~~~~~~~~~~~~~~~~~~rl~~~~~~ 179 (247)
T PF03710_consen 111 LAARYGRPPDEDGEPAGFAVIAMGKLGGRELNYSSDIDLIFVYDPDGETGRRSISNQEFFTRLAQRLIR 179 (247)
T ss_dssp HHHHCTSCCCCTTCC-SEEEEE-HHHHTT---TT--EEEEEEE---TT-SSS-SBHHHHHHHHHHHHHH
T ss_pred HHHHcCCCCcccCCcCCeEEEEeccccccccCCccCCceEEEeccccccccChhhHHHHHHHHHHHHHH
Confidence 44556665321 1123678888898888888999999999987643221 13689888777665
No 47
>PRK01293 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=57.26 E-value=19 Score=37.34 Aligned_cols=44 Identities=25% Similarity=0.246 Sum_probs=30.0
Q ss_pred CeEEEEeeeecc----cC--cCCCCCeeEEeecCCccCchhhHHHHHHHHHH
Q 005394 90 NALIFTFGSYRL----GV--HGPGADIDALCVGPSYVSREEDFFFILHNILA 135 (698)
Q Consensus 90 ~~~I~~FGSy~l----Gv--~~p~SDID~l~v~P~~v~re~~Ff~~l~~~L~ 135 (698)
+...-+|||... |+ -.++||||+++.+|..... +-+..+.+.|.
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 567789999764 33 3589999999999876654 33444444444
No 48
>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=57.17 E-value=9.5 Score=39.73 Aligned_cols=26 Identities=27% Similarity=0.256 Sum_probs=22.3
Q ss_pred eEEEEeeeecccCcCCCCCeeEEeec
Q 005394 91 ALIFTFGSYRLGVHGPGADIDALCVG 116 (698)
Q Consensus 91 ~~I~~FGSy~lGv~~p~SDID~l~v~ 116 (698)
.-...+||.+-|+.+|+||.|+-.|.
T Consensus 21 l~~~~sGS~a~G~~s~dSD~D~r~vy 46 (247)
T PF10127_consen 21 LYACESGSRAYGFASPDSDYDVRGVY 46 (247)
T ss_pred EEEecccccccCCCCCCcCcccchhc
Confidence 45667899999999999999997655
No 49
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=57.13 E-value=33 Score=34.59 Aligned_cols=80 Identities=21% Similarity=0.192 Sum_probs=45.7
Q ss_pred CeEEEEeeeecc----cCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhcc-CCceEEEeccCccceEEEEecCeeee
Q 005394 90 NALIFTFGSYRL----GVHGPGADIDALCVGPSYVSREEDFFFILHNILAEME-EVTELQPVLDAHVPVMKFKFDGLSID 164 (698)
Q Consensus 90 ~~~I~~FGSy~l----Gv~~p~SDID~l~v~P~~v~re~~Ff~~l~~~L~~~~-~V~el~~I~~ArVPIIKf~~~GI~iD 164 (698)
+.+.+..|++++ |.--...|||+.+..+.... +.++|..+..... .+ +-+.+ ...-.++++...++.||
T Consensus 16 gv~~~ivGG~av~l~~g~~r~T~DIDlfi~~~~~~~-~~~~~~~~a~~~g-~~~~~~~~----~~~~~~~~~~~~~v~ID 89 (181)
T PF09970_consen 16 GVEYVIVGGAAVNLAYGRRRTTKDIDLFIENPSPNL-EADALREVAEENG-WDLGWTDF----GTPRYVVKVGGEDVRID 89 (181)
T ss_pred CCeEEEECHHHHHHHhCCCCCCCCeEEEeCCCchHH-HHHHHHHHHHHcC-CCcCcccc----CCCceEEEeCCCCeEEE
Confidence 557899999864 55567899999876664432 2244444332111 11 11111 22334566666899999
Q ss_pred EEeeeccccccc
Q 005394 165 LLYASISRLVVR 176 (698)
Q Consensus 165 Lsfa~l~~~~vp 176 (698)
| +.++....+|
T Consensus 90 l-~~ni~~~~v~ 100 (181)
T PF09970_consen 90 L-LENIGDFYVP 100 (181)
T ss_pred c-hhccCCcccC
Confidence 9 5555544444
No 50
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=56.56 E-value=34 Score=41.49 Aligned_cols=51 Identities=16% Similarity=0.159 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCCCCeeEEeecCCc
Q 005394 55 EKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (698)
Q Consensus 55 ~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (698)
+.|+++.+.-..+++.. +++ .+.-|...|+|+=|=-.|.||||++++.+..
T Consensus 6 ~~~~~~~~~~~~~~~~~--------~~~------~~~aLvAvGGYGR~EL~P~SDIDLLiL~~~~ 56 (693)
T PRK00227 6 QLREDAEASALALLGSL--------QLP------PGTALAATGSLARREMTPYSDLDLILLHPPG 56 (693)
T ss_pred HHHHHHHHHHHHHHHhc--------CCC------CCeEEEEeccccccCcCCCcCceEEEEeCCc
Confidence 45666666666666643 333 2678999999999999999999999998743
No 51
>PRK03059 PII uridylyl-transferase; Provisional
Probab=51.49 E-value=48 Score=41.14 Aligned_cols=54 Identities=24% Similarity=0.369 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCCCCeeEEeecCC
Q 005394 59 QVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPS 118 (698)
Q Consensus 59 ~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~ 118 (698)
+++..+..++..+++..-...+.+ .+.-|...|+|+=|--.|.||||++++.+.
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 366666777777766543333322 357899999999999999999999999863
No 52
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=49.06 E-value=63 Score=40.29 Aligned_cols=56 Identities=21% Similarity=0.264 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCCCCeeEEeecCCc
Q 005394 60 VLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (698)
Q Consensus 60 VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (698)
++..+..++.+.++.+-.....+ ...+.-|...|.|+=|--.|.||||++++.+..
T Consensus 52 ~~~~~s~~~d~~l~~~~~~~~~~----~~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~ 107 (895)
T PRK00275 52 LIEDRAWFVDQILQQAWHQFDWS----DDADIALVAVGGYGRGELHPYSDIDLLILLDSA 107 (895)
T ss_pred HHHHHHHHHHHHHHHHHHHhccC----CCCCEEEEEcCCccccCcCCCCCceEEEEecCC
Confidence 44444555554444433332222 223589999999999999999999999998754
No 53
>PRK04374 PII uridylyl-transferase; Provisional
Probab=47.53 E-value=65 Score=40.12 Aligned_cols=54 Identities=19% Similarity=0.263 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCCCCeeEEeecCC
Q 005394 60 VLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPS 118 (698)
Q Consensus 60 VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~ 118 (698)
++..+..++..+++.+-.... + ...+.-|...|+|+=|=-.|.||||++++.+.
T Consensus 47 ~~~~~s~~~D~~l~~~~~~~~-~----~~~~~alvAvGgYGR~EL~p~SDIDLliL~~~ 100 (869)
T PRK04374 47 LLALRARAVDQLMRNAWTRCI-P----ADSGLSLHAVGGYGRGELFPRSDVDLLVLGET 100 (869)
T ss_pred HHHHHHHHHHHHHHHHHHHhC-C----CcCCEEEEEcCCccccccCCcccceEEEEecC
Confidence 444545555555554433222 2 11358899999999999999999999999874
No 54
>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=45.96 E-value=26 Score=36.43 Aligned_cols=46 Identities=15% Similarity=0.194 Sum_probs=30.7
Q ss_pred eEEEEeeeecccCcCCCCCeeEEeecCCccCch-hhHHHHHHHHHHh
Q 005394 91 ALIFTFGSYRLGVHGPGADIDALCVGPSYVSRE-EDFFFILHNILAE 136 (698)
Q Consensus 91 ~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re-~~Ff~~l~~~L~~ 136 (698)
--||.-||..+=-.++.||+|+=++.....+.+ ...++.-++.|.+
T Consensus 98 ~GlY~MGS~gSi~Qs~~SDlDiWvCh~~~L~~~~~~~Lq~K~~~i~~ 144 (204)
T PF12633_consen 98 LGLYSMGSTGSIGQSSSSDLDIWVCHDSDLSPEERQLLQQKCDLIEQ 144 (204)
T ss_pred EEEEecCCCccccCCCCCCCeEEEEcCCCCCHHHHHHHHHHHHHHHH
Confidence 569999999999999999999955554444432 1233333444444
No 55
>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=45.50 E-value=71 Score=39.43 Aligned_cols=31 Identities=26% Similarity=0.389 Sum_probs=27.6
Q ss_pred CCeEEEEeeeecccCcCCCCCeeEEeecCCc
Q 005394 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (698)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (698)
.+.-|...|||+=|=-.|.||||++++.+..
T Consensus 42 ~~~aliA~GgyGR~El~p~SDiDll~l~~~~ 72 (850)
T TIGR01693 42 SGIALVAVGGYGRGELAPYSDIDLLFLHDGK 72 (850)
T ss_pred CCeEEEEeCCccccCcCCCCCCeEEEEeCCC
Confidence 4688999999999999999999999998643
No 56
>COG2413 Predicted nucleotidyltransferase [General function prediction only]
Probab=45.29 E-value=40 Score=35.16 Aligned_cols=28 Identities=29% Similarity=0.430 Sum_probs=23.1
Q ss_pred eEEEEeeeecccCcCCCCCeeEEeecCC
Q 005394 91 ALIFTFGSYRLGVHGPGADIDALCVGPS 118 (698)
Q Consensus 91 ~~I~~FGSy~lGv~~p~SDID~l~v~P~ 118 (698)
..-+.+||.+.|=--|+||+|+.+.-|.
T Consensus 38 ie~~v~gSvarGDV~p~SDvDV~I~~~v 65 (228)
T COG2413 38 IEAVVYGSVARGDVRPGSDVDVAIPEPV 65 (228)
T ss_pred chhEEEeeeeccCcCCCCCceEEEecCC
Confidence 3456789999998889999999887643
No 57
>PRK03381 PII uridylyl-transferase; Provisional
Probab=45.12 E-value=52 Score=40.36 Aligned_cols=29 Identities=14% Similarity=0.166 Sum_probs=26.9
Q ss_pred CCeEEEEeeeecccCcCCCCCeeEEeecC
Q 005394 89 ANALIFTFGSYRLGVHGPGADIDALCVGP 117 (698)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P 117 (698)
...-|...|+|+=|--.|.||||++++.+
T Consensus 56 ~~~alvAvg~~gr~el~p~SD~Dll~l~~ 84 (774)
T PRK03381 56 SGVALVAVGGLGRRELLPYSDLDLVLLHD 84 (774)
T ss_pred CCeEEEEeCCcCCcCcCCCCCCeEEEEeC
Confidence 35889999999999999999999999987
No 58
>PF03296 Pox_polyA_pol: Poxvirus poly(A) polymerase nucleotidyltransferase domain; InterPro: IPR024231 Poly(A) polymerase (2.7.7.19 from EC) catalyses template-independent extension of the 3'-end of a DNA or RNA strand by one nucleotide at a time. The Poxvirus enzyme creates the 3'(poly)A tail of mRNAs, and is a heterodimer of a catalytic and a regulatory subunit. This entry represents the nucleotidyltransferase domain of the catalytic subunit [].; PDB: 3ERC_C 3ER8_D 3OWG_A 2GA9_D 2GAF_D 3ER9_B.
Probab=43.04 E-value=35 Score=33.59 Aligned_cols=78 Identities=19% Similarity=0.397 Sum_probs=38.4
Q ss_pred HHHHHHHcCCCCCHHHHHHHHHH---HHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCC---CCee
Q 005394 38 LEKFLVEAGLYESKEEDEKREQV---LGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPG---ADID 111 (698)
Q Consensus 38 L~~~L~~~~l~pS~EE~~~R~~V---L~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~---SDID 111 (698)
..+.|..+++..-.++...|..| +..+..++++.+++ + +-....||||.+-+--|+ .|||
T Consensus 9 a~~~l~s~~v~~~~~~~~grh~vS~lV~~V~klmeEyLrr----h----------Nk~CicYGSyslhllN~~I~YgDID 74 (149)
T PF03296_consen 9 ASDYLNSYNVANPSGKVMGRHNVSDLVENVNKLMEEYLRR----H----------NKSCICYGSYSLHLLNPNIKYGDID 74 (149)
T ss_dssp HHHHHHHH--S-------------THHHHHHHHHHHHHHH---------------TTTEEEESHHHHHTTSTTS--SS-E
T ss_pred HHHHHHHhcccccCccccccccCcHHHHHHHHHHHHHHHh----h----------CCCeEEeeeeeEEecCCCcccCcch
Confidence 34566777777667777777765 45556666666654 2 344788999998777664 7999
Q ss_pred EEeecCCccCchhhHHHHHHHHHH
Q 005394 112 ALCVGPSYVSREEDFFFILHNILA 135 (698)
Q Consensus 112 ~l~v~P~~v~re~~Ff~~l~~~L~ 135 (698)
++=... ..|+-.|.-++.
T Consensus 75 ilqTNa------r~flI~laflI~ 92 (149)
T PF03296_consen 75 ILQTNA------RTFLINLAFLIK 92 (149)
T ss_dssp EEESTH------HHHHHHHHHHHH
T ss_pred hhhccc------HHHHHHHHHHHh
Confidence 863331 255544444444
No 59
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=37.95 E-value=79 Score=40.02 Aligned_cols=48 Identities=17% Similarity=0.144 Sum_probs=37.1
Q ss_pred CCeEEEEeeeecccCcCCCCCeeEEeecCCccC-c---hhhHHHHHHHHHHh
Q 005394 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVS-R---EEDFFFILHNILAE 136 (698)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~-r---e~~Ff~~l~~~L~~ 136 (698)
.+.-|..+|+|.=+=-.+.||||++++...... . ...||..+.+.+..
T Consensus 722 ~~~avia~Gk~Gr~EL~~~SDlDl~fl~~~~~~~~~~~~~~~~~rlaq~l~~ 773 (1007)
T PRK14109 722 ARIAVIGMGRLGGRELGYGSDADVMFVHEPAPGADEAEAVRWATAVAEELRR 773 (1007)
T ss_pred CCEEEEEeccccccccCCCCCCcEEEEeCCCCCCCchhHHHHHHHHHHHHHH
Confidence 468999999999999999999999999863211 1 12688888777765
No 60
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=36.14 E-value=1.3e+02 Score=38.27 Aligned_cols=48 Identities=13% Similarity=0.066 Sum_probs=36.6
Q ss_pred CCeEEEEeeeecccCcCCCCCeeEEeecCCccCch----hhHHHHHHHHHHh
Q 005394 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSRE----EDFFFILHNILAE 136 (698)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re----~~Ff~~l~~~L~~ 136 (698)
.+.-|..+|+|.-+=-.++||||++++.+...... ..||..+.+.|..
T Consensus 214 ~~~aviamGklG~~EL~~~SDiDLi~ly~~~~~~~~~~~~~~~~rl~q~l~~ 265 (1007)
T PRK14109 214 VRLAVIAMGKCGARELNYVSDVDVIFVAEPAEGVDEAAALAVATRLASELMR 265 (1007)
T ss_pred CCeEEEEeccccccccCCccCCCEEEEeCCCCCcccccHHHHHHHHHHHHHH
Confidence 46799999999999999999999999986432110 2577777777665
No 61
>COG3541 Predicted nucleotidyltransferase [General function prediction only]
Probab=36.00 E-value=17 Score=38.61 Aligned_cols=20 Identities=30% Similarity=0.350 Sum_probs=17.2
Q ss_pred EeeeecccCcCCCCCeeEEe
Q 005394 95 TFGSYRLGVHGPGADIDALC 114 (698)
Q Consensus 95 ~FGSy~lGv~~p~SDID~l~ 114 (698)
--||+.-|+..|+||+|+=-
T Consensus 15 esGS~~yGf~spdSDyDvR~ 34 (248)
T COG3541 15 ESGSHLYGFPSPDSDYDVRG 34 (248)
T ss_pred cccccccCCCCCCCccceee
Confidence 34999999999999999833
No 62
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=34.06 E-value=87 Score=34.73 Aligned_cols=70 Identities=24% Similarity=0.230 Sum_probs=55.0
Q ss_pred eEEEEeeeecccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEecCeeeeEEeee
Q 005394 91 ALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYAS 169 (698)
Q Consensus 91 ~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~~Ff~~l~~~L~~~~~V~el~~I~~ArVPIIKf~~~GI~iDLsfa~ 169 (698)
.++-.-||.|=|-.+ .+|||++|.... .. . +.+.|.+++.+.++.+-.+.+|-++.--..|++||+-++.
T Consensus 181 ~~~~~aGs~RR~ret-v~DiD~~~s~~~-~~---~----v~~~~~~~~~~~~vi~~G~~k~s~~~~~~~~~svD~r~v~ 250 (326)
T COG1796 181 IQASIAGSLRRGRET-VGDIDILISTSH-PE---S----VLEELLEMPNVQEVIAKGETKVSMLLILDEGTSVDFRVVP 250 (326)
T ss_pred heeeeccchhhcccc-ccceeeEeccCC-cH---H----HHHHHhcCCCcceeeecCCceeeEEEEecCCCeeEEEEcC
Confidence 566777899888776 689999765532 21 1 5666777899999999899999988888899999998765
No 63
>KOG2708 consensus Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones]
Probab=33.12 E-value=6.6e+02 Score=27.21 Aligned_cols=104 Identities=20% Similarity=0.294 Sum_probs=59.0
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeecccCcCCCCCeeEEeec--CCccCc
Q 005394 45 AGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVG--PSYVSR 122 (698)
Q Consensus 45 ~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~--P~~v~r 122 (698)
.|..|.+....+|..+|..+++.+.+- .....|||++|.. |..-..
T Consensus 38 ~GFlP~~TA~HHr~~il~Lv~~al~ea--------------------------------~v~~~diD~icyTKGPGmgaP 85 (336)
T KOG2708|consen 38 EGFLPRDTARHHRAWILGLVKQALEEA--------------------------------GVTSDDIDCICYTKGPGMGAP 85 (336)
T ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHc--------------------------------CCChhhCCEEEEcCCCCCCCc
Confidence 477888888899999999888877641 2236799999964 332111
Q ss_pred hhhHHHHHHH---HHHhccC---------CceEEEeccCccceEEEEecCeeeeEEeeecccccccccccc
Q 005394 123 EEDFFFILHN---ILAEMEE---------VTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDI 181 (698)
Q Consensus 123 e~~Ff~~l~~---~L~~~~~---------V~el~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~~vp~~l~i 181 (698)
-.--..... +|-+.|- |+-=+.|..|.-|++-..-.|--==+-|..--...+.+.+||
T Consensus 86 -L~~vaivaRtlsllw~kPlv~VNHCigHIEMGR~iTgA~nPvvLYvSGGNTQvIAYse~rYrIFGETlDI 155 (336)
T KOG2708|consen 86 -LSVVAIVARTLSLLWNKPLVGVNHCIGHIEMGREITGAQNPVVLYVSGGNTQVIAYSEKRYRIFGETLDI 155 (336)
T ss_pred -hhhHHHHHHHHHHHhCCCcccchhhhhhhhhcceeccCCCCEEEEEeCCceEEEEEccceeeeecceehh
Confidence 011122222 3333332 222367889999998877655332233333222234444444
No 64
>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=31.72 E-value=38 Score=25.58 Aligned_cols=31 Identities=19% Similarity=0.429 Sum_probs=24.4
Q ss_pred hHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 005394 35 NRELEKFLVEAGLYESKEEDEKREQVLGRIRQ 66 (698)
Q Consensus 35 t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~ 66 (698)
+.+|.++|...|+..++.. ..|+++|+.++.
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 4679999999998766554 679998887764
No 65
>PHA02603 nrdC.11 hypothetical protein; Provisional
Probab=28.99 E-value=31 Score=38.30 Aligned_cols=25 Identities=28% Similarity=0.307 Sum_probs=21.0
Q ss_pred EEEEeeeecccCcCCCCCeeEEeec
Q 005394 92 LIFTFGSYRLGVHGPGADIDALCVG 116 (698)
Q Consensus 92 ~I~~FGSy~lGv~~p~SDID~l~v~ 116 (698)
-+..+||...|+.+|+||+|.--|+
T Consensus 5 ~~~~~GShaYG~~tp~SD~D~rGV~ 29 (330)
T PHA02603 5 MKGLFGSHLYGTSTPESDVDYKGIF 29 (330)
T ss_pred EEEecccceeCCCCCCcccccceee
Confidence 3567999999999999999995444
No 66
>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=28.06 E-value=25 Score=37.69 Aligned_cols=21 Identities=43% Similarity=0.680 Sum_probs=17.1
Q ss_pred eCChhhhhhhhhhhHhhHHHH
Q 005394 378 AANADDLLAWKGWVESRLRQL 398 (698)
Q Consensus 378 a~~~e~~~~w~GwVESRlR~L 398 (698)
-+|.-+...++||||||+-.+
T Consensus 95 DSn~~EGAVLKGWVESRFGL~ 115 (262)
T PF07357_consen 95 DSNSPEGAVLKGWVESRFGLL 115 (262)
T ss_pred CCCChhhhhhhhhhhhccCcC
Confidence 356678899999999999755
No 67
>PRK11072 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed
Probab=26.68 E-value=2e+02 Score=36.43 Aligned_cols=48 Identities=25% Similarity=0.287 Sum_probs=35.8
Q ss_pred CCeEEEEeeeecccCcCCCCCeeEEeecCCc-cC----c---hhhHHHHHHHHHHh
Q 005394 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSY-VS----R---EEDFFFILHNILAE 136 (698)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~-v~----r---e~~Ff~~l~~~L~~ 136 (698)
.+..|+-.|-|.-+=-.+.||||++++.+.. .+ + ...||..+.+.|-.
T Consensus 153 ~~~aViamGKlG~~ELn~~SDIDLifly~~~~~~~~~~~~~~~~~~f~rl~q~li~ 208 (943)
T PRK11072 153 QPLLILGMGKLGGRELNFSSDIDLIFTYPEHGETQGGRRSIDNQQFFTRLGQRLIK 208 (943)
T ss_pred CCEEEEEeccccCccCCCccCCceEEEeCCCCCCCCCcccchHHHHHHHHHHHHHH
Confidence 4678888898888888999999999998732 11 1 13688888776654
No 68
>PRK05092 PII uridylyl-transferase; Provisional
Probab=26.10 E-value=1.3e+02 Score=37.66 Aligned_cols=30 Identities=33% Similarity=0.583 Sum_probs=27.2
Q ss_pred CCeEEEEeeeecccCcCCCCCeeEEeecCC
Q 005394 89 ANALIFTFGSYRLGVHGPGADIDALCVGPS 118 (698)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~ 118 (698)
.+.-|...|.|+-|--.|.||||++++.+.
T Consensus 104 ~~~alvA~GgyGr~EL~p~SDiDLl~l~~~ 133 (931)
T PRK05092 104 ERLAVLAVGGYGRGELAPGSDIDLLFLLPY 133 (931)
T ss_pred CceEEEEecCcCCcccCCCCCceEEEEeCC
Confidence 357899999999999999999999999874
No 69
>PRK11072 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed
Probab=25.72 E-value=2.1e+02 Score=36.18 Aligned_cols=60 Identities=12% Similarity=0.245 Sum_probs=40.5
Q ss_pred HhhcCCCccc-cccCCeEEEEeeeecccCcCCCCCeeEEeecCC----------ccCchhhHHHHHHHHHHh
Q 005394 76 TRLRGYSDQM-VEDANALIFTFGSYRLGVHGPGADIDALCVGPS----------YVSREEDFFFILHNILAE 136 (698)
Q Consensus 76 ~~~~g~~~~~-~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~----------~v~re~~Ff~~l~~~L~~ 136 (698)
+..+|.+... ....+.-|.-+|-+.-+=-+-+||||++.+... ...- ..||..+.+.|.+
T Consensus 666 ~~~~G~p~~~~~~~~~~aViamGKlGg~EL~y~SDlDlifvy~~~~~~~t~g~~~~~~-~~~~~rl~qrli~ 736 (943)
T PRK11072 666 VKRHGEPPHLEGRERGFAVIGYGKLGGKELGYASDLDLVFLHDCPEDAMTDGDKSIDG-RQFYLRLAQRIIH 736 (943)
T ss_pred HHHhCCCCCccCCCCCEEEEeecCccCCccCCcccceEEEEeecCccccCCCCCcccH-HHHHHHHHHHHHH
Confidence 4456775321 112356888888888777788999999998851 1111 3689988887775
No 70
>COG1391 GlnE Glutamine synthetase adenylyltransferase [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms]
Probab=22.74 E-value=6.4e+02 Score=32.08 Aligned_cols=47 Identities=23% Similarity=0.294 Sum_probs=28.3
Q ss_pred CeEEEEeeeecccCcCCCCCeeEEeecCCccCc------hhhHHHHHHHHHHh
Q 005394 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVSR------EEDFFFILHNILAE 136 (698)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~r------e~~Ff~~l~~~L~~ 136 (698)
+..|.--|-..-+==.=.||||++++.|..-.. ..+||+.+.+.|-+
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 344444333332222358999999988765433 13599988776654
No 71
>PRK14108 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=20.23 E-value=5e+02 Score=33.13 Aligned_cols=48 Identities=19% Similarity=0.273 Sum_probs=35.6
Q ss_pred CCeEEEEeeeecccCcCCCCCeeEEeecCCcc-C--c---hhhHHHHHHHHHHh
Q 005394 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYV-S--R---EEDFFFILHNILAE 136 (698)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v-~--r---e~~Ff~~l~~~L~~ 136 (698)
.+.-|.-.|-|.-+=-.++||||++++.+... + + ...||..+.+.|-.
T Consensus 185 ~~~aViamGklGg~ELn~~SDiDLifly~~~~~~~~~~~~~~~~~~rl~q~li~ 238 (986)
T PRK14108 185 SGLIVLGMGKLGAGELNYSSDIDLIVFFDETAPILGDPIEAQPFFVRLTRRLVR 238 (986)
T ss_pred CCeEEEeeccccccccCCCCCCceEEEeCCCCCCccccchHHHHHHHHHHHHHH
Confidence 35789999999988889999999999887321 1 1 13688887776554
Done!