Query 004736
Match_columns 732
No_of_seqs 258 out of 718
Neff 4.7
Searched_HMMs 46136
Date Thu Mar 28 12:02:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004736.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004736hhsearch_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-140 2E-145 1143.3 40.3 490 1-499 1-500 (562)
2 PTZ00418 Poly(A) polymerase; P 100.0 8E-134 2E-138 1125.1 52.9 483 11-497 47-540 (593)
3 COG5186 PAP1 Poly(A) polymeras 100.0 9E-121 2E-125 956.9 33.3 478 13-495 4-525 (552)
4 PF04928 PAP_central: Poly(A) 100.0 5.7E-73 1.2E-77 585.8 21.1 254 13-362 1-254 (254)
5 COG5260 TRF4 DNA polymerase si 100.0 2.4E-31 5.1E-36 291.5 24.0 263 31-347 54-342 (482)
6 PF04926 PAP_RNA-bind: Poly(A) 100.0 7.6E-32 1.6E-36 259.9 9.1 135 363-498 1-156 (157)
7 KOG1906 DNA polymerase sigma [ 100.0 8E-30 1.7E-34 284.4 23.7 267 28-347 57-341 (514)
8 cd05402 NT_PAP_TUTase Nucleoti 99.8 7.6E-19 1.7E-23 159.8 13.2 110 56-210 1-113 (114)
9 KOG2277 S-M checkpoint control 99.7 2.1E-16 4.6E-21 180.2 20.5 251 48-348 126-431 (596)
10 TIGR03671 cca_archaeal CCA-add 99.6 5.9E-13 1.3E-17 146.7 29.3 343 39-461 3-364 (408)
11 PRK13300 tRNA CCA-pyrophosphor 99.6 1.4E-12 3E-17 145.5 31.0 303 39-411 4-323 (447)
12 COG1746 CCA1 tRNA nucleotidylt 99.2 3E-09 6.5E-14 117.1 22.8 305 37-413 6-326 (443)
13 PF03813 Nrap: Nrap protein; 99.1 1.5E-08 3.3E-13 123.2 28.6 343 98-461 1-426 (972)
14 KOG2054 Nucleolar RNA-associat 98.2 2.8E-05 6.1E-10 93.0 16.7 290 91-391 148-478 (1121)
15 smart00572 DZF domain in DSRM 98.1 0.00012 2.6E-09 76.8 17.3 213 93-346 5-230 (246)
16 cd05400 NT_2-5OAS_ClassI-CCAas 97.7 0.00029 6.2E-09 66.7 11.1 77 90-169 27-110 (143)
17 PF03828 PAP_assoc: Cid1 famil 97.6 3.1E-05 6.8E-10 63.4 2.7 55 261-319 1-59 (60)
18 cd05397 NT_Pol-beta-like Nucle 97.5 0.00017 3.7E-09 57.8 4.9 26 90-115 17-42 (49)
19 PF01909 NTP_transf_2: Nucleot 97.4 0.00023 4.9E-09 62.0 5.5 32 90-121 14-45 (93)
20 PF09249 tRNA_NucTransf2: tRNA 97.4 0.00064 1.4E-08 63.8 7.6 93 221-335 3-97 (114)
21 PF03813 Nrap: Nrap protein; 97.1 0.0044 9.6E-08 76.4 13.9 157 200-361 668-839 (972)
22 cd05403 NT_KNTase_like Nucleot 96.9 0.0013 2.7E-08 56.7 4.6 31 91-121 19-49 (93)
23 PF14091 DUF4269: Domain of un 95.7 0.096 2.1E-06 51.9 10.5 117 93-236 18-144 (152)
24 COG1669 Predicted nucleotidylt 95.4 0.028 6.1E-07 51.7 5.4 60 57-136 7-68 (97)
25 PF07528 DZF: DZF domain; Int 95.3 0.65 1.4E-05 49.4 15.8 209 96-346 2-232 (248)
26 PRK13746 aminoglycoside resist 94.4 0.08 1.7E-06 56.6 6.3 31 91-121 29-59 (262)
27 PF10421 OAS1_C: 2'-5'-oligoad 94.4 0.076 1.6E-06 54.3 5.8 47 214-260 41-88 (190)
28 COG1708 Predicted nucleotidylt 94.1 0.042 9.2E-07 49.8 3.2 28 90-117 26-53 (128)
29 cd00141 NT_POLXc Nucleotidyltr 91.7 3 6.4E-05 45.5 13.4 113 89-241 159-277 (307)
30 PRK02098 phosphoribosyl-dephos 90.7 0.46 9.9E-06 49.7 5.8 32 90-121 120-157 (221)
31 TIGR03135 malonate_mdcG holo-A 89.9 0.57 1.2E-05 48.3 5.6 32 90-121 108-145 (202)
32 PF14792 DNA_pol_B_palm: DNA p 88.0 2.6 5.7E-05 39.4 8.2 52 89-141 23-77 (112)
33 cd05401 NT_GlnE_GlnD_like Nucl 87.3 2.9 6.3E-05 41.0 8.5 48 89-136 54-101 (172)
34 PF03445 DUF294: Putative nucl 83.2 9.2 0.0002 36.9 9.6 49 88-136 47-96 (138)
35 KOG2054 Nucleolar RNA-associat 82.9 7 0.00015 48.7 10.4 112 202-319 806-926 (1121)
36 COG1665 Predicted nucleotidylt 81.2 0.25 5.4E-06 53.1 -2.1 25 95-119 126-150 (315)
37 COG2844 GlnD UTP:GlnB (protein 74.4 11 0.00025 46.2 8.6 58 61-122 41-98 (867)
38 PF03281 Mab-21: Mab-21 protei 71.4 1.4E+02 0.003 31.8 15.3 100 206-340 184-289 (292)
39 PRK05007 PII uridylyl-transfer 70.0 17 0.00037 45.3 9.1 57 60-120 54-110 (884)
40 PRK01759 glnD PII uridylyl-tra 66.2 21 0.00046 44.3 8.8 56 60-119 30-85 (854)
41 PF10620 MdcG: Phosphoribosyl- 63.8 12 0.00026 38.9 5.2 31 90-120 116-152 (213)
42 PRK08609 hypothetical protein; 62.6 46 0.00099 39.6 10.3 108 90-241 175-283 (570)
43 smart00483 POLXc DNA polymeras 62.5 92 0.002 34.5 12.1 29 90-119 164-192 (334)
44 PF03710 GlnE: Glutamate-ammon 60.8 30 0.00065 36.6 7.7 62 75-136 111-179 (247)
45 PF10127 Nuc-transf: Predicted 59.0 8.4 0.00018 40.3 3.2 27 91-117 21-47 (247)
46 PF09970 DUF2204: Nucleotidyl 58.4 30 0.00065 35.1 6.9 80 90-176 16-100 (181)
47 PRK00227 glnD PII uridylyl-tra 58.4 27 0.00058 42.6 7.6 52 54-119 5-56 (693)
48 PRK03059 PII uridylyl-transfer 55.1 40 0.00087 42.0 8.5 54 59-118 36-89 (856)
49 PRK00275 glnD PII uridylyl-tra 53.3 49 0.0011 41.5 8.9 32 89-120 77-108 (895)
50 PRK04374 PII uridylyl-transfer 53.3 48 0.001 41.4 8.8 55 60-119 47-101 (869)
51 KOG2534 DNA polymerase IV (fam 52.8 53 0.0011 36.7 7.9 49 88-137 169-217 (353)
52 KOG3793 Transcription factor N 52.3 2.2E+02 0.0048 31.3 12.2 212 31-275 38-264 (362)
53 PRK03381 PII uridylyl-transfer 51.3 50 0.0011 40.7 8.4 29 89-117 56-84 (774)
54 TIGR01693 UTase_glnD [Protein- 50.6 52 0.0011 40.8 8.5 31 89-119 42-72 (850)
55 PRK01293 phosphoribosyl-dephos 48.2 40 0.00086 35.3 6.0 33 90-122 109-147 (207)
56 PF02937 COX6C: Cytochrome c o 46.1 18 0.00039 32.0 2.6 39 683-725 3-43 (73)
57 COG2413 Predicted nucleotidylt 41.6 43 0.00093 35.2 4.9 27 92-118 39-65 (228)
58 PRK14109 bifunctional glutamin 38.5 74 0.0016 40.4 7.3 48 89-136 722-773 (1007)
59 PF10281 Ish1: Putative stress 36.1 31 0.00067 26.3 2.2 31 35-66 6-36 (38)
60 PRK14109 bifunctional glutamin 35.7 1.3E+02 0.0028 38.4 8.7 48 89-136 214-265 (1007)
61 COG3541 Predicted nucleotidylt 35.7 18 0.00038 38.8 1.2 21 96-116 16-36 (248)
62 PF03296 Pox_polyA_pol: Poxvir 35.2 55 0.0012 32.5 4.3 77 39-135 10-92 (149)
63 PRK05092 PII uridylyl-transfer 33.6 1.4E+02 0.003 37.6 8.6 31 89-119 104-134 (931)
64 COG1796 POL4 DNA polymerase IV 31.8 1E+02 0.0022 34.5 6.2 70 91-169 181-250 (326)
65 PF07357 DRAT: Dinitrogenase r 28.7 24 0.00051 38.2 0.7 21 378-398 95-115 (262)
66 PRK11072 bifunctional glutamin 27.3 1.9E+02 0.0041 36.7 8.2 48 89-136 153-208 (943)
67 PHA02603 nrdC.11 hypothetical 26.0 38 0.00081 37.9 1.7 25 92-116 5-29 (330)
68 PRK11072 bifunctional glutamin 22.8 2.5E+02 0.0055 35.7 8.1 60 76-136 666-736 (943)
69 PRK14108 bifunctional glutamin 22.7 4E+02 0.0087 34.1 9.8 48 89-136 185-238 (986)
70 KOG2708 Predicted metalloprote 21.4 7.7E+02 0.017 27.0 10.1 83 45-160 38-134 (336)
71 COG1391 GlnE Glutamine synthet 20.9 6.9E+02 0.015 32.0 10.9 47 90-136 173-225 (963)
No 1
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=100.00 E-value=1.1e-140 Score=1143.29 Aligned_cols=490 Identities=54% Similarity=0.942 Sum_probs=465.1
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 004736 1 MSSSERMSSPPPPKQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRG 80 (732)
Q Consensus 1 ~~~~~~~~s~~~~~~~Gvt~PiS~~~Pt~~D~~~s~eL~~~L~~~~l~pSeEE~~~R~~VL~~L~~iVk~wv~~v~~~~g 80 (732)
|.+.. +.....++.||||+|||+++||++|+++|.+|+++|+++|+||++||..+|++||++|++||++|++++++++|
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 CCccccccCCeEEEEeccccccCCCCCCCeeEEeecCCccCccchHHHHHHHHHHhccCCceEEEeccCccceEEEEecC
Q 004736 81 YSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDG 160 (732)
Q Consensus 81 ~~~~~~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~re~dFF~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~G 160 (732)
+++++..+++|+|+||||||||||+||||||+|||+|+|++|+ |||..|.++|+++++|++|++|++|+||||||+|+|
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 ceeeEEeeeccccccccccccccccccCCCCcccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCC
Q 004736 161 LSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGF 240 (732)
Q Consensus 161 I~iDLsfa~l~~~~ipe~l~l~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~ 240 (732)
|+|||+||+++.+.+|++|+|.||++|+||||+|+||||||||||+||+|||+.+.||.+|||||+|||+||||+|.+||
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 004736 241 LGGVNWALLVARVCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCM 320 (732)
Q Consensus 241 LGG~swaiLVa~icQlyPn~s~~~LL~~FF~~Ys~wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~ 320 (732)
|||++|||||||+||||||++++.||.+||.+|++|+||+||+|++++++.+++++|||+.|++||+|+||||||+||+|
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 004736 321 NSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTL 400 (732)
Q Consensus 321 Nsa~NVs~sTl~vI~~EF~RA~~Il~~i~~~~~~W~~Lfep~~FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~ 400 (732)
|++||||+||+++|.+||+||++||++|+.++.+|++|||+++||.+|||||+|+++|.++|++.+|.||||||+|+|+.
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 004736 401 MIERDTYGKLQCHPYPHEYVDTSK----PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSIN----MYMFWKPG- 471 (732)
Q Consensus 401 ~LE~~~~~~l~ahp~P~~f~~~~~----~~~~~~ffIGL~~~~~~~~~~~~~~dl~~~v~eF~~~i~----~~~~~~~~- 471 (732)
+||+. ..++.|||+|+.|.++.. ..+...|||||....+ .++||+..+++|...++ ....+.+|
T Consensus 399 klE~~-~~i~~ahp~P~~f~~~~~~~~~~~~~~~~~igl~~~e~------~~~Dlt~~iq~f~~~v~~q~~~~~~~~~g~ 471 (562)
T KOG2245|consen 399 KLERN-QVILIAHPNPKKFKDTYNCPLEEDPESLWFIGLEFDEN------VKIDLTKDIQSFKKNVERQAVNLTLIKAGC 471 (562)
T ss_pred HHHhh-cceEEecCCcccccccccCCcccchhHhhhhccccccc------ccchhhhhHHHhhhhhhhcceeeeeeeccc
Confidence 99995 467889999999988753 2356789999987654 34999999999999887 45678899
Q ss_pred -eEEEEEeeccCCCCCCcCCCCccccCCC
Q 004736 472 -MEICVSHIRRKQIPPYVFPEGYKRTRHP 499 (732)
Q Consensus 472 -m~i~v~~vkr~~LP~~v~~~g~~~~~~~ 499 (732)
|.+.+.|+||++|+.+++++++++.|.-
T Consensus 472 ~~~~~~~~~krr~l~~~~~~~~l~~~k~~ 500 (562)
T KOG2245|consen 472 DVEIDFGHVKRRSLIQTITKEFLRLCKQY 500 (562)
T ss_pred ccccccccccccccccccCHHHhhHHHhh
Confidence 7778889999999999999988775544
No 2
>PTZ00418 Poly(A) polymerase; Provisional
Probab=100.00 E-value=7.7e-134 Score=1125.06 Aligned_cols=483 Identities=43% Similarity=0.790 Sum_probs=459.0
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCC
Q 004736 11 PPPKQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDAN 90 (732)
Q Consensus 11 ~~~~~~Gvt~PiS~~~Pt~~D~~~s~eL~~~L~~~~l~pSeEE~~~R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~ 90 (732)
.+++.||||+|||+++||++|++.+++|+++|+++|+|||+||.++|++||++|+++|++|+++++.++|++++++.+++
T Consensus 47 ~~~~~~Gvt~Pis~~~Pt~~d~~~s~~L~~~L~~~~~fes~ee~~kR~~vL~~L~~iv~~wv~~vs~~k~~~~~~~~~~~ 126 (593)
T PTZ00418 47 ECALSYGVTDPISLNGPTEEDLKLSNELINLLKSYNLYETEEGKKKRERVLGSLNKLVREFVVEASIEQGINEEEASQIS 126 (593)
T ss_pred CcccccCCCCCccCCCCChHHHhhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhHHhcCC
Confidence 46778999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEeccccccCCCCCCCeeEEeecCCccCccchHHHHHHHHHHhccCCceEEEeccCccceEEEEecCceeeEEeeec
Q 004736 91 ALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASI 170 (732)
Q Consensus 91 ~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~re~dFF~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l 170 (732)
++|+|||||+||||+|+||||+|||+|.|++|+ +||..|.++|++.++|++|++|++|+||||||+++||+|||+||++
T Consensus 127 g~I~tfGSYrLGV~~pgSDID~L~V~P~~vtre-dFF~~f~~~L~~~~~V~eL~~V~~A~VPiIk~~~~GI~iDL~fa~l 205 (593)
T PTZ00418 127 GKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRE-SFFSDFYAKLQQDPNITKLQPVPDAYTPVIKFVYDGIDIDLLFANL 205 (593)
T ss_pred eEEEEeccccccCCCCCCcccEEEECCCCCCHH-HHHHHHHHHHhcCCCcceeeccCccccCeEEEEECCEEEeeeeccc
Confidence 999999999999999999999999999999996 9999999999999999999999999999999999999999999999
Q ss_pred ccccccccccccccc-ccCCCCcccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCcchHHHHHH
Q 004736 171 SRLVVREDLDISDMS-VLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALL 249 (732)
Q Consensus 171 ~~~~ipe~l~l~~d~-lL~~lDe~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaiL 249 (732)
+...+|+++++.+|+ +|++||++++|||||+||+|+|+++||+.+.||.+||+||+|||+||||+|++||||||+||||
T Consensus 206 ~~~~vp~~~~~l~d~~lL~nlde~s~rSLNG~Rvtd~Il~lVPn~~~Fr~aLR~IKlWAkrRGIYsNv~GflGGV~wAIL 285 (593)
T PTZ00418 206 PLPTIPDCLNSLDDDYILRNVDEKTVRSLNGCRVADLILASVPNKDYFRTTLRFIKLWAKRRGIYSNVLGYLGGVSWAIL 285 (593)
T ss_pred CCCCCCccccccCchhhhhcCCHHHhhhhccHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccccccccccchHHHHHH
Confidence 999999999988886 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhCCCCCHHHHHHHHHHHhhcCCCCCceeeccccc-----cccCcccccCCCCCCCCCCceeEeCCCCCCCCcCC
Q 004736 250 VARVCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDE-----AELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSY 324 (732)
Q Consensus 250 Va~icQlyPn~s~~~LL~~FF~~Ys~wdW~~pV~l~~i~~-----g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~ 324 (732)
|||+||+|||+++++||.+||.+|++|+||+||+|+++++ |.+++++|||+.|++|++|+||||||+||+||+||
T Consensus 286 vARVCQLyPna~~s~Lv~~FF~iys~W~Wp~PV~L~~i~~~~~~~g~~~~~VWdPr~~~~dr~h~MPIITPayP~mNst~ 365 (593)
T PTZ00418 286 TARICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKEVPNIPGLMNFKVWDPRVNPQDRAHLMPIITPAFPSMNSTH 365 (593)
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHhhcCCCCCCeEcccccccccCCcccCCcccCCCCCcccccccCCeecCCCCCccccc
Confidence 9999999999999999999999999999999999998875 66789999999999999999999999999999999
Q ss_pred ccCHhHHHHHHHHHHHHHHHHHHhhh-cCCCccccccccchhhhcccEEEEEEEeCChhhhhhhhhHHHHHHHHHHHHhh
Q 004736 325 NVSTSTLRVMMDQFQYGNTICEEVEL-NKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIE 403 (732)
Q Consensus 325 NVs~sTl~vI~~EF~RA~~Il~~i~~-~~~~W~~Lfep~~FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE 403 (732)
|||.+|+++|++||+||++|++++.. ++.+|++||+|++||.+||+||+|++.+.+++++..|.||||||||.|+.+||
T Consensus 366 nVt~sT~~vI~~Ef~Ra~~i~~~i~~~~~~~W~~Lfep~~Ff~~Yk~yl~V~v~a~~~~~~~~w~G~VESRlR~Lv~~LE 445 (593)
T PTZ00418 366 NVTYTTKRVITEEFKRAHEIIKYIEKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKKLE 445 (593)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHcCCcchhhhcceEEEEEEEECCHHHhhhhhhHHHHHHHHHHHHhh
Confidence 99999999999999999999999988 88999999999999999999999999999999999999999999999999999
Q ss_pred hcccCceeeccCCCCCcCCCC-CCceeeEEEeeeecCCCccCCCceecchHHHHHHHHHHhhcc---ccCCceEEEEEee
Q 004736 404 RDTYGKLQCHPYPHEYVDTSK-PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSINMYM---FWKPGMEICVSHI 479 (732)
Q Consensus 404 ~~~~~~l~ahp~P~~f~~~~~-~~~~~~ffIGL~~~~~~~~~~~~~~dl~~~v~eF~~~i~~~~---~~~~~m~i~v~~v 479 (732)
+. +.+.+||||++|.+... ..|.++|||||.++.+.. .+..++||+.++++|++.|++|. .|.++|||+|+||
T Consensus 446 ~~--~~i~~~p~P~~f~~~~~~~~~~~~ffIGL~~~~~~~-~~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~~i~v~~V 522 (593)
T PTZ00418 446 TL--NNLKIRPYPKFFKYQDDGWDYASSFFIGLVFFSKNV-YNNSTFDLRYAIRDFVDIINNWPEMEKYPDQIDINIKYL 522 (593)
T ss_pred cc--CCceEeecCcccccCCCCceeEEEEEEeEeeccCCC-CCCceEecHHHHHHHHHHHHhhhhcccCCCCceEEEEEe
Confidence 74 34678999999988753 357789999999876543 23358999999999999999886 3678899999999
Q ss_pred ccCCCCCCcCCCCccccC
Q 004736 480 RRKQIPPYVFPEGYKRTR 497 (732)
Q Consensus 480 kr~~LP~~v~~~g~~~~~ 497 (732)
|+++||++||++|++|++
T Consensus 523 k~~~Lp~~v~~~~~~~~~ 540 (593)
T PTZ00418 523 KKSQLPAFVLSQTPEEPV 540 (593)
T ss_pred ehHhCCHhhccCCCcCCC
Confidence 999999999999987744
No 3
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=100.00 E-value=8.6e-121 Score=956.87 Aligned_cols=478 Identities=42% Similarity=0.753 Sum_probs=457.1
Q ss_pred CCCCCCCCCCCCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeE
Q 004736 13 PKQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANAL 92 (732)
Q Consensus 13 ~~~~Gvt~PiS~~~Pt~~D~~~s~eL~~~L~~~~l~pSeEE~~~R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~k 92 (732)
.++||||+|||+.+.|+++.+++.+|+++|++.|+|+++.|.+.|.+||..|+.+++++++++++.+|+.+.|+.+++++
T Consensus 4 ~k~~GiTgP~ST~~aTe~En~Ln~~li~eLk~~g~FE~~~E~~~Rv~VL~~Lq~~~~eFV~~vs~~K~m~dgmar~aGGK 83 (552)
T COG5186 4 KKKYGITGPLSTREATEEENRLNGELIKELKERGFFEDDKEGQTRVRVLGKLQFMVREFVARVSRNKGMGDGMARPAGGK 83 (552)
T ss_pred cccccccCCcccccccHHHhhhhHHHHHHHHHcCCcCCchhhhhHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCce
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeccccccCCCCCCCeeEEeecCCccCccchHHHHHHHHHHhccCCceEEEeccCccceEEEEecCceeeEEeeeccc
Q 004736 93 IFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISR 172 (732)
Q Consensus 93 I~~FGSy~lGv~~p~SDIDll~v~P~~v~re~dFF~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~ 172 (732)
|++|||||||||+||||||++||.|.|++|+ |||..|..+|++.++++++.+|++|+||||||+|+||+|||.||++..
T Consensus 84 IFTyGSYRLGVhgpGsDIDtLvvVPkHVsR~-dFFt~f~~~Lrer~ei~eva~vpDAfVPIIK~KF~GIsIDLifARLs~ 162 (552)
T COG5186 84 IFTYGSYRLGVHGPGSDIDTLVVVPKHVSRS-DFFTHFYEELRERPEIEEVAKVPDAFVPIIKLKFQGISIDLIFARLSI 162 (552)
T ss_pred eeeecceeeeccCCCCCcceEEEecccccHH-HHHHHHHHHhccCcchhhhccCCcccceeEEEEecCccceeeeeeccC
Confidence 9999999999999999999999999999996 999999999999999999999999999999999999999999999999
Q ss_pred cccccccccccccccCCCCcccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCcchHHHHHHHHH
Q 004736 173 LVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVAR 252 (732)
Q Consensus 173 ~~ipe~l~l~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaiLVa~ 252 (732)
+.+|..|+++|+++|++|||+|++||||.||+|+|+++||+...|+.+||+||+||++|.||.|.+||.||++|+|||||
T Consensus 163 P~Vp~~l~Lsd~nLLk~~dEkcilsLNGtRVTDeiL~LVP~~~vF~~ALRaIK~WAqRRavYaN~~GfpGGVAwam~VAR 242 (552)
T COG5186 163 PVVPDGLNLSDDNLLKSMDEKCILSLNGTRVTDEILNLVPSVKVFHSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVAR 242 (552)
T ss_pred CcCCCcccccchhhhhcchHHHHHhhcCceehHHHHHhCCchHHHHHHHHHHHHHHHhhhhhccccCCcchHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCCHHHHHHHHHHHhhcCCCCCceeeccccccccCcccccCCCCCCCCCCceeEeCCCCCCCCcCCccCHhHHH
Q 004736 253 VCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLR 332 (732)
Q Consensus 253 icQlyPn~s~~~LL~~FF~~Ys~wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~NVs~sTl~ 332 (732)
+||||||++...++.+||+++++|+||+||+|+||++|+++.++|||+.|+.|+.|+||||||+||+||.|||||.||..
T Consensus 243 iCQLYPNA~S~vIv~kFF~ils~WnWPqPviLkPieDgplqvrvWnPKvYpsDk~HRMPvITPAYPSMCATHNit~STq~ 322 (552)
T COG5186 243 ICQLYPNASSFVIVCKFFEILSSWNWPQPVILKPIEDGPLQVRVWNPKVYPSDKYHRMPVITPAYPSMCATHNITNSTQH 322 (552)
T ss_pred HHhhccCcchHhHHHHHHHHHHhcCCCCCeEeeeccCCCeeEEeeCCccCcccccccCccccCCchhhhhhccccchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCccccccccchhhhcccEEEEEEEeCChhhhhhhhhHHHHHHHHHHHHhhhcccCceee
Q 004736 333 VMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQC 412 (732)
Q Consensus 333 vI~~EF~RA~~Il~~i~~~~~~W~~Lfep~~FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~a 412 (732)
+|..||-||++|+++|..+..+|..||+..+||.+||+||.|++.+.++|++.+|.|+||||+|.|+.+||.. .+++.|
T Consensus 323 vIl~EfvRa~~I~~di~~n~~~w~~lFek~DFF~RYk~yleitA~s~~~E~~lKW~GlvESKiR~Lv~klE~v-d~i~~A 401 (552)
T COG5186 323 VILMEFVRAHKILSDIERNALDWRRLFEKSDFFSRYKLYLEITAMSSCEEDFLKWEGLVESKIRILVSKLEAV-DDILYA 401 (552)
T ss_pred hHHHHHHHHHHhhhhHhhccccHHHHHHhhhHHHHHhHhhhhhhhhcchhhhhhhhhHHHHHHHHHHHHHHHh-hhhhhc
Confidence 9999999999999999998899999999999999999999999999999999999999999999999999975 466889
Q ss_pred ccCCCCCcCCC----------------------------------C---------CCceeeEEEeeeecCCCccCCCcee
Q 004736 413 HPYPHEYVDTS----------------------------------K---------PCAHCAFFMGLQRKPGEVVQEGQQF 449 (732)
Q Consensus 413 hp~P~~f~~~~----------------------------------~---------~~~~~~ffIGL~~~~~~~~~~~~~~ 449 (732)
||||+.|...- . ..|-+.|||||+.... ..++++
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 1255689999997653 345789
Q ss_pred cchHHHHHHHHHHhhcccc-CCceEEEEEeeccCCCCCCcCCCCccc
Q 004736 450 DIRGSVEEFKLSINMYMFW-KPGMEICVSHIRRKQIPPYVFPEGYKR 495 (732)
Q Consensus 450 dl~~~v~eF~~~i~~~~~~-~~~m~i~v~~vkr~~LP~~v~~~g~~~ 495 (732)
||..+++||.+.++.|+++ ..+|.|.|+.+|+++||+-||.+|+.|
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 9999999999999999655 477999999999999999999988755
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=5.7e-73 Score=585.79 Aligned_cols=254 Identities=59% Similarity=1.048 Sum_probs=204.0
Q ss_pred CCCCCCCCCCCCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeE
Q 004736 13 PKQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANAL 92 (732)
Q Consensus 13 ~~~~Gvt~PiS~~~Pt~~D~~~s~eL~~~L~~~~l~pSeEE~~~R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~k 92 (732)
.++||||+|||+++||++|++.+++|+++|++++++||+||.++|++||++|+++|++|+++
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 37899999999999999999999999999999999999999999999999999999999953
Q ss_pred EEEeccccccCCCCCCCeeEEeecCCccCccchHHHHHHHHHHhccCCceEEEeccCccceEEEEecCceeeEEeeeccc
Q 004736 93 IFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISR 172 (732)
Q Consensus 93 I~~FGSy~lGv~~p~SDIDll~v~P~~v~re~dFF~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~ 172 (732)
..
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 cccccccccccccccCCCCcccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCcchHHHHHHHHH
Q 004736 173 LVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVAR 252 (732)
Q Consensus 173 ~~ipe~l~l~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaiLVa~ 252 (732)
..+|+++++.++++|++||++|++||||+||+++|+++||+.+.||.++|+||+|||+||||+|++||||||+||||||+
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 004736 253 VCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLR 332 (732)
Q Consensus 253 icQlyPn~s~~~LL~~FF~~Ys~wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~NVs~sTl~ 332 (732)
+||+|||+++++||.+||.+|++|+|++||+++++.++.+++++|+|+.|++|++|+|||+||+||+||+|+|||.+|++
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 004736 333 VMMDQFQYGNTICEEVELNKAQWSALFEPY 362 (732)
Q Consensus 333 vI~~EF~RA~~Il~~i~~~~~~W~~Lfep~ 362 (732)
+|++||+||+++++++..++.+|++||+|+
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=2.4e-31 Score=291.48 Aligned_cols=263 Identities=22% Similarity=0.250 Sum_probs=210.8
Q ss_pred HHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCCCCe
Q 004736 31 DMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADI 110 (732)
Q Consensus 31 D~~~s~eL~~~L~~~~l~pSeEE~~~R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDI 110 (732)
...++.+|.++.. .+.|+.+|.+.|...|++|++++++-+ + ++.+++|||+.+|+++|+|||
T Consensus 54 ~~~lt~el~~~y~--~I~ps~eEl~~R~~~leklr~~lk~~~--------------p--da~l~vFGS~~t~L~l~~SDi 115 (482)
T COG5260 54 SDELTSELLEFYD--YIAPSDEELKRRKALLEKLRTLLKKEF--------------P--DADLKVFGSTETGLALPKSDI 115 (482)
T ss_pred HHHHHHHHHHHHH--hhCCCHHHHHHHHHHHHHHHHHHHHhC--------------C--ccceeEecccccccccCcccc
Confidence 3455666666665 488999999999999999999997422 2 469999999999999999999
Q ss_pred eEEeecCCccCccchHHHHHHHHHHhccCCceEEEeccCccceEEEEe--cCceeeEEeeeccccccccccccccccccC
Q 004736 111 DALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKF--DGLSIDLLYASISRLVVREDLDISDMSVLN 188 (732)
Q Consensus 111 Dll~v~P~~v~re~dFF~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~--~GI~iDLsfa~l~~~~ipe~l~l~~d~lL~ 188 (732)
|++++.+....++..-...++..|.......++.+|..|+||||||.. .|++|||+|++.
T Consensus 116 Dl~I~s~~~~~~et~~~~~l~~~l~~~~~~~~~~~v~tarVPIIKl~d~~s~l~~Disfn~~------------------ 177 (482)
T COG5260 116 DLCIISDPRGYKETRNAGSLASHLFKKNLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNT------------------ 177 (482)
T ss_pred cEEEecCCccccccccHHHHHHHHHHhccCeeeEEEEecccceEEEecCccceEEEeecCch------------------
Confidence 999999776665422212455555555677889999999999999997 699999999983
Q ss_pred CCCcccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCcchHHHHHHHHHHHhhCCC---------
Q 004736 189 DVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPN--------- 259 (732)
Q Consensus 189 ~lDe~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaiLVa~icQlyPn--------- 259 (732)
+|++.|..++.++-..+++|+|+.+||+||++|.++++.+|+|+||++++||..++|++|.
T Consensus 178 ----------~~~~~akl~~~~~~~~P~lrpLvliIKhwl~~R~ln~~~~GtL~sy~i~cmV~sfLq~~~~~~~~~~~~~ 247 (482)
T COG5260 178 ----------NGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPFLFFDNGLL 247 (482)
T ss_pred ----------hHHHHHHHHHHHHhcCcccchHHHHHHHHHHHHhhcccccCcchhhhhHHHHHHHHHhCCcccccccccc
Confidence 6888999999999999999999999999999999999999999999999999999999982
Q ss_pred ---------CCHHHHHHHHHHHhh-cCCCCCceeecccccc-c---cCcccccCCCCCCCCCCceeEeCCC-CCCCCcCC
Q 004736 260 ---------AVPSMLVSRFFRVYT-MWRWPNPVMLCAIDEA-E---LGFSVWDPRKNRRDKTHHMPIITPA-YPCMNSSY 324 (732)
Q Consensus 260 ---------~s~~~LL~~FF~~Ys-~wdW~~pV~l~~i~~g-~---lg~~~W~p~~~~~dr~~~MpIiTP~-~P~~Nsa~ 324 (732)
.+++.|+.+||++|+ .|+|..-++... .| . ...+.|--. . +...++|++|. ++..+++.
T Consensus 248 ~~l~~~~~~~~lgvLf~dFf~~yG~~f~Y~~~~~si~--~g~~~~~K~e~g~~~~---~-~p~~LsiqdP~td~n~~~~a 321 (482)
T COG5260 248 SPLKYNKNIDNLGVLFDDFFELYGKSFNYSLVVLSIN--SGDFYLPKYEKGWLKP---S-KPNSLSIQDPGTDRNNDISA 321 (482)
T ss_pred chhhccccccccchHHHHHHHHhccccChhheEEEec--CCceeeehhhcccccc---c-CCCcEeecCCCCCccccccc
Confidence 248999999999999 599987555432 22 1 111344311 1 13789999999 66554432
Q ss_pred ccCHhHHHHHHHHHHHHHHHHHH
Q 004736 325 NVSTSTLRVMMDQFQYGNTICEE 347 (732)
Q Consensus 325 NVs~sTl~vI~~EF~RA~~Il~~ 347 (732)
..-+.+.|+.+|.+|.+++.+
T Consensus 322 --~s~~ik~i~~~F~~aF~lls~ 342 (482)
T COG5260 322 --VSFNIKDIKAAFIRAFELLSN 342 (482)
T ss_pred --ccchHHHHHHHHHHHHHHHhh
Confidence 334689999999999999987
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=7.6e-32 Score=259.94 Aligned_cols=135 Identities=36% Similarity=0.714 Sum_probs=104.9
Q ss_pred chhhhcccEEEEEEEeCChhhhhhhhhHHHHHHHHHHHHhhhcccCceeeccCCCCCc------------------CCCC
Q 004736 363 LFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYV------------------DTSK 424 (732)
Q Consensus 363 ~FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~------------------~~~~ 424 (732)
+||.+|||||+|+|+|.+++++.+|.||||||||.||.+||+.. .+..|||||++|. +...
T Consensus 1 ~FF~~Yk~yl~I~~~a~~~~~~~~W~G~VESrlR~Lv~~LE~~~-~i~~ahp~pk~f~~~~~~~~~~~~~~~~~~~~~~~ 79 (157)
T PF04926_consen 1 DFFSRYKHYLQIDVSAKNEEDHRKWSGWVESRLRHLVQKLERNP-GIKLAHPFPKRFERVYECSEQADENNDEEEEEDPE 79 (157)
T ss_dssp -HHHH-SEEEEEEEEECSHHHHHHHHHHHHCCHHHHHHHHHTST-TEEEEEE-SS-EEEEEE-EBECTTCTTSHHCHCTS
T ss_pred ChhHhCceeEEEEEEeCCHHHHHHhhhHHHHHHHHHHHHHccCC-CeeEecCCCCccccccccccccccccccccccCCC
Confidence 69999999999999999999999999999999999999999865 4678999999998 1122
Q ss_pred CCceeeEEEeeeecCCCccCCCceecchHHHHHHHHHHhhccc---cCCceEEEEEeeccCCCCCCcCCCCccccCC
Q 004736 425 PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSINMYMF---WKPGMEICVSHIRRKQIPPYVFPEGYKRTRH 498 (732)
Q Consensus 425 ~~~~~~ffIGL~~~~~~~~~~~~~~dl~~~v~eF~~~i~~~~~---~~~~m~i~v~~vkr~~LP~~v~~~g~~~~~~ 498 (732)
..+.++|||||++......+.++++||+.++++|++.|++|.. +.++|+|+|+||||+|||++||++|.+|+++
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 3578999999999876543334679999999999999999754 6688999999999999999999999888654
No 7
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=99.97 E-value=8e-30 Score=284.42 Aligned_cols=267 Identities=22% Similarity=0.334 Sum_probs=212.6
Q ss_pred CHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHhhcCCCccccccCCeEEEEeccccccCCCC
Q 004736 28 TEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAK-DWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGP 106 (732)
Q Consensus 28 t~~D~~~s~eL~~~L~~~~l~pSeEE~~~R~~VL~~L~~iVk-~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p 106 (732)
.+.=..++++++.+++ .+.||.+|.+.|.++++++++.|+ .| ..+.|++||||.+|+++|
T Consensus 57 ~~~s~~l~~eI~~fv~--~l~pt~~e~~~R~~~~~~i~~~v~~~~-----------------~~a~v~~FGS~~tglyLP 117 (514)
T KOG1906|consen 57 NLVSERLRNEILDFVQ--YLIPTPEEIEVRSELVEKIRDVVKQKW-----------------PDASVYVFGSVPTGLYLP 117 (514)
T ss_pred chhHHHHHHHHHHHHH--HhcCCchHHHHHHHHHHHHHHHHHHhc-----------------ccceeEEeeeeecccccc
Confidence 4555566778888887 589999999999999999999997 33 269999999999999999
Q ss_pred CCCeeEEeecCCccCccchHHHHHHHHHHh--ccCCceEEEeccCccceEEEEe--cCceeeEEeeeccccccccccccc
Q 004736 107 GADIDALCVGPSYVSREEDFFFILHNILAE--MEEVTELQPVLDAHVPVMKFKF--DGLSIDLLYASISRLVVREDLDIS 182 (732)
Q Consensus 107 ~SDIDll~v~P~~v~re~dFF~~l~~~L~~--~~~V~~l~~I~~ArVPIIKf~~--~GI~iDLsfa~l~~~~ipe~l~l~ 182 (732)
+||||+++..+....++ +....+.-++.. ...-..+..|..|+||||||+. .+|.|||+|++.
T Consensus 118 ~sDIDl~v~~~~~~~~e-~~~~~~~l~~~~e~~~~~~~v~~v~karvpiik~~d~~s~i~vDISFn~~------------ 184 (514)
T KOG1906|consen 118 DSDIDLVVLSKFLNDKE-DRAVKLELALELEEDNSAFHVKVVQKARVPIIKFKDPVSNIHVDISFNQT------------ 184 (514)
T ss_pred ccceEEEEecccccCch-hhHHHHHHHHhhhhccccceEEEeeeeeeeeEEeecCccceEEEeeeccc------------
Confidence 99999999999777664 555555444443 2233568889999999999996 799999999983
Q ss_pred cccccCCCCcccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCcchHHHHHHHHHHHhhCCCC--
Q 004736 183 DMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPNA-- 260 (732)
Q Consensus 183 ~d~lL~~lDe~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaiLVa~icQlyPn~-- 260 (732)
|||+.++.|..++.+.+.+|.++.++|+|...|++++.++|+++||++++||..++|++|..
T Consensus 185 ----------------~G~~aa~~i~~~~~~~p~~~~lvlvlk~fl~~r~ln~v~tGgisSyal~~Lv~~fl~l~~~~~s 248 (514)
T KOG1906|consen 185 ----------------NGVKAAKFIKDFLRDHPFLRSLVLVLKQFLYERRLNGVHTGGISSYALELLVLSFLQLHPRSKS 248 (514)
T ss_pred ----------------CchhHHHHHHHHHhcCccchhHHHHHHHHHHhhcccccccccchHHHHHHHHHHHHhhcccccC
Confidence 78999999999999999999999999999999999999999999999999999999999864
Q ss_pred -------CHHHHHHHHHHHhh-cCCCCC-ceeeccccccccC--cccccCCCCCCCCCCceeEeCCCCCCCCcCCccCHh
Q 004736 261 -------VPSMLVSRFFRVYT-MWRWPN-PVMLCAIDEAELG--FSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTS 329 (732)
Q Consensus 261 -------s~~~LL~~FF~~Ys-~wdW~~-pV~l~~i~~g~lg--~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~NVs~s 329 (732)
.++.|+.+||++|+ +|++.. -|.+....+ ..+ ...|- .+...+...++|+||..|..+.++.- .
T Consensus 249 ~~~~~~~~~~vll~~f~e~yG~~f~~~k~~i~~~~~g~-~~~~~~~~~~--~~~~~~~~~LsieDP~~P~ndigr~s--~ 323 (514)
T KOG1906|consen 249 GRLAVLKNLGVLLIKFFELYGRNFGYDKLGISLSLGGE-YVSKELTGFF--NNSLERPGSLSIEDPVDPTNDIGRSS--F 323 (514)
T ss_pred CccchhcccchHHHHHHHHhccccCchhhceeccCCcc-cccHHhhhhh--cccccCCCccccCCCCCccccccccc--c
Confidence 36789999999999 566654 233221111 011 11121 12234566799999999977665332 4
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 004736 330 TLRVMMDQFQYGNTICEE 347 (732)
Q Consensus 330 Tl~vI~~EF~RA~~Il~~ 347 (732)
.+..|+.+|..|+.++..
T Consensus 324 ~~~~v~~~F~~af~~l~~ 341 (514)
T KOG1906|consen 324 NFSQVKGAFAYAFKVLTN 341 (514)
T ss_pred cHHHHHHHHHHHHHHHhh
Confidence 588999999999988876
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=99.79 E-value=7.6e-19 Score=159.79 Aligned_cols=110 Identities=39% Similarity=0.751 Sum_probs=97.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCCCCeeEEeecCCc-cCccchHHHHHHHHH
Q 004736 56 KREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY-VSREEDFFFILHNIL 134 (732)
Q Consensus 56 ~R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~-v~re~dFF~~l~~~L 134 (732)
.|++++++|++++++|. .++++++|||+++|+++|+||||+++..|.. ... ..++..+.+.|
T Consensus 1 ~r~~i~~~l~~~i~~~~----------------~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~~~~~-~~~l~~l~~~l 63 (114)
T cd05402 1 KREEVLDRLQELIKEWF----------------PGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDR-EDFLRKLAKLL 63 (114)
T ss_pred CHHHHHHHHHHHHHHHC----------------CCCEEEEecccccCCCCCCCCeeEEEEeCCCCccH-HHHHHHHHHHH
Confidence 38899999999999873 2689999999999999999999999999976 333 58999999999
Q ss_pred HhccCCceEEEeccCccceEEEEec--CceeeEEeeeccccccccccccccccccCCCCcccccccchhhHHHHHHHh
Q 004736 135 AEMEEVTELQPVLDAHVPVMKFKFD--GLSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKL 210 (732)
Q Consensus 135 ~~~~~V~~l~~I~~ArVPIIKf~~~--GI~iDLsfa~l~~~~ipe~l~l~~d~lL~~lDe~svrSLNG~Rvtd~Ilrl 210 (732)
++...+.++..|.+|+||||||.+. |++|||+|++ .||++.+++|..+
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 9999999997 4788888877765
No 9
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=99.72 E-value=2.1e-16 Score=180.19 Aligned_cols=251 Identities=23% Similarity=0.318 Sum_probs=188.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCCCCeeEEeec-CCccCc----
Q 004736 48 YESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVG-PSYVSR---- 122 (732)
Q Consensus 48 ~pSeEE~~~R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~-P~~v~r---- 122 (732)
.+...+...|......++.++..-+ +.....+..|||..+|+....+|+| +|+. ......
T Consensus 126 ~~~~~~~~~~~~~~~~l~~~~~~~~--------------p~~~~~~~~~gs~~~~~~~~~~d~d-~~~~~~~~~~~~~~~ 190 (596)
T KOG2277|consen 126 KLPHSDVKTRKLILDKLRALASLLF--------------PDSILSLYLFGSSDLGLGERSSDLD-LCVDFTSSFLSFEKI 190 (596)
T ss_pred CCCccccchHHHHHHHHHHHHHHhc--------------CCCcceeeccCcccccccccccCcc-eeecccccccccchh
Confidence 3455566667777777777776422 2223347899999999999999999 4543 222111
Q ss_pred -cchHHHHHHHHHHhccC--CceEEEeccCccceEEEEe--cCceeeEEeeeccccccccccccccccccCCCCcccccc
Q 004736 123 -EEDFFFILHNILAEMEE--VTELQPVLDAHVPVMKFKF--DGLSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRS 197 (732)
Q Consensus 123 -e~dFF~~l~~~L~~~~~--V~~l~~I~~ArVPIIKf~~--~GI~iDLsfa~l~~~~ipe~l~l~~d~lL~~lDe~svrS 197 (732)
...++..+.+.|+...+ +..++.|..|+||||||.. .++++|+++.+..
T Consensus 191 ~~~~~~~l~~~~~~~~~~~~~~~~~~i~~A~vPiik~~~~~~~~~~d~s~~n~~-------------------------- 244 (596)
T KOG2277|consen 191 KGLEILKLLAKCLASLLEEGVREVQQILSARVPIIKFNDSGSGLECDLSVNNSD-------------------------- 244 (596)
T ss_pred hhHHHHHHHHHHHHhccccccceeeeeeecCCCEEEecCCCCCCceeeeeccch--------------------------
Confidence 13456667777776543 7889999999999999965 6899999998642
Q ss_pred cchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCcc-hHHHHHHHHHHHhhCCCC----------------
Q 004736 198 LNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLG-GVNWALLVARVCQLYPNA---------------- 260 (732)
Q Consensus 198 LNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~LG-G~swaiLVa~icQlyPn~---------------- 260 (732)
|.+.+..+..+...+++|++|...||+||+++++++...|.+. +|++.+||++++|.++..
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 3445566666666678999999999999999999999999998 699999999999986310
Q ss_pred ---------------------------CHHHHHHHHHHHhh-cCCCCCceeeccccccccCcccccCCCCCCCCCCceeE
Q 004736 261 ---------------------------VPSMLVSRFFRVYT-MWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPI 312 (732)
Q Consensus 261 ---------------------------s~~~LL~~FF~~Ys-~wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpI 312 (732)
+++.|+..||.||+ .|||++-++--......... |. ......+.|
T Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~f~~yy~~~Fdf~~~~I~~r~~~~l~~~--~~-----~~~~~~l~i 395 (596)
T KOG2277|consen 323 KPVVKKKVLCSFLRVFQRNPSNSQNTGSLGELLLGFFSYYASLFDFRKNAISIRRGRALKRA--KK-----IKSKKFLCI 395 (596)
T ss_pred ccchhhhhhhccccccccccccccccchHHHHHHHHHHHHhhhcccccceeeeeeccccccc--ch-----hhhccceee
Confidence 25689999999999 79999866532221110000 11 112356999
Q ss_pred eCCCCCCCCcCCccCHhHHHHHHHHHHHHHHHHHHh
Q 004736 313 ITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEV 348 (732)
Q Consensus 313 iTP~~P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~~i 348 (732)
++|++...|.+..++...+..|+.+|+....++...
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=99.60 E-value=5.9e-13 Score=146.67 Aligned_cols=343 Identities=20% Similarity=0.233 Sum_probs=208.0
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCC-CCCeeEEeecC
Q 004736 39 EKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGP-GADIDALCVGP 117 (732)
Q Consensus 39 ~~~L~~~~l~pSeEE~~~R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p-~SDIDll~v~P 117 (732)
.+.|+ .+-||+||.++-+.+.+.|...+++++++. ...++++.|||++-|.|++ +||||++++.|
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 478999999999999999999998877531 1247999999999999999 99999999999
Q ss_pred CccCccchHH---HHHHHHHHhc-cCCceEEEeccCccceEEEEecCceeeEEeeecccccccccccccccc-ccCCCCc
Q 004736 118 SYVSREEDFF---FILHNILAEM-EEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDMS-VLNDVDE 192 (732)
Q Consensus 118 ~~v~re~dFF---~~l~~~L~~~-~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~~ipe~l~l~~d~-lL~~lDe 192 (732)
....++ ++= ..+...+.+. +.. ...-|--|-++..+.|++|||.=|- ++.+.+ +...+|-
T Consensus 69 ~~~~~e-~l~~~gl~i~~~~~~~~~~~----~~~yaeHpYv~~~~~G~~VDiVPcy----------~v~~g~~~~taVDR 133 (408)
T TIGR03671 69 KDTSRE-ELEEYGLEIGHEVLKRGGNY----EERYAEHPYVSGEIEGFEVDVVPCY----------KVESGEEIISAVDR 133 (408)
T ss_pred CCCCHH-HHHHHHHHHHHHHHhhCCCH----hheeccCceEEEEEccEEEEEEeeE----------EccCcCeeeccccC
Confidence 877764 332 1222222221 111 1347777999999999999998442 122211 1112221
Q ss_pred ccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCC--CCCCCcchHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 004736 193 PTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYS--NVTGFLGGVNWALLVARVCQLYPNAVPSMLVSRFF 270 (732)
Q Consensus 193 ~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIys--n~~G~LGG~swaiLVa~icQlyPn~s~~~LL~~FF 270 (732)
. ..-+++++.-.. ..++..+|++|.|+|.-|+|+ -+.++++||..-||++++ -+-..++..+
T Consensus 134 t-------p~H~~fv~~rl~--~~~~d~VRLlK~f~k~igvYGsE~~~~GFSGYl~ELLv~~y------G~F~~~l~~a- 197 (408)
T TIGR03671 134 T-------PFHTRYVLERLD--GKLRDDVRLLKQFLKGIGVYGSELKTRGFSGYLCELLVIHY------GSFENVLKAA- 197 (408)
T ss_pred c-------hHHHHHHHHhhh--hhHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHh------CCHHHHHHHH-
Confidence 1 122456655443 248899999999999999996 567899999999999995 2223333322
Q ss_pred HHhhcCCCCCceeeccccccccCcccccCCCCCCCCCCceeEeCCCCCCCCcCCccCHhHHHHHHHHHHHHHHHHHHhhh
Q 004736 271 RVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVEL 350 (732)
Q Consensus 271 ~~Ys~wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~~i~~ 350 (732)
++ |..++.+.... +... .-.+++.|+||.+|..|+|.++|..++..+...-+++. ++
T Consensus 198 ---~~--wk~~~~id~~~--------~~~~----~f~~PlvViDPvDp~RNVAaalS~~~~~~fv~aar~fl---~~--- 254 (408)
T TIGR03671 198 ---SK--WKPGVVIDIEE--------HGTK----KFDDPLVVIDPVDPKRNVAAALSLENLARFILAARMFL---KN--- 254 (408)
T ss_pred ---Hh--cCCCeEEecCc--------cccc----cCCCCEEEeCCCCCcchHHHHcCHHHHHHHHHHHHHHH---HC---
Confidence 33 44556663211 1111 12468999999999999999999988877765443332 22
Q ss_pred cCCCcccccccc-----chh---hh-cccEEEEEEEeCChhhhhhhhhHHHHHHHHHHHHhhhcccCceeeccCCCCCcC
Q 004736 351 NKAQWSALFEPY-----LFF---ES-YRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYVD 421 (732)
Q Consensus 351 ~~~~W~~Lfep~-----~FF---~~-Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~~ 421 (732)
+=..+|.|. ++- .+ -.+.+.|..-..+.-+- ..-|-++--.+.|...||+.....+....| .+
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-ILYPQLERSGRSLVKLLEREGFEVLRYGVW----AD 326 (408)
T ss_pred ---CCHHHcCCCCCChHHHHHHHhhcCcEEEEEEeCCCCCCcc-chhHHHHHHHHHHHHHHHHCCCEEEEeeee----cC
Confidence 122344332 111 22 22334444433332222 334666666777777788765444444434 12
Q ss_pred CCCCCceeeEEEeeeecCC--CccCCCceecchHHHHHHHHH
Q 004736 422 TSKPCAHCAFFMGLQRKPG--EVVQEGQQFDIRGSVEEFKLS 461 (732)
Q Consensus 422 ~~~~~~~~~ffIGL~~~~~--~~~~~~~~~dl~~~v~eF~~~ 461 (732)
. -.|..++=|....- -....|.++.-+.-...|.+.
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 12444445543221 111234445555667788764
No 11
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=99.59 E-value=1.4e-12 Score=145.48 Aligned_cols=303 Identities=20% Similarity=0.231 Sum_probs=189.5
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCC-CCCeeEEeecC
Q 004736 39 EKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGP-GADIDALCVGP 117 (732)
Q Consensus 39 ~~~L~~~~l~pSeEE~~~R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p-~SDIDll~v~P 117 (732)
.+.|+ .+-||+||.++-.++.+.|...+++++++ .+. .++++.+|||+-|.|++ +||||+.++.|
T Consensus 4 ~evl~--~i~Ps~eE~~~l~~~~~~l~~~L~~~~~~----~~~--------~~~V~l~GS~ArgT~L~GdsDIDIFv~fp 69 (447)
T PRK13300 4 EEVLE--RIKPTEEEREKLKKVAEELIERLEEAIKE----LGL--------DAEVELVGSTARGTWLSGDRDIDIFVLFP 69 (447)
T ss_pred HHHHH--hcCCCHHHHHHHHHHHHHHHHHHHHHHHh----cCC--------ceEEEEEeeecCCcccCCCCceeEEEEeC
Confidence 44455 37899999999999999999999887643 221 38999999999999999 78999999999
Q ss_pred CccCccchHH----HHHHHHHHhccCCceEEEeccCccceEEEEecCceeeEEeeeccccccccccccccc-cccCCCCc
Q 004736 118 SYVSREEDFF----FILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDM-SVLNDVDE 192 (732)
Q Consensus 118 ~~v~re~dFF----~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~~ipe~l~l~~d-~lL~~lDe 192 (732)
....++ ++= ......++..-.-.+++ -|-=|-++..+.|++|||.=|- ++.+. .+...+|-
T Consensus 70 ~~~~~e-~L~~~gl~i~~~~~~~~~~~~~~~---yaeHpyv~~~~~G~~VDiVPcy----------~v~~~~~~~saVDR 135 (447)
T PRK13300 70 KDTSRE-ELEEKGLEIGKEVAKELLGDYEER---YAEHPYVTGEIDGFEVDIVPCY----------KVESGEEIISAVDR 135 (447)
T ss_pred CCCCHH-HHHHHHHHHHHHHHHhhCCcceee---eccCceEEEEECCEEEEEEeeE----------EccCcCcccccccC
Confidence 887764 221 11222333211122333 4788999999999999998542 12221 11122221
Q ss_pred ccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCC--CCCCCcchHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 004736 193 PTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYS--NVTGFLGGVNWALLVARVCQLYPNAVPSMLVSRFF 270 (732)
Q Consensus 193 ~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIys--n~~G~LGG~swaiLVa~icQlyPn~s~~~LL~~FF 270 (732)
. ..-+++|+.-.. +.++..+|++|.|+|.-|+|+ -+.++++||..-||++++ -+-..++..+
T Consensus 136 t-------p~H~~fv~~rl~--~~~~d~VRLlK~f~k~~gvYGsE~k~~GFSGYl~ELLv~~y------G~F~~~l~~a- 199 (447)
T PRK13300 136 T-------PFHTKYVKERLK--GKLEDEVRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHY------GSFENVLKAA- 199 (447)
T ss_pred c-------hHHHHHHHHhhh--hhHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHh------CCHHHHHHHH-
Confidence 1 122566665542 348899999999999999996 567999999999999995 2333333332
Q ss_pred HHhhcCCCCCceeeccccccccCcccccCCCCCCCCCCceeEeCCCCCCCCcCCccCHhHHHHHHHHHHHHHHHHHHhhh
Q 004736 271 RVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVEL 350 (732)
Q Consensus 271 ~~Ys~wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~~i~~ 350 (732)
++| .-++.+...+ |... ....+++.|+||.+|..|+|.++|..++..+... |..-+.+
T Consensus 200 ---~~w--~~~~~I~~~~--------~~~~---~~f~~PlvViDPvDp~RNVAaa~S~~~~~~fv~a---ar~fL~~--- 257 (447)
T PRK13300 200 ---SKW--KPPVKIDLEK--------HGKE---YKFDDPLVVIDPVDPNRNVAAALSLENLATFILA---AREFLKN--- 257 (447)
T ss_pred ---HhC--CCCceEeccc--------cCcc---ccCCCCEEEeCCCCCcchHHHHcCHHHHHHHHHH---HHHHHhC---
Confidence 334 3345543211 1100 0224689999999999999999998877666532 2223333
Q ss_pred cCCCccccccccc-----h---hh-hcccEEEEEEEeCChhhhhhhhhHHHHHHHHHHHHhhhcccCcee
Q 004736 351 NKAQWSALFEPYL-----F---FE-SYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQ 411 (732)
Q Consensus 351 ~~~~W~~Lfep~~-----F---F~-~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ 411 (732)
+=...|.|.+ . +. +-.+.+.|..-..+.-+- ..-|-++--.+.|...||+.....+.
T Consensus 258 ---Ps~~fF~~~~~~~~~~~~~l~~R~t~~~~v~f~~p~~v~D-il~pQl~r~~~~i~~~L~~~gF~v~~ 323 (447)
T PRK13300 258 ---PSLEFFFPSDLSPEEILEELERRGTTVLALEFPRPDIVED-ILYPQLERSLRSIVKLLEREGFEVLR 323 (447)
T ss_pred ---CCHHhcCCCCCChHHHHHHHhhcCceEEEEEeCCCCCCcc-chhHHHHHHHHHHHHHHHHCCCEEEE
Confidence 2223333333 1 11 112444555444433222 23466666677777778876544343
No 12
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=99.18 E-value=3e-09 Score=117.08 Aligned_cols=305 Identities=19% Similarity=0.200 Sum_probs=185.6
Q ss_pred HHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCC-CCCeeEEee
Q 004736 37 ELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGP-GADIDALCV 115 (732)
Q Consensus 37 eL~~~L~~~~l~pSeEE~~~R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p-~SDIDll~v 115 (732)
.|.+.|+. +.||+||.++=+.+.+.|...+++-. +++|+ .+.+...||++=|.|++ +.|||+-|.
T Consensus 6 ~l~evl~~--i~P~~eE~~~~~~~~e~l~~~~~~~~----~e~~~--------~aev~lVGS~AkgTwL~gd~DIDvFi~ 71 (443)
T COG1746 6 VLEEVLKR--IKPTEEERKKLKEVAEELRERINEII----EELGI--------DAEVVLVGSYAKGTWLRGDHDIDVFIA 71 (443)
T ss_pred HHHHHHHH--cCCCHHHHHHHHHHHHHHHHHHHHHH----HhcCC--------cceEEEEeecccCcccCCCcceeEEEE
Confidence 45555654 67999999988888888888877654 34444 58899999999999999 779999999
Q ss_pred cCCccCccchH----HHHHHHHHHhccCCceEEEeccCccceEEEEecCceeeEEeeeccccccccccccccccccCCCC
Q 004736 116 GPSYVSREEDF----FFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDMSVLNDVD 191 (732)
Q Consensus 116 ~P~~v~re~dF----F~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~~ipe~l~l~~d~lL~~lD 191 (732)
.|....++ .. .......|.+ .--.+.-|-=|-+.-.+.|+++|+.=|-... -++ .+...+|
T Consensus 72 Fp~d~~~e-el~~~GL~ig~~~l~~-----~~~~~~YAeHPYV~g~v~G~eVDvVPCy~v~--~~~-------~~~sAVD 136 (443)
T COG1746 72 FPKDTSEE-ELEEKGLEIGREVLKR-----GNYEERYAEHPYVTGEVDGYEVDVVPCYKVE--DGE-------KIISAVD 136 (443)
T ss_pred CCCCCCHH-HHHHHHHHHHHHHhcC-----CchhhhhccCCeeEEEEccEEEEEEeccccc--Ccc-------ccccccc
Confidence 99887764 11 1122233332 0112456777999999999999998553210 011 1111222
Q ss_pred cccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCC--CCCCcchHHHHHHHHHHHhhCCCCCHHHHHHHH
Q 004736 192 EPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSN--VTGFLGGVNWALLVARVCQLYPNAVPSMLVSRF 269 (732)
Q Consensus 192 e~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn--~~G~LGG~swaiLVa~icQlyPn~s~~~LL~~F 269 (732)
-.- -=+.++..-+-... +.=+|++|.|.|.=|+|++ +.++++||.--||+++|= .|
T Consensus 137 RTp-------lHt~yv~e~L~~~~--~deVrLLK~FlK~iGvYGaE~rt~GFSGYL~ELLII~yG-------------sF 194 (443)
T COG1746 137 RTP-------LHTRYVEEHLKGRQ--KDEVRLLKQFLKGIGVYGAELRTQGFSGYLCELLIIHYG-------------SF 194 (443)
T ss_pred Ccc-------hhHHHHHHHhcccc--hhHHHHHHHHHhccCccceeeeeccchHHHHHHHHhhhc-------------cH
Confidence 111 11345554443322 2347899999999999996 579999999999999872 23
Q ss_pred HHHhhcC-CCCCceeeccccccccCcccccCCCCCCCCCCceeEeCCCCCCCCcCCccCHhHHHHHHHHHHHHHHHHHHh
Q 004736 270 FRVYTMW-RWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEV 348 (732)
Q Consensus 270 F~~Ys~w-dW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~~i 348 (732)
=..--.. +|.-+++|..- .|..+.. ...+|.|+||.+|..|+|.+||..++..++ .|.+..-.
T Consensus 195 e~vl~~a~~wrp~~~ID~~--------~~~~e~f---~d~PliVvDPVDP~RNVAAalSl~~la~f~----~aar~FL~- 258 (443)
T COG1746 195 ENVLKAASRWRPGKIIDLE--------GHKRERF---EDEPLIVVDPVDPKRNVAAALSLENLARFV----HAAREFLK- 258 (443)
T ss_pred HHHHHHHhccCCCeEEecc--------chhhhcc---CCCCeEecCCCCCccchhhhcCHHHHHHHH----HHHHHHhc-
Confidence 3333222 37777776531 1211111 224899999999999999999987765543 33322211
Q ss_pred hhcCCCccccccccc--------hhhhcccEEEEEEEeCChhhhhhhhhHHHHHHHHHHHHhhhcccCceeec
Q 004736 349 ELNKAQWSALFEPYL--------FFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCH 413 (732)
Q Consensus 349 ~~~~~~W~~Lfep~~--------FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ah 413 (732)
.+=...|.|.. ...+=.+-+.+..-..+.-+ ...-|-++---+.|...||......+..+
T Consensus 259 ----~PS~efF~p~~~~~~~~~~~~~rgt~v~~l~~~~pd~vd-DilypQl~r~~~~l~r~Le~~gF~vl~~~ 326 (443)
T COG1746 259 ----NPSPEFFFPRKPKPLLLSKLRRRGTHVLALVFPKPDLVD-DILYPQLERTARSLFRALEEEGFRVLRSG 326 (443)
T ss_pred ----CCChhhcCCCCcCcccccchhhcCceEEEEEeCCCCCCc-chhhHHHHHHHHHHHHHHHHcCCEEeeee
Confidence 12222332211 11111222333333334322 23447777777888888887654444433
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=99.14 E-value=1.5e-08 Score=123.17 Aligned_cols=343 Identities=15% Similarity=0.212 Sum_probs=206.7
Q ss_pred cccccCCC---CCCCeeEEeecCCccCccchHH------------HHHHHHH--HhccCCceEEEe---ccCccceEEEE
Q 004736 98 SYRLGVHG---PGADIDALCVGPSYVSREEDFF------------FILHNIL--AEMEEVTELQPV---LDAHVPVMKFK 157 (732)
Q Consensus 98 Sy~lGv~~---p~SDIDll~v~P~~v~re~dFF------------~~l~~~L--~~~~~V~~l~~I---~~ArVPIIKf~ 157 (732)
||.++... ++-.||+.+.-|..+-.++||. ..++..| .+...+.++... .+.+-||+.+.
T Consensus 1 S~~l~t~~k~~~~~~VDl~v~mP~~~fq~KDyln~RY~~KRA~YLa~iA~~L~~~~~~~~~~v~~~~~~gd~~kPil~l~ 80 (972)
T PF03813_consen 1 SYALKTMIKSKPNLTVDLAVEMPKSLFQEKDYLNYRYFHKRALYLAYIAAHLQKKKSKLFVDVSFEYLNGDPLKPILVLR 80 (972)
T ss_pred CcccccccccCCCCeeEEEEeCChhhcCchhhccchHHHHHHHHHHHHHHHHhhhccccceeEEEEeCCCCCCCCeEEEE
Confidence 56666554 5779999999998765555543 2455667 223333344332 67888999998
Q ss_pred ec-----C------ceeeEEeeecccc-c----cccccc------------------cccccccCCCCcccccccchhhH
Q 004736 158 FD-----G------LSIDLLYASISRL-V----VREDLD------------------ISDMSVLNDVDEPTVRSLNGCRV 203 (732)
Q Consensus 158 ~~-----G------I~iDLsfa~l~~~-~----ipe~l~------------------l~~d~lL~~lDe~svrSLNG~Rv 203 (732)
-. + +.|-|..+..... . .|..-+ ..|..+|.++- =..-
T Consensus 81 p~~~~~~~~~~~~~~~iRi~~~~~~~~F~~~rl~P~rnnvR~~~~~~~~~~~~~pTP~YNssIL~D~~--------~~~~ 152 (972)
T PF03813_consen 81 PKGKKDSDDFSKTKFRIRIIPSIPSDTFPLSRLAPSRNNVRPSWFDEEDSSSLPPTPHYNSSILEDML--------MEEH 152 (972)
T ss_pred ECCccccccccCCcEEEEEEecCCcccCCHHhcCCCCCccCcCcccccccCCCCCCCcchHHHHHHHh--------HHHH
Confidence 42 2 4455554432211 0 111000 11111221110 0112
Q ss_pred HHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCC-CCCcchHHHHHHHHHHHhh---------CCCCCHHHHHHHHHHHh
Q 004736 204 ADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNV-TGFLGGVNWALLVARVCQL---------YPNAVPSMLVSRFFRVY 273 (732)
Q Consensus 204 td~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~-~G~LGG~swaiLVa~icQl---------yPn~s~~~LL~~FF~~Y 273 (732)
...+.+.....+.|+.+++++|.||++||+.+.. .|++||+-|+||+++.+|- .+..+.-+|+..+.++.
T Consensus 153 l~~l~~~~~~~p~f~dA~iLlkvWl~QRg~~~~~~~~Gf~~f~~s~lla~Ll~~g~~~~~~~l~~~mSsyQlFr~~l~fL 232 (972)
T PF03813_consen 153 LKYLHEASKSSPAFRDACILLKVWLRQRGFGSGISQGGFGGFEWSMLLAYLLQGGGRNGKKKLSKSMSSYQLFRAVLQFL 232 (972)
T ss_pred HHHHHHHHhcCHHHHHHHHHHHHHHhcCCCCcccCCCCcchHHHHHHHHHHHcCCCccCCcccCCCCCHHHHHHHHHHHH
Confidence 3344455566799999999999999999999875 5899999999999999976 34567889999999999
Q ss_pred hcCCC-CCceeeccccccccCcccccCCCCCCCCCCceeEeCCCCCCCCcCCccCHhHHHHHHHHHHHHHHHHHHhhhcC
Q 004736 274 TMWRW-PNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNK 352 (732)
Q Consensus 274 s~wdW-~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~~i~~~~ 352 (732)
+..|| .+|+.++.-.+.......| .+.+....+||. =.+|...+++.++++.++.|-+++.+++.+.. .
T Consensus 233 A~~d~~~~~l~~~~~~~~~~~~~~~-------~~~~~~vf~D~s-g~~Nl~~~ms~~s~~~L~~eA~~tl~lL~~~~--~ 302 (972)
T PF03813_consen 233 ATTDLSKKPLFFKSSSDSTESLEEF-------HSAFDPVFVDPS-GGLNLLAKMSPSSYEELQHEAKLTLELLDDSS--D 302 (972)
T ss_pred hccccccCceEEecCCCccchhhhh-------hccCCeEEEeCC-CCEEEEEcCCHHHHHHHHHHHHHHHHHhcccc--c
Confidence 99999 6688887643211111111 123456666664 56899999999999999999999999998632 3
Q ss_pred CCcccccc-c-cchhhhcccEEEEE---EE----eCChhhhhhhhhHHHHHHHHHHH-HhhhcccCceeeccC---CCCC
Q 004736 353 AQWSALFE-P-YLFFESYRNYLQVD---IV----AANADDLLAWKGWVESRLRQLTL-MIERDTYGKLQCHPY---PHEY 419 (732)
Q Consensus 353 ~~W~~Lfe-p-~~FF~~Yk~yl~I~---v~----a~~~e~~~~w~GwVESRlR~Lv~-~LE~~~~~~l~ahp~---P~~f 419 (732)
.....+|- + ..+..+|.+++.|. .. .....+...|...++.++-.|+. .|..... .++++ +.++
T Consensus 303 d~F~~lFl~~~~~~~~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lL~raLgdR~~---~i~v~~~~~~~w 379 (972)
T PF03813_consen 303 DGFDSLFLTKVDPPALRFDHVLRISPDSLLSSFSPDESLDFLSFSNYLLRKIYRLLKRALGDRAK---LIRVLRPSQPPW 379 (972)
T ss_pred cchhhhhcccCCcccccCCEEEEEcchhhcccccccccccccchhHHHHHHHHHHHHHHHHHHHH---eEEEeCCCCCCc
Confidence 45777774 4 46778999999991 11 11223333444456667766664 3543221 22333 2222
Q ss_pred cCCCC--CCceeeEEEeeeecCCCc---cCCCceecchHHHHHHHHH
Q 004736 420 VDTSK--PCAHCAFFMGLQRKPGEV---VQEGQQFDIRGSVEEFKLS 461 (732)
Q Consensus 420 ~~~~~--~~~~~~ffIGL~~~~~~~---~~~~~~~dl~~~v~eF~~~ 461 (732)
.-... ........|||..++... ...|-..|-.....+|++.
T Consensus 380 ~i~~~~~~~~~~~l~vGl~ln~~~~~r~vd~GP~a~d~~ea~~FR~F 426 (972)
T PF03813_consen 380 SISSKPPKSKPKTLTVGLILNPENAFRLVDRGPSAEDKEEAAAFREF 426 (972)
T ss_pred ccCCCCCCCCCceEEEEEEEchhhceeeeeeCcCCcCcHHHHHHHHH
Confidence 11111 111226789998875211 1111122334566778763
No 14
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=98.21 E-value=2.8e-05 Score=92.98 Aligned_cols=290 Identities=17% Similarity=0.204 Sum_probs=170.2
Q ss_pred eEEE-EeccccccC-CCCCCCeeEEeecCCccCccchHH------------HHHHHHHHhccCCceEEEe---ccCccce
Q 004736 91 ALIF-TFGSYRLGV-HGPGADIDALCVGPSYVSREEDFF------------FILHNILAEMEEVTELQPV---LDAHVPV 153 (732)
Q Consensus 91 ~kI~-~FGSy~lGv-~~p~SDIDll~v~P~~v~re~dFF------------~~l~~~L~~~~~V~~l~~I---~~ArVPI 153 (732)
+++. ..||+.+|. ..|+.-+|+++..|+..-..+|++ +.+...|.+.+....+... .+-.-||
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 556666654 468899999999996543333433 2233333333433333332 2345588
Q ss_pred EEEEecCceeeEEeeeccccccccccc-cccccccCCCC----------cccccccchh--------hHHHHHHHhCCCc
Q 004736 154 MKFKFDGLSIDLLYASISRLVVREDLD-ISDMSVLNDVD----------EPTVRSLNGC--------RVADQILKLVPNV 214 (732)
Q Consensus 154 IKf~~~GI~iDLsfa~l~~~~ipe~l~-l~~d~lL~~lD----------e~svrSLNG~--------Rvtd~IlrlVP~~ 214 (732)
+.+.-.|-..|+.-.+.+..-+|..+. ..++.+|-... +..---.|-. ....++.+.....
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 877765555555443322222222211 11111111100 0000001111 0112333444556
Q ss_pred hhHHHHHHHHHHHHHHhCCCCCCCCCcchHHHHHHHHHHHh---hCCCCCHHHHHHHHHHHhhcCCCCC-ceeecccccc
Q 004736 215 EHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQ---LYPNAVPSMLVSRFFRVYTMWRWPN-PVMLCAIDEA 290 (732)
Q Consensus 215 ~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaiLVa~icQ---lyPn~s~~~LL~~FF~~Ys~wdW~~-pV~l~~i~~g 290 (732)
+.|+.++.+.|.|+++|-. +-..|++||+-|++++++... ++-+.+..+++..-+++.+.|||.. -+-+++-. .
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 224689999999999998874 4566778899999999999999986 45554310 0
Q ss_pred ccCcccccCCCCCCCCCCceeEeCCCCCCCCcCCccCHhHHHHHHHHHHHHHHHHHHhhhcCCCccccc-cccchhhhcc
Q 004736 291 ELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALF-EPYLFFESYR 369 (732)
Q Consensus 291 ~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~~i~~~~~~W~~Lf-ep~~FF~~Yk 369 (732)
.. |....-+..+....++ ..-..|...|++.++++.+++|.+-+..++.+.. ...++.+| ++.+.|..|.
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 0000001112333333 2345788999999999999999999999999765 35678777 7899999999
Q ss_pred cEEEEEEEeCChhhhhhhhhHH
Q 004736 370 NYLQVDIVAANADDLLAWKGWV 391 (732)
Q Consensus 370 ~yl~I~v~a~~~e~~~~w~GwV 391 (732)
|-+.+.--..-+.....-.||.
T Consensus 457 h~l~l~~~~~l~~~~~~~~~~~ 478 (1121)
T KOG2054|consen 457 HVLHLSPLSRLQAAEHLLSGFC 478 (1121)
T ss_pred eeeeccccchhhhHHhhcccch
Confidence 9887765433333333444443
No 15
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=98.12 E-value=0.00012 Score=76.77 Aligned_cols=213 Identities=16% Similarity=0.150 Sum_probs=146.1
Q ss_pred EEEeccccccCCCCCC-CeeEEeecCCccCccchHHHHHHH----HHHhccCCceEEEeccCccceEEEEec----Ccee
Q 004736 93 IFTFGSYRLGVHGPGA-DIDALCVGPSYVSREEDFFFILHN----ILAEMEEVTELQPVLDAHVPVMKFKFD----GLSI 163 (732)
Q Consensus 93 I~~FGSy~lGv~~p~S-DIDll~v~P~~v~re~dFF~~l~~----~L~~~~~V~~l~~I~~ArVPIIKf~~~----GI~i 163 (732)
|.-.||+.-|+.+.|. +.|+++++....+. .....+.+ -|+...+=.....|..+.+|.++..+. -...
T Consensus 5 V~rVG~~aKG~ll~Gd~~~~lVv~c~~~PT~--~ll~~v~~~l~e~l~~~~~~e~~~~~~~~~~~~~~~~i~ltSp~~r~ 82 (246)
T smart00572 5 VMRVGSFAKGTLLKGDNVAELVLLCKEKPTS--ELVARLARKLPEQLKAVTEDEALIIVTSTKEPTMEVGILITSPLARV 82 (246)
T ss_pred eEEeeeeccCceecCCCceeEEEEecCCCcH--HHHHHHHHHHHHHHhhcCcccceeeeeccCCCceeEEEEEecccccc
Confidence 5678999999999876 78999999877665 34444433 333321112233456777788877752 2233
Q ss_pred eEEeeeccccccccccccccccccCCCC-cccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCcc
Q 004736 164 DLLYASISRLVVREDLDISDMSVLNDVD-EPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLG 242 (732)
Q Consensus 164 DLsfa~l~~~~ipe~l~l~~d~lL~~lD-e~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~LG 242 (732)
+...+. +|+++.-.+ +-.-+| +.|+.+|-.+|-+.+..........|+.++|++|-|.++....+ -|.
T Consensus 83 ~~~~~~-----~~~~~~~~~--p~~~ld~~~cl~aLAalRhakWFq~~a~~l~s~~iviRilKd~~~R~~~~~----pL~ 151 (246)
T smart00572 83 ELLITT-----VPENLRKLD--PEDHLDRKKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQ----PLS 151 (246)
T ss_pred cccccc-----cCcccccCC--ccccCCHHHHHHHHHHHHHhHHHHHhccCCcchhhHHHHHHHHHHhccccc----ccc
Confidence 333322 233332111 112234 35888888999999999998888899999999999999876554 389
Q ss_pred hHHHHHHHHHHHhhCCC-CCHHHHHHHHHHHhhc-CCCCCceeeccccccccCcccccCCCCCCCCCCceeEeCCCCC-C
Q 004736 243 GVNWALLVARVCQLYPN-AVPSMLVSRFFRVYTM-WRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYP-C 319 (732)
Q Consensus 243 G~swaiLVa~icQlyPn-~s~~~LL~~FF~~Ys~-wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P-~ 319 (732)
++.+-+++++.+--... .++++-+.+||++.++ .-+|.- --|.||..+ .
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 99999999998853221 3589999999999884 212210 136788886 7
Q ss_pred CCcCCccCHhHHHHHHHHHHHHHHHHH
Q 004736 320 MNSSYNVSTSTLRVMMDQFQYGNTICE 346 (732)
Q Consensus 320 ~Nsa~NVs~sTl~vI~~EF~RA~~Il~ 346 (732)
.|++...|.-....|...-+.+.+++.
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=97.74 E-value=0.00029 Score=66.71 Aligned_cols=77 Identities=27% Similarity=0.317 Sum_probs=56.1
Q ss_pred CeEEEEeccccccCCCC-CCCeeEEeecCCccC----ccchHHHHHHHHHHhccCCceEEEeccCccceEEEEec--Cce
Q 004736 90 NALIFTFGSYRLGVHGP-GADIDALCVGPSYVS----REEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFD--GLS 162 (732)
Q Consensus 90 ~~kI~~FGSy~lGv~~p-~SDIDll~v~P~~v~----re~dFF~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~--GI~ 162 (732)
...++.||||+.|...+ .||||++++.+.... ...++...+.+.|.+...- -.. ....-|.|.+.+. +++
T Consensus 27 ~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~~~~~~~~~~~~l~~~L~~~~~~--~~~-~~~~~~~v~v~~~~~~~~ 103 (143)
T cd05400 27 VAEVFLQGSYARGTALRGDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEYYGA--NEE-VKAQHRSVTVKFKGQGFH 103 (143)
T ss_pred ccEEEEEcceeCCCCCCCCCceeEEEEEcCcccccccCHHHHHHHHHHHHHHhcCc--ccc-cccCceEEEEEEcCCCeE
Confidence 47899999999999977 899999999886543 1146667777777764321 112 2455578888886 899
Q ss_pred eeEEeee
Q 004736 163 IDLLYAS 169 (732)
Q Consensus 163 iDLsfa~ 169 (732)
+||.-+.
T Consensus 104 vDvvP~~ 110 (143)
T cd05400 104 VDVVPAF 110 (143)
T ss_pred EEEEEEe
Confidence 9997654
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=97.64 E-value=3.1e-05 Score=63.41 Aligned_cols=55 Identities=20% Similarity=0.344 Sum_probs=36.5
Q ss_pred CHHHHHHHHHHHhh-cCCCCCceeeccccccc-c--CcccccCCCCCCCCCCceeEeCCCCCC
Q 004736 261 VPSMLVSRFFRVYT-MWRWPNPVMLCAIDEAE-L--GFSVWDPRKNRRDKTHHMPIITPAYPC 319 (732)
Q Consensus 261 s~~~LL~~FF~~Ys-~wdW~~pV~l~~i~~g~-l--g~~~W~p~~~~~dr~~~MpIiTP~~P~ 319 (732)
++++||.+||+||+ .|||.+-|+.... |. . ....|.. ....+...|+|++|+.|+
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 8999997775432 21 1 1233431 112345789999999885
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=97.49 E-value=0.00017 Score=57.76 Aligned_cols=26 Identities=35% Similarity=0.532 Sum_probs=24.5
Q ss_pred CeEEEEeccccccCCCCCCCeeEEee
Q 004736 90 NALIFTFGSYRLGVHGPGADIDALCV 115 (732)
Q Consensus 90 ~~kI~~FGSy~lGv~~p~SDIDll~v 115 (732)
..+++.||||+.|.+.+.||||++|+
T Consensus 17 ~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 17 GYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred CcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 47899999999999999999999987
No 19
>PF01909 NTP_transf_2: Nucleotidyltransferase domain A subset of this Pfam family; InterPro: IPR002934 A small region that overlaps with a nuclear localization signal and binds to the RNA primer contains three aspartates that are essential for catalysis. Sequence and secondary structure comparisons of regions surrounding these aspartates with sequences of other polymerases revealed a significant homology to the palm structure of DNA polymerase beta, terminal deoxynucleotidyltransferase and DNA polymerase IV of Saccharomyces cerevisiae, all members of the family X of polymerases. This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor [, ]. Proteins containing this domain include kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase inactivates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. In experiments, Mn2+ strongly stimulated this reaction due to a 50-fold lower Ki for 8-azido-ATP in the presence of Mn2+. Mutations of the highly conserved Asp residues 113, 115, and 167, critical for metal binding in the catalytic domain of bovine poly(A) polymerase, led to a strong reduction of cross-linking efficiency, and Mn2+ no longer stimulated the reaction. Mutations in the region of the "helical turn motif" (a domain binding the triphosphate moiety of the nucleotide) and in the suspected nucleotide-binding helix of bovine poly(A) polymerase impaired ATP binding and catalysis. The results indicate that ATP is bound in part by the helical turn motif and in part by a region that may be a structural analogue of the fingers domain found in many polymerases.; GO: 0016779 nucleotidyltransferase activity; PDB: 4EBK_B 4EBJ_A 1KNY_A 2B4V_A 2B56_A 2B51_A 1NO5_B 1Q79_A 1Q78_A 1F5A_A ....
Probab=97.43 E-value=0.00023 Score=61.99 Aligned_cols=32 Identities=34% Similarity=0.464 Sum_probs=29.5
Q ss_pred CeEEEEeccccccCCCCCCCeeEEeecCCccC
Q 004736 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVS 121 (732)
Q Consensus 90 ~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~ 121 (732)
...|+.|||++.|.+.|+||||++++.+....
T Consensus 14 ~~~v~lfGS~a~g~~~~~SDIDl~i~~~~~~~ 45 (93)
T PF01909_consen 14 VAEVYLFGSYARGDATPDSDIDLLIILDEPED 45 (93)
T ss_dssp TEEEEEEHHHHHTSSCTTSCEEEEEEESSTSC
T ss_pred CCEEEEECCcccCcCCCCCCEEEEEEeCCccc
Confidence 58999999999999999999999999987754
No 20
>PF09249 tRNA_NucTransf2: tRNA nucleotidyltransferase, second domain; InterPro: IPR015329 This domain adopts a structure consisting of a five helical bundle core. It is predominantly found in Archaeal tRNA nucleotidyltransferases, following the catalytic nucleotidyltransferase domain []. ; GO: 0004810 tRNA adenylyltransferase activity, 0016437 tRNA cytidylyltransferase activity; PDB: 3OUY_B 2ZHB_A 2ZH1_A 2ZH2_A 1UET_A 2ZH7_A 1R8B_A 2DR5_A 1TFW_C 3OVA_A ....
Probab=97.35 E-value=0.00064 Score=63.82 Aligned_cols=93 Identities=24% Similarity=0.345 Sum_probs=59.2
Q ss_pred HHHHHHHHHHhCCCCC--CCCCcchHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhhcCCCCCceeeccccccccCccccc
Q 004736 221 LRCLKFWAKRRGVYSN--VTGFLGGVNWALLVARVCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWD 298 (732)
Q Consensus 221 lr~IK~WAK~RGIysn--~~G~LGG~swaiLVa~icQlyPn~s~~~LL~~FF~~Ys~wdW~~pV~l~~i~~g~lg~~~W~ 298 (732)
+|++|.++|.-|+|++ ++++++||..-+||+++=- +....+.-+ +|..|+.|..-..+...
T Consensus 3 VrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~yGs----------F~~~l~~a~--~W~~~~~Id~~~~~~~~----- 65 (114)
T PF09249_consen 3 VRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHYGS----------FENVLEAAA--KWKPPVVIDLEDHGEPS----- 65 (114)
T ss_dssp HHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHHHSS----------HHHHHHHHT--T--TTEEEETT-TTE-------
T ss_pred hHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHHHCC----------HHHHHHHHH--hcCCCeEEccCccchhh-----
Confidence 6899999999999996 4799999999999998721 223333334 67778887642111100
Q ss_pred CCCCCCCCCCceeEeCCCCCCCCcCCccCHhHHHHHH
Q 004736 299 PRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMM 335 (732)
Q Consensus 299 p~~~~~dr~~~MpIiTP~~P~~Nsa~NVs~sTl~vI~ 335 (732)
+.-..++.|+||.+|..|+|.+||..++..+.
T Consensus 66 -----~~f~~PlvviDPvDp~RNVAAalS~~~~~~fv 97 (114)
T PF09249_consen 66 -----KKFDDPLVVIDPVDPNRNVAAALSLENLAEFV 97 (114)
T ss_dssp -----EEE-SS-EEEETTEEEEETTTTS-HHHHHHHH
T ss_pred -----hhcCCCeEEcCCCCCCchHhHhcCHHHHHHHH
Confidence 11236899999999999999999987766544
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=97.13 E-value=0.0044 Score=76.40 Aligned_cols=157 Identities=23% Similarity=0.344 Sum_probs=108.8
Q ss_pred hhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCcchHHHHHHHHHHH-hhCC---CCCHHHHHHHHHHHhhc
Q 004736 200 GCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVC-QLYP---NAVPSMLVSRFFRVYTM 275 (732)
Q Consensus 200 G~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaiLVa~ic-QlyP---n~s~~~LL~~FF~~Ys~ 275 (732)
..+-+..|..+.-.++.|.+++|++|.|...+-+ .|++.--.+=||||++. +-+| ..++..=+.+|.++-++
T Consensus 668 ~p~h~~~i~~l~~~~p~fs~tvRL~KrW~~shlL----s~~i~~E~vELlva~vfl~~~p~~~P~S~~~GFlRfL~lLs~ 743 (972)
T PF03813_consen 668 LPKHTSAIHGLHTRFPSFSPTVRLAKRWLSSHLL----SGHISEEAVELLVASVFLSPAPWSPPSSPQTGFLRFLHLLST 743 (972)
T ss_pred hHHHHHHHHHHHhhCCchhHHHHHHHHHHHhccC----cccCCHHHHHHHHHHHhcCCCCCCCCCCHhHHHHHHHHHHHh
Confidence 3445666777777789999999999999999977 46788899999999987 3344 34555667777788899
Q ss_pred CCCCC-ceeeccccccc--------cCcccccCCCCCCCCCCceeEeCCCCCCCCc--CCccCHhHHHHHHHHHHHHHHH
Q 004736 276 WRWPN-PVMLCAIDEAE--------LGFSVWDPRKNRRDKTHHMPIITPAYPCMNS--SYNVSTSTLRVMMDQFQYGNTI 344 (732)
Q Consensus 276 wdW~~-pV~l~~i~~g~--------lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Ns--a~NVs~sTl~vI~~EF~RA~~I 344 (732)
|||.+ |++++...+-. ..|..|.. ..+......|.|.||.+|.-.. ...-+..-+++|+.--+.+.++
T Consensus 744 ~dW~~~PLiVd~~~~l~~~~~~~i~~~f~~~R~-~dp~~~~p~~~IaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~sl~~ 822 (972)
T PF03813_consen 744 WDWREEPLIVDFNNELTEEDRAEIETNFDAWRK-IDPAMNLPAMFIATPYDPEGSLWTRNGPSKVVAKRLTALAKASLKL 822 (972)
T ss_pred CCCCcCCEEEECCCCCCHHHHHHHHHHHHHhhc-cCccccCCcEEEEeCCCCCCCEeECCCCCHHHHHHHHHHHHHHHHH
Confidence 99996 88876432110 12333432 2344455789999999986432 1234455577777666667777
Q ss_pred HHHhhhcCCCccccccc
Q 004736 345 CEEVELNKAQWSALFEP 361 (732)
Q Consensus 345 l~~i~~~~~~W~~Lfep 361 (732)
++.-..+..+|..||.|
T Consensus 823 l~~~~~~~~~~~~lF~~ 839 (972)
T PF03813_consen 823 LEEQGLSDLDWKSLFRP 839 (972)
T ss_pred HHhcCCCCCCHHHhcCC
Confidence 77433346789999976
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=96.90 E-value=0.0013 Score=56.69 Aligned_cols=31 Identities=32% Similarity=0.532 Sum_probs=28.4
Q ss_pred eEEEEeccccccCCCCCCCeeEEeecCCccC
Q 004736 91 ALIFTFGSYRLGVHGPGADIDALCVGPSYVS 121 (732)
Q Consensus 91 ~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~ 121 (732)
..++.|||++.|-+.++||||++++.+....
T Consensus 19 ~~i~LfGS~arg~~~~~SDiDl~vi~~~~~~ 49 (93)
T cd05403 19 EKVYLFGSYARGDARPDSDIDLLVIFDDPLD 49 (93)
T ss_pred cEEEEEeeeecCCCCCCCCeeEEEEeCCCCC
Confidence 6899999999999999999999999987654
No 23
>PF14091 DUF4269: Domain of unknown function (DUF4269)
Probab=95.69 E-value=0.096 Score=51.85 Aligned_cols=117 Identities=23% Similarity=0.376 Sum_probs=74.1
Q ss_pred EEEeccccccCCCCCCCeeEEeecCCccCccchHHHHHHHHHHhccCCceE-EEeccCccceEEEEecCceeeEEeeecc
Q 004736 93 IFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTEL-QPVLDAHVPVMKFKFDGLSIDLLYASIS 171 (732)
Q Consensus 93 I~~FGSy~lGv~~p~SDIDll~v~P~~v~re~dFF~~l~~~L~~~~~V~~l-~~I~~ArVPIIKf~~~GI~iDLsfa~l~ 171 (732)
-...|.+.+|+..|+||||++|..+.. +.|-..+.....+.++.+-- ..|..-..=+..|.+.|..+-|---+.
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 456799999999999999999998742 13333344444444443211 223444455677888999988753222
Q ss_pred ccccccccccccccccCCCCcccccccchhhHHHHHHHhCCCc-hhHHHHHHHHH--------HHHHHhCCCCC
Q 004736 172 RLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNV-EHFCTTLRCLK--------FWAKRRGVYSN 236 (732)
Q Consensus 172 ~~~ipe~l~l~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVP~~-~~FR~llr~IK--------~WAK~RGIysn 236 (732)
.++.-||+|=...-.+++... +.||.-+|-+| +||+--||-++
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 133468887554444555444 78999888888 46666666544
No 24
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=95.41 E-value=0.028 Score=51.72 Aligned_cols=60 Identities=27% Similarity=0.350 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCCCCeeEEeecCCccCccchHHH--HHHHHH
Q 004736 57 REQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFF--ILHNIL 134 (732)
Q Consensus 57 R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~re~dFF~--~l~~~L 134 (732)
.+++++++...+++|. | -.++-.||||+=|=..|+||||+++-..... .+|. .+...|
T Consensus 7 ~~~~lr~~~~~l~~k~-------g---------v~~~~vFGS~aRgE~~~~SDIDILVef~~~~----~ll~~~~l~~~L 66 (97)
T COG1669 7 LKKILRKIKPELKEKY-------G---------VKRVAVFGSYARGEQKPDSDIDILVEFEPGK----TLLDLVRLEDEL 66 (97)
T ss_pred HHHHHHHHHHHHHHHh-------C---------CceEEEeeeeecCCCCCCCCceeEEeecCCc----cHHHHHHHHHHH
Confidence 3344666666666554 2 2679999999999999999999999654332 4443 234555
Q ss_pred Hh
Q 004736 135 AE 136 (732)
Q Consensus 135 ~~ 136 (732)
.+
T Consensus 67 ~~ 68 (97)
T COG1669 67 SD 68 (97)
T ss_pred HH
Confidence 54
No 25
>PF07528 DZF: DZF domain; InterPro: IPR006561 This domain is found in proteins containing the double-stranded RNA-binding motif, DSRM (IPR001159 from INTERPRO), or the zinc finger domain C2H2 (IPR007087 from INTERPRO). This domain is found exclusively in the metazoa.
Probab=95.27 E-value=0.65 Score=49.36 Aligned_cols=209 Identities=14% Similarity=0.165 Sum_probs=132.1
Q ss_pred eccccccCCCCCC-CeeEEeecCCccCccchHHHHHHHHHHh----c-cCCceEEEe------ccCccceEEEEe--c--
Q 004736 96 FGSYRLGVHGPGA-DIDALCVGPSYVSREEDFFFILHNILAE----M-EEVTELQPV------LDAHVPVMKFKF--D-- 159 (732)
Q Consensus 96 FGSy~lGv~~p~S-DIDll~v~P~~v~re~dFF~~l~~~L~~----~-~~V~~l~~I------~~ArVPIIKf~~--~-- 159 (732)
.||+.-|+.+.|. ++|+|+++..-.+. ++...+.+.|.+ . ++ +-...+ ...+.|.+...+ .
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 89999999877774 566665554443 1 22 111112 222335555443 2
Q ss_pred CceeeEEeeeccccccccccccccccccCCCCc-ccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCC
Q 004736 160 GLSIDLLYASISRLVVREDLDISDMSVLNDVDE-PTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVT 238 (732)
Q Consensus 160 GI~iDLsfa~l~~~~ipe~l~l~~d~lL~~lDe-~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~ 238 (732)
.+.+.+..+. .+++..- .+.-..+|. .+..+|-.+|-+.++.+........+.++|++|-..+|--- +
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 111123444 57888888999999999988888899999999999887533 5
Q ss_pred CCcchHHHHHHHHHHHhhCCC---CCHHHHHHHHHHHhhc-CCCCCceeeccccccccCcccccCCCCCCCCCCceeEeC
Q 004736 239 GFLGGVNWALLVARVCQLYPN---AVPSMLVSRFFRVYTM-WRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIIT 314 (732)
Q Consensus 239 G~LGG~swaiLVa~icQlyPn---~s~~~LL~~FF~~Ys~-wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiT 314 (732)
+.|+++.+-+|+-+..---|+ .++++-+.+||+..|. +--|.- . -|.|
T Consensus 148 ~~L~~W~leLL~~~~i~~~~~~~~l~~g~a~RRvle~lasGillp~~----------~------------------gl~D 199 (248)
T PF07528_consen 148 QPLSSWALELLVEKAISNNSSRQPLSPGDAFRRVLECLASGILLPGS----------P------------------GLRD 199 (248)
T ss_pred CCCChhHHHHHHHHHeeeCCCCCCCChHHHHHHHHHHHhCceecCCC----------C------------------CCcC
Confidence 678999888888777653333 4689999999999874 322210 0 1335
Q ss_pred CCC-CCCCcCCccCHhHHHHHHHHHHHHHHHHH
Q 004736 315 PAY-PCMNSSYNVSTSTLRVMMDQFQYGNTICE 346 (732)
Q Consensus 315 P~~-P~~Nsa~NVs~sTl~vI~~EF~RA~~Il~ 346 (732)
|+. ...++..+.|.-....|..--|.+.+++.
T Consensus 200 PcE~~~~~~~~~lt~qq~e~it~sAQ~~LRlla 232 (248)
T PF07528_consen 200 PCEKDPVDVLDTLTLQQREDITSSAQTALRLLA 232 (248)
T ss_pred CCCCCCceeeccCCHHHHHHHHHHHHHHHHHHH
Confidence 555 44677777777777777776666665553
No 26
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=94.39 E-value=0.08 Score=56.55 Aligned_cols=31 Identities=29% Similarity=0.269 Sum_probs=28.1
Q ss_pred eEEEEeccccccCCCCCCCeeEEeecCCccC
Q 004736 91 ALIFTFGSYRLGVHGPGADIDALCVGPSYVS 121 (732)
Q Consensus 91 ~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~ 121 (732)
.-|+.|||+..|-..|.||||++++.....+
T Consensus 29 ~~vyLfGS~~~G~~~p~SDIDllvvv~~~l~ 59 (262)
T PRK13746 29 LAIHLYGSAVDGGLKPHSDIDLLVTVAVPLD 59 (262)
T ss_pred EEEEEECCcccCCCCCCCceeEEEEeCCCCC
Confidence 4689999999999999999999999987765
No 27
>PF10421 OAS1_C: 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus ; InterPro: IPR018952 This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between residues 320 and 344 at the extreme C-terminal end []. Oligoadenylate synthetases are antiviral enzymes that counteract viral attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesise 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication []. This domain is often associated with IPR002934 from INTERPRO. ; PDB: 1PX5_B.
Probab=94.36 E-value=0.076 Score=54.27 Aligned_cols=47 Identities=13% Similarity=0.051 Sum_probs=33.2
Q ss_pred chhHHHHHHHHHHHHHHhCCCCCCC-CCcchHHHHHHHHHHHhhCCCC
Q 004736 214 VEHFCTTLRCLKFWAKRRGVYSNVT-GFLGGVNWALLVARVCQLYPNA 260 (732)
Q Consensus 214 ~~~FR~llr~IK~WAK~RGIysn~~-G~LGG~swaiLVa~icQlyPn~ 260 (732)
....+.|+|+||+|-+...-..... +-+.+|++-||+++.-..-.+.
T Consensus 41 P~klK~LIrLVKhWy~~~~~~~~~~~~lPpsYaLELLtIyAWE~g~~~ 88 (190)
T PF10421_consen 41 PTKLKNLIRLVKHWYQQCKKKKCGGGSLPPSYALELLTIYAWEQGCGA 88 (190)
T ss_dssp -HHHHHHHHHHHHHHHHHHCC--HTT-S--HHHHHHHHHHHHHHHT-S
T ss_pred CHHHHHHHHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHhcCCC
Confidence 3678999999999999766653333 4567999999999998765544
No 28
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=94.11 E-value=0.042 Score=49.77 Aligned_cols=28 Identities=43% Similarity=0.630 Sum_probs=26.2
Q ss_pred CeEEEEeccccccCCCCCCCeeEEeecC
Q 004736 90 NALIFTFGSYRLGVHGPGADIDALCVGP 117 (732)
Q Consensus 90 ~~kI~~FGSy~lGv~~p~SDIDll~v~P 117 (732)
...++.|||++-|=+.+.||||++++++
T Consensus 26 ~~~v~LfGS~arG~~~~~SDiDv~vv~~ 53 (128)
T COG1708 26 DLLIYLFGSYARGDFVKESDIDLLVVSD 53 (128)
T ss_pred CeEEEEEccCcccccccCCCeeEEEEcC
Confidence 5899999999999999999999999983
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=91.70 E-value=3 Score=45.48 Aligned_cols=113 Identities=24% Similarity=0.252 Sum_probs=71.6
Q ss_pred CCeEEEEeccccccCCCCCCCeeEEeecCCccCccchHHHHHHHHHHhccCCceEEEeccCccceEEEEe------cCce
Q 004736 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKF------DGLS 162 (732)
Q Consensus 89 ~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~re~dFF~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~------~GI~ 162 (732)
...++.+-||||=|-.+ .+|||+|+..+.... ..++..+...|.+.+.+..+. ..-..-....+ .|+.
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 36899999999999876 579999998876543 256777888888777654321 11111122222 2899
Q ss_pred eeEEeeeccccccccccccccccccCCCCcccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCc
Q 004736 163 IDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFL 241 (732)
Q Consensus 163 iDLsfa~l~~~~ipe~l~l~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~L 241 (732)
|||.++.... . .-.++-.-.+.. -.|-++.||++||..=+.+|..
T Consensus 233 VDl~~~p~~~------~------------------------~~all~fTGs~~----~nr~lR~~A~~~G~~L~~~GL~ 277 (307)
T cd00141 233 VDLRVVPPEE------F------------------------GAALLYFTGSKQ----FNRALRRLAKEKGLKLNEYGLF 277 (307)
T ss_pred EEEEEeCHHH------H------------------------HHHHHHhhCCHH----HHHHHHHHHHHcCCeeeccccc
Confidence 9999876321 0 112222222222 2456699999999887777764
No 30
>PRK02098 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=90.68 E-value=0.46 Score=49.72 Aligned_cols=32 Identities=25% Similarity=0.308 Sum_probs=27.4
Q ss_pred CeEEEEecccc----ccC--CCCCCCeeEEeecCCccC
Q 004736 90 NALIFTFGSYR----LGV--HGPGADIDALCVGPSYVS 121 (732)
Q Consensus 90 ~~kI~~FGSy~----lGv--~~p~SDIDll~v~P~~v~ 121 (732)
+..+-+|||+. +|+ -.++||||+++-.|....
T Consensus 120 g~~~gv~GS~a~qlaTG~~~l~~~SDLDLLi~~~~~~~ 157 (221)
T PRK02098 120 GVDCRVFGSLAWQALTGLPYLSASSDLDLLWPLPAAAQ 157 (221)
T ss_pred CCcEEEeeehHHHHhhCCcccCCCCCeeEEEecCChhh
Confidence 56899999999 999 799999999998875443
No 31
>TIGR03135 malonate_mdcG holo-ACP synthase, malonate decarboxylase-specific. Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A. Members of this protein family are the phosphoribosyl-dephospho-CoA transferase specific to the malonate decarboxylase system. This enzyme can also be designated holo-ACP synthase (2.7.7.61). The corresponding component of the citrate lyase system, CitX, shows little or no sequence similarity to this family.
Probab=89.88 E-value=0.57 Score=48.33 Aligned_cols=32 Identities=28% Similarity=0.304 Sum_probs=27.6
Q ss_pred CeEEEEeccc----cccC--CCCCCCeeEEeecCCccC
Q 004736 90 NALIFTFGSY----RLGV--HGPGADIDALCVGPSYVS 121 (732)
Q Consensus 90 ~~kI~~FGSy----~lGv--~~p~SDIDll~v~P~~v~ 121 (732)
+..+-+|||+ .+|+ -.++||||+++-.|....
T Consensus 108 ~~~~gv~GS~~~qlaTg~~~~~~~SDLDLLi~~~~~~~ 145 (202)
T TIGR03135 108 GVPWGVYGSAGWQLLTGLPYLHASSDLDLLLRAPSPLS 145 (202)
T ss_pred CCcEEEecchHHHHhcCCcccCCCCCeeEEEcCCChhh
Confidence 5689999999 8999 799999999998875544
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=87.97 E-value=2.6 Score=39.40 Aligned_cols=52 Identities=33% Similarity=0.319 Sum_probs=38.9
Q ss_pred CCeEEEEeccccccCCCCCCCeeEEeecCCccCc---cchHHHHHHHHHHhccCCc
Q 004736 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSR---EEDFFFILHNILAEMEEVT 141 (732)
Q Consensus 89 ~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~r---e~dFF~~l~~~L~~~~~V~ 141 (732)
.+.++..-||||=|-...+ |||+++..|..... ...++..+...|.+..-++
T Consensus 23 p~~~v~i~GSyRRGK~~~g-DiDiLIt~~~~~~~~~~~~~~l~~lv~~L~~~g~i~ 77 (112)
T PF14792_consen 23 PGLEVEICGSYRRGKETSG-DIDILITHPDPSSVSKKLEGLLEKLVKRLEEKGFIT 77 (112)
T ss_dssp TT-EEEEEHHHHTT-SEES-SEEEEEEETTCSTTTCSTTCHHHHHHHHHHHTTSEE
T ss_pred CCcEEEEccccccCCCcCC-CeEEEEeCCCcCcchhhHHHHHHHHHHHHHhCCeEE
Confidence 4689999999999988755 99999999876542 1368888888898754443
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=87.27 E-value=2.9 Score=40.99 Aligned_cols=48 Identities=23% Similarity=0.275 Sum_probs=36.7
Q ss_pred CCeEEEEeccccccCCCCCCCeeEEeecCCccCccchHHHHHHHHHHh
Q 004736 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAE 136 (732)
Q Consensus 89 ~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~re~dFF~~l~~~L~~ 136 (732)
...-++.+|||+-|=-.+.||||++++.+........+|..+.+.+.+
T Consensus 54 ~~~~~la~Gs~GR~E~~~~SD~D~~~v~~~~~~~~~~~~~~l~~~i~~ 101 (172)
T cd05401 54 VPFALLALGSYGRGELNPSSDQDLLLLYDDDGDEVAAYFEELAERLIK 101 (172)
T ss_pred CcEEEEEeCCcccCCcCCCcCcceEEEeCCCCchHHHHHHHHHHHHHH
Confidence 468999999999999999999999999875432113567666665554
No 34
>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=83.25 E-value=9.2 Score=36.91 Aligned_cols=49 Identities=20% Similarity=0.148 Sum_probs=38.1
Q ss_pred cCCeEEEEeccccccCCCCCCCeeEEeecCCccCcc-chHHHHHHHHHHh
Q 004736 88 DANALIFTFGSYRLGVHGPGADIDALCVGPSYVSRE-EDFFFILHNILAE 136 (732)
Q Consensus 88 ~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~re-~dFF~~l~~~L~~ 136 (732)
....-++.+||++=+=.++.||+|..+|.......+ ..+|..|.+.+..
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 357899999999999999999999999998732222 4677776665553
No 35
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=82.86 E-value=7 Score=48.70 Aligned_cols=112 Identities=19% Similarity=0.232 Sum_probs=70.3
Q ss_pred hHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCcchHHHHHHHHHHHhh-C---CCCCHHHHHHHHHHHhhcCC
Q 004736 202 RVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQL-Y---PNAVPSMLVSRFFRVYTMWR 277 (732)
Q Consensus 202 Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaiLVa~icQl-y---Pn~s~~~LL~~FF~~Ys~wd 277 (732)
|.+-.|-.+-..++.|-.++|+-|.|...+=+-+ |.+ -=++-+|||...+. + |..++-.=..+|..+-|+||
T Consensus 806 ~ht~aL~~l~qsh~~ys~vvrLaKrWl~shLL~~---h~~-De~iELLva~lf~~p~p~~~psS~~~gFlRfL~llS~~d 881 (1121)
T KOG2054|consen 806 LHTLALQSLSQSHPFYSSVVRLAKRWLGSHLLSG---HHL-DEAIELLVAALFLKPGPLVPPSSPENGFLRFLSLLSTWD 881 (1121)
T ss_pred HHHHHHHHHhhcccchhHHHHHHHHHHHHHhhcc---chH-HHHHHHHHHHHhcCccCCCCCCCcchhHHHHHHHHhcCc
Confidence 4455555566667899999999999999875543 223 55678888877643 3 34556666788888999999
Q ss_pred CCC-ceeeccccccccCcc----cccCCCCCCCCCCceeEeCCCCCC
Q 004736 278 WPN-PVMLCAIDEAELGFS----VWDPRKNRRDKTHHMPIITPAYPC 319 (732)
Q Consensus 278 W~~-pV~l~~i~~g~lg~~----~W~p~~~~~dr~~~MpIiTP~~P~ 319 (732)
|.. |.+++-. + ..... .-+.-...|.....|.|+||-+-.
T Consensus 882 W~~~PLIvd~n-n-~~~ed~~~e~~e~f~s~R~~lp~m~vit~yD~~ 926 (1121)
T KOG2054|consen 882 WKFDPLIVDFN-N-GFPEDERSELEEKFISARKQLPPMVVITPYDHL 926 (1121)
T ss_pred ccCCceEEEcC-C-CCcHHHHHHHHHHHhhhcccCCceEEeeccccc
Confidence 986 7776531 1 11000 000000112234589999997553
No 36
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=81.25 E-value=0.25 Score=53.10 Aligned_cols=25 Identities=32% Similarity=0.480 Sum_probs=22.0
Q ss_pred EeccccccCCCCCCCeeEEeecCCc
Q 004736 95 TFGSYRLGVHGPGADIDALCVGPSY 119 (732)
Q Consensus 95 ~FGSy~lGv~~p~SDIDll~v~P~~ 119 (732)
.-||..+|++..+||||+++.|+.+
T Consensus 126 VTGSiL~gl~~~nSDIDfVVYG~~~ 150 (315)
T COG1665 126 VTGSILLGLYDENSDIDFVVYGQMW 150 (315)
T ss_pred ccccccccccCCCCCceEEEEcHHH
Confidence 4599999999999999999999543
No 37
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=74.35 E-value=11 Score=46.18 Aligned_cols=58 Identities=21% Similarity=0.354 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCCCCeeEEeecCCccCc
Q 004736 61 LGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSR 122 (732)
Q Consensus 61 L~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~r 122 (732)
++....++..|..++-...|.++ ..+.-|...|.|+=|--.|.||||++++.|...+.
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 34445555566666656677764 34789999999999999999999999999987653
No 38
>PF03281 Mab-21: Mab-21 protein
Probab=71.43 E-value=1.4e+02 Score=31.77 Aligned_cols=100 Identities=17% Similarity=0.148 Sum_probs=65.3
Q ss_pred HHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCcchHHHHHHHHHHHhhCCCC-C-----HHHHHHHHHHHhhcCCCC
Q 004736 206 QILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPNA-V-----PSMLVSRFFRVYTMWRWP 279 (732)
Q Consensus 206 ~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaiLVa~icQlyPn~-s-----~~~LL~~FF~~Ys~wdW~ 279 (732)
.+++.+ ....+.+++++|....+.. ...+.|++|++-.++.+.|..+|.. . +++.+.+.+...-.
T Consensus 184 ~ll~~~--~~~~~~~l~llk~l~~~~~---~~~~~l~syhLkt~ll~~~~~~p~~~~W~~~~l~~~l~~~l~~L~~---- 254 (292)
T PF03281_consen 184 QLLKNL--NGCRKKCLRLLKALRDRHL---TNLSGLSSYHLKTVLLWLCEKHPSSSDWSEENLGERLLDLLDFLIK---- 254 (292)
T ss_pred HHHHhc--cccHHHHHHHHHHHHHhcc---ccCCCccHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHHHHH----
Confidence 344443 4567889999999987766 5568899999999999999999876 1 34444444333221
Q ss_pred CceeeccccccccCcccccCCCCCCCCCCceeEeCCCCCCCCcCCccCHhHHHHHHHHHHH
Q 004736 280 NPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQY 340 (732)
Q Consensus 280 ~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~NVs~sTl~vI~~EF~R 340 (732)
...++.+ + .-+.|.+|.=.+.+..++..+..++.+
T Consensus 255 ------~L~~~~L----------p----------hff~~~~NLf~~~~~~~~~~~~~~~~~ 289 (292)
T PF03281_consen 255 ------CLQEGRL----------P----------HFFIPNLNLFQHLSPEELDELARKLER 289 (292)
T ss_pred ------HHhcCCC----------C----------ccCCCCcccCCCCCHHHHHHHHHHHHH
Confidence 1111111 0 124677888888888777777766553
No 39
>PRK05007 PII uridylyl-transferase; Provisional
Probab=70.04 E-value=17 Score=45.26 Aligned_cols=57 Identities=18% Similarity=0.282 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCCCCeeEEeecCCcc
Q 004736 60 VLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYV 120 (732)
Q Consensus 60 VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v 120 (732)
++..+..++.++++.+-...+.+ ...+.-|+..|+|+=|=-.|.||||++++.+...
T Consensus 54 ~~~~~s~~~D~~l~~l~~~~~~~----~~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~ 110 (884)
T PRK05007 54 LVEARTEFIDQLLQRLWIEAGFD----QIPDLALVAVGGYGRGELHPLSDIDLLILSRKKL 110 (884)
T ss_pred HHHHHHHHHHHHHHHHHHHccCC----CcCceEEEecCCCCCcccCCcccceEEEEeCCCC
Confidence 45555555666655544444443 1246899999999999999999999999998443
No 40
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=66.22 E-value=21 Score=44.29 Aligned_cols=56 Identities=14% Similarity=0.199 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCCCCeeEEeecCCc
Q 004736 60 VLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (732)
Q Consensus 60 VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~ 119 (732)
++.....++.++++.+-...+.+. ..+.-|+..|+|+=|=-.|.||||++++.+..
T Consensus 30 ~~~~~~~~~D~~l~~l~~~~~~~~----~~~iaLvAvGGYGR~eL~P~SDIDlliL~~~~ 85 (854)
T PRK01759 30 LIENRSDFYDQLLIHLWQQFGLEE----QSDLALIAVGGYGRREMFPLSDLDILILTEQP 85 (854)
T ss_pred HHHHHHHHHHHHHHHHHHHccCCC----CCCeEEEEeCCcccccCCCcccceEEEEeCCC
Confidence 666666666666665433333221 13588999999999999999999999998744
No 41
>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=63.77 E-value=12 Score=38.94 Aligned_cols=31 Identities=26% Similarity=0.270 Sum_probs=24.8
Q ss_pred CeEEEEecccc----ccCC--CCCCCeeEEeecCCcc
Q 004736 90 NALIFTFGSYR----LGVH--GPGADIDALCVGPSYV 120 (732)
Q Consensus 90 ~~kI~~FGSy~----lGv~--~p~SDIDll~v~P~~v 120 (732)
+...-+|||+. +|+. .++||||+++-.+...
T Consensus 116 ~~~~gv~GS~g~qlaTGl~~l~~~SDLDLli~~~~~~ 152 (213)
T PF10620_consen 116 GLRWGVYGSLGFQLATGLPYLHADSDLDLLIRPPSPS 152 (213)
T ss_pred CCCEEEehhHHHHHHhCccccCCCCCceEEEeCCChh
Confidence 67899999985 4443 6999999999888665
No 42
>PRK08609 hypothetical protein; Provisional
Probab=62.61 E-value=46 Score=39.57 Aligned_cols=108 Identities=17% Similarity=0.169 Sum_probs=61.9
Q ss_pred CeEEEEeccccccCCCCCCCeeEEeecCCccCccchHHHHHHHHHHhccCCceEEEeccCccceEEEEe-cCceeeEEee
Q 004736 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKF-DGLSIDLLYA 168 (732)
Q Consensus 90 ~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~re~dFF~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~-~GI~iDLsfa 168 (732)
..++..-||||=|--+ ..|||+|+..+.. ..+.+.|.+.+.++++..-...+.-+ .+.. .|+.|||-+.
T Consensus 175 ~~~v~~~GS~RR~~et-~gDiDili~~~~~--------~~~~~~l~~~~~v~~~~~~g~~~~~~-~~~~~~~~~vDl~~v 244 (570)
T PRK08609 175 IIRFSRAGSLRRARET-VKDLDFIIATDEP--------EAVREQLLQLPNIVEVIAAGDTKVSV-ELEYEYTISVDFRLV 244 (570)
T ss_pred ccEEEeccchhccccc-cCCeeEEEecCCH--------HHHHHHHHcCccHHHHHhcCCceEEE-EEecCCCeEEEEEEe
Confidence 5789999999999776 5799999977542 11233444444443322111212211 1222 4999999987
Q ss_pred eccccccccccccccccccCCCCcccccccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCc
Q 004736 169 SISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFL 241 (732)
Q Consensus 169 ~l~~~~ipe~l~l~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~L 241 (732)
.... + .-.++-.-.. ..| .|-++.||++||+.-|-+|..
T Consensus 245 ~~~~------~------------------------~~aL~yfTGS-~~h---n~~lr~~A~~~g~~l~e~gl~ 283 (570)
T PRK08609 245 EPEA------F------------------------ATTLHHFTGS-KDH---NVRMRQLAKERGEKISEYGVE 283 (570)
T ss_pred CHHH------H------------------------HHHHHHHhcc-HHH---HHHHHHHHHHcCCcccccccc
Confidence 6321 0 0111212122 222 345589999999988888875
No 43
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=62.50 E-value=92 Score=34.53 Aligned_cols=29 Identities=34% Similarity=0.564 Sum_probs=24.6
Q ss_pred CeEEEEeccccccCCCCCCCeeEEeecCCc
Q 004736 90 NALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (732)
Q Consensus 90 ~~kI~~FGSy~lGv~~p~SDIDll~v~P~~ 119 (732)
..++..-||||=|-.+ ..|||+|+..+..
T Consensus 164 ~~~v~i~GSyRRgket-~gDIDili~~~~~ 192 (334)
T smart00483 164 DAIVTLTGSFRRGKET-GHDVDFLITSPHP 192 (334)
T ss_pred CcEEEEecccccCCCc-CCCeeEEEecCCc
Confidence 5789999999999776 5799999988764
No 44
>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=60.79 E-value=30 Score=36.55 Aligned_cols=62 Identities=21% Similarity=0.168 Sum_probs=35.2
Q ss_pred HHhhcCCCccc-cccCCeEEEEeccccccCCCCCCCeeEEeecCCccCc------cchHHHHHHHHHHh
Q 004736 75 LTRLRGYSDQM-VEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSR------EEDFFFILHNILAE 136 (732)
Q Consensus 75 v~~~~g~~~~~-~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~r------e~dFF~~l~~~L~~ 136 (732)
+....|.+... -...+.-|+-.|-+.-+=-..+||||+++|.+..-.. ...||..+.+.+.+
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 34455665321 1123689999999999999999999999998743321 13688888876664
No 45
>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=58.98 E-value=8.4 Score=40.32 Aligned_cols=27 Identities=26% Similarity=0.214 Sum_probs=23.1
Q ss_pred eEEEEeccccccCCCCCCCeeEEeecC
Q 004736 91 ALIFTFGSYRLGVHGPGADIDALCVGP 117 (732)
Q Consensus 91 ~kI~~FGSy~lGv~~p~SDIDll~v~P 117 (732)
.-...+||..-|+.+|+||.|+-.|.-
T Consensus 21 l~~~~sGS~a~G~~s~dSD~D~r~vy~ 47 (247)
T PF10127_consen 21 LYACESGSRAYGFASPDSDYDVRGVYI 47 (247)
T ss_pred EEEecccccccCCCCCCcCcccchhcc
Confidence 456678999999999999999987654
No 46
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=58.40 E-value=30 Score=35.07 Aligned_cols=80 Identities=21% Similarity=0.192 Sum_probs=46.7
Q ss_pred CeEEEEeccccc----cCCCCCCCeeEEeecCCccCccchHHHHHHHHHHhcc-CCceEEEeccCccceEEEEecCceee
Q 004736 90 NALIFTFGSYRL----GVHGPGADIDALCVGPSYVSREEDFFFILHNILAEME-EVTELQPVLDAHVPVMKFKFDGLSID 164 (732)
Q Consensus 90 ~~kI~~FGSy~l----Gv~~p~SDIDll~v~P~~v~re~dFF~~l~~~L~~~~-~V~~l~~I~~ArVPIIKf~~~GI~iD 164 (732)
+.+++..|++.+ |.--.+.|||+.+..+.... +.+++..++.... .+ +-+.+ ...-.++++...++.||
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 457899999864 66678999999887764432 2234444332111 11 11111 22334556666899999
Q ss_pred EEeeeccccccc
Q 004736 165 LLYASISRLVVR 176 (732)
Q Consensus 165 Lsfa~l~~~~ip 176 (732)
| +.++....+|
T Consensus 90 l-~~ni~~~~v~ 100 (181)
T PF09970_consen 90 L-LENIGDFYVP 100 (181)
T ss_pred c-hhccCCcccC
Confidence 9 6665555555
No 47
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=58.37 E-value=27 Score=42.56 Aligned_cols=52 Identities=15% Similarity=0.154 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCCCCeeEEeecCCc
Q 004736 54 DEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (732)
Q Consensus 54 ~~~R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~ 119 (732)
.+.|+++.+.-..+++.. +++ .+.-|...|+|+=|=-.|.||||++++.+..
T Consensus 5 ~~~~~~~~~~~~~~~~~~--------~~~------~~~aLvAvGGYGR~EL~P~SDIDLLiL~~~~ 56 (693)
T PRK00227 5 AQLREDAEASALALLGSL--------QLP------PGTALAATGSLARREMTPYSDLDLILLHPPG 56 (693)
T ss_pred HHHHHHHHHHHHHHHHhc--------CCC------CCeEEEEeccccccCcCCCcCceEEEEeCCc
Confidence 345667766666666642 333 2578999999999999999999999999743
No 48
>PRK03059 PII uridylyl-transferase; Provisional
Probab=55.15 E-value=40 Score=41.98 Aligned_cols=54 Identities=24% Similarity=0.369 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCCCCeeEEeecCC
Q 004736 59 QVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPS 118 (732)
Q Consensus 59 ~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~ 118 (732)
+++..+..++.++++..-...+.+ .+.-|+..|+|+=|--.|.||||++++.+.
T Consensus 36 ~~~~~~s~l~d~~l~~~~~~~~~~------~~~alvAvGgyGR~EL~p~SDiDll~l~~~ 89 (856)
T PRK03059 36 ALLHALSRLVDQALRRLWQECGLP------AGAALVAVGGYGRGELFPYSDVDLLVLLPD 89 (856)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCC------CCeEEEEcCCCCCcccCCCCCCEEEEEecC
Confidence 356666666666665543222222 257899999999999999999999999863
No 49
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=53.34 E-value=49 Score=41.47 Aligned_cols=32 Identities=31% Similarity=0.343 Sum_probs=28.5
Q ss_pred CCeEEEEeccccccCCCCCCCeeEEeecCCcc
Q 004736 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYV 120 (732)
Q Consensus 89 ~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v 120 (732)
.+.-|+..|.|+=|--.|.||||++++.+...
T Consensus 77 ~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~ 108 (895)
T PRK00275 77 ADIALVAVGGYGRGELHPYSDIDLLILLDSAD 108 (895)
T ss_pred CCEEEEEcCCccccCcCCCCCceEEEEecCCC
Confidence 35899999999999999999999999987543
No 50
>PRK04374 PII uridylyl-transferase; Provisional
Probab=53.29 E-value=48 Score=41.41 Aligned_cols=55 Identities=18% Similarity=0.245 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCCCCeeEEeecCCc
Q 004736 60 VLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (732)
Q Consensus 60 VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~ 119 (732)
++..+..++.++++.+-.... + ...+.-|+..|+|+=|=-.|.||||++++.+..
T Consensus 47 ~~~~~s~~~D~~l~~~~~~~~-~----~~~~~alvAvGgYGR~EL~p~SDIDLliL~~~~ 101 (869)
T PRK04374 47 LLALRARAVDQLMRNAWTRCI-P----ADSGLSLHAVGGYGRGELFPRSDVDLLVLGETA 101 (869)
T ss_pred HHHHHHHHHHHHHHHHHHHhC-C----CcCCEEEEEcCCccccccCCcccceEEEEecCC
Confidence 444444455555544322222 1 113488999999999999999999999998743
No 51
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=52.83 E-value=53 Score=36.68 Aligned_cols=49 Identities=31% Similarity=0.482 Sum_probs=37.6
Q ss_pred cCCeEEEEeccccccCCCCCCCeeEEeecCCccCccchHHHHHHHHHHhc
Q 004736 88 DANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEM 137 (732)
Q Consensus 88 ~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~re~dFF~~l~~~L~~~ 137 (732)
++++.+..-|||+=| ...+.|||+|+..|..-+.+.-.+..+...|.+.
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 347899999999998 4568999999999876543345677777777764
No 52
>KOG3793 consensus Transcription factor NFAT, subunit NF45 [Transcription]
Probab=52.27 E-value=2.2e+02 Score=31.35 Aligned_cols=212 Identities=17% Similarity=0.198 Sum_probs=106.0
Q ss_pred HHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCCCCe
Q 004736 31 DMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADI 110 (732)
Q Consensus 31 D~~~s~eL~~~L~~~~l~pSeEE~~~R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDI 110 (732)
|-..+++|++ +++++.|+.+|...=-..+.+++.++.+-+. .|+- .-.-..|--.|||..|..+-++|.
T Consensus 38 D~~f~~alLk--RnqdL~P~~~~q~~I~~~vtKV~~vLdn~~~-----~~L~----~~~ieevrqVGSF~k~T~~tg~~~ 106 (362)
T KOG3793|consen 38 DTSFSEALLK--RNQDLAPNSAEQASILSLVTKVNNVLDNLVA-----PGLF----EVQIEEVRQVGSFKKGTMTTGHNV 106 (362)
T ss_pred chHHHHHHHh--hhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-----CCce----EeehhhhhhccceeccccccCCcc
Confidence 6666666655 3358999999877666666666666654321 1221 111245677899999999998886
Q ss_pred -eEEeecCCccCcc--chHHHHHHHHHHhc-c-CCceEEEeccCccceEEEE--e--cCceeeEEeeecccccccccccc
Q 004736 111 -DALCVGPSYVSRE--EDFFFILHNILAEM-E-EVTELQPVLDAHVPVMKFK--F--DGLSIDLLYASISRLVVREDLDI 181 (732)
Q Consensus 111 -Dll~v~P~~v~re--~dFF~~l~~~L~~~-~-~V~~l~~I~~ArVPIIKf~--~--~GI~iDLsfa~l~~~~ipe~l~l 181 (732)
|+|++-.--.+.| ...-.++.+-|+.. + ++-. |-+.+-- + ..-.+-|+++. +|+++.
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 6665543222222 01122233333321 1 1111 1111111 1 12334444443 344332
Q ss_pred ccccccCCCCcccc-cccchhhHHHHHHHhCCCchhHHHHHHHHHHHHHHhCCCCCCCCCcchHHHHH-HHHHHHhhC-C
Q 004736 182 SDMSVLNDVDEPTV-RSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWAL-LVARVCQLY-P 258 (732)
Q Consensus 182 ~~d~lL~~lDe~sv-rSLNG~Rvtd~IlrlVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swai-LVa~icQly-P 258 (732)
.-+++-.||-+-+ ..+-.+|-+.++-+. ......+.++|++|---.+ +-||=-=-.|+| |++++|-+. |
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 1112223333211 122333433333222 2234567788888865443 234422223444 567777553 4
Q ss_pred C---CCHHHHHHHHHHHhhc
Q 004736 259 N---AVPSMLVSRFFRVYTM 275 (732)
Q Consensus 259 n---~s~~~LL~~FF~~Ys~ 275 (732)
+ +.++.-..+||++.+.
T Consensus 245 ~RQ~l~ln~Afrr~~qilaA 264 (362)
T KOG3793|consen 245 TRQPLALNVAYRRCLQILAA 264 (362)
T ss_pred ccccchhhHHHHHHHHHHHh
Confidence 4 3477889999999884
No 53
>PRK03381 PII uridylyl-transferase; Provisional
Probab=51.34 E-value=50 Score=40.69 Aligned_cols=29 Identities=14% Similarity=0.166 Sum_probs=27.0
Q ss_pred CCeEEEEeccccccCCCCCCCeeEEeecC
Q 004736 89 ANALIFTFGSYRLGVHGPGADIDALCVGP 117 (732)
Q Consensus 89 ~~~kI~~FGSy~lGv~~p~SDIDll~v~P 117 (732)
...-|...|+|+-|--.|.||||++++.+
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 54
>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=50.56 E-value=52 Score=40.77 Aligned_cols=31 Identities=26% Similarity=0.389 Sum_probs=27.8
Q ss_pred CCeEEEEeccccccCCCCCCCeeEEeecCCc
Q 004736 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (732)
Q Consensus 89 ~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~ 119 (732)
.+.-|+..|||+=|=-.|.||||++++.+..
T Consensus 42 ~~~aliA~GgyGR~El~p~SDiDll~l~~~~ 72 (850)
T TIGR01693 42 SGIALVAVGGYGRGELAPYSDIDLLFLHDGK 72 (850)
T ss_pred CCeEEEEeCCccccCcCCCCCCeEEEEeCCC
Confidence 3688999999999999999999999998744
No 55
>PRK01293 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=48.23 E-value=40 Score=35.27 Aligned_cols=33 Identities=24% Similarity=0.261 Sum_probs=25.2
Q ss_pred CeEEEEecccc----ccC--CCCCCCeeEEeecCCccCc
Q 004736 90 NALIFTFGSYR----LGV--HGPGADIDALCVGPSYVSR 122 (732)
Q Consensus 90 ~~kI~~FGSy~----lGv--~~p~SDIDll~v~P~~v~r 122 (732)
+...-+|||.. +|+ -.++||||+++..|....+
T Consensus 109 ~~~wgv~GS~g~qlaTGl~~l~~~SDLDLlir~~~~l~~ 147 (207)
T PRK01293 109 GLAWGVTGSAGFELATGIPVLHADSDLDLLIRAPQPLAR 147 (207)
T ss_pred CCceeeehhHHHHHhhCCccccCCCCccEeecCCCcccH
Confidence 46678999975 443 3699999999999876654
No 56
>PF02937 COX6C: Cytochrome c oxidase subunit VIc; InterPro: IPR004204 Cytochrome c oxidase, a 13 subunit complex, 1.9.3.1 from EC is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIc.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3AG4_I 2DYS_V 3ASO_I 2EIK_V 2EIM_I 1OCC_V 1V54_V 1OCO_V 3ASN_V 2EIL_I ....
Probab=46.06 E-value=18 Score=31.96 Aligned_cols=39 Identities=28% Similarity=0.433 Sum_probs=23.3
Q ss_pred ccccchhhHHHH--HHHHhHHHHhhhcCchhhhhHHHhhhhhhcc
Q 004736 683 VVQKPVMRHVLF--IIFGLCLCFILCTNFTLYCSFCWLFGHFYSR 725 (732)
Q Consensus 683 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 725 (732)
.+.||.||.+|. +-+.+..+|++| +-|..+|-|++.-.|
T Consensus 3 ~l~KP~mrgll~~~l~~~i~~a~~ls----~~~~~~~kf~v~~pR 43 (73)
T PF02937_consen 3 ALAKPQMRGLLAKRLKRHIVVAFVLS----LGVAAAYKFGVAEPR 43 (73)
T ss_dssp -------BSHHHHHHHHHHHHHHHHH----HHHHHHHHHHTHHHH
T ss_pred cccCchhhhHHHHHHHHHHHHHHHHH----HHHHHHHHHHHhhHH
Confidence 578999998874 667777777777 457788888886544
No 57
>COG2413 Predicted nucleotidyltransferase [General function prediction only]
Probab=41.60 E-value=43 Score=35.24 Aligned_cols=27 Identities=30% Similarity=0.455 Sum_probs=23.1
Q ss_pred EEEEeccccccCCCCCCCeeEEeecCC
Q 004736 92 LIFTFGSYRLGVHGPGADIDALCVGPS 118 (732)
Q Consensus 92 kI~~FGSy~lGv~~p~SDIDll~v~P~ 118 (732)
.-+.+||.+.|=--|+||+|+.+..|-
T Consensus 39 e~~v~gSvarGDV~p~SDvDV~I~~~v 65 (228)
T COG2413 39 EAVVYGSVARGDVRPGSDVDVAIPEPV 65 (228)
T ss_pred hhEEEeeeeccCcCCCCCceEEEecCC
Confidence 456789999998899999999997753
No 58
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=38.46 E-value=74 Score=40.43 Aligned_cols=48 Identities=19% Similarity=0.169 Sum_probs=37.3
Q ss_pred CCeEEEEeccccccCCCCCCCeeEEeecCCccC-cc---chHHHHHHHHHHh
Q 004736 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVS-RE---EDFFFILHNILAE 136 (732)
Q Consensus 89 ~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~-re---~dFF~~l~~~L~~ 136 (732)
.+.-|+.+|+|+=+=-.+.||||++++...... ++ ..||..+.+.+..
T Consensus 722 ~~~avia~Gk~Gr~EL~~~SDlDl~fl~~~~~~~~~~~~~~~~~rlaq~l~~ 773 (1007)
T PRK14109 722 ARIAVIGMGRLGGRELGYGSDADVMFVHEPAPGADEAEAVRWATAVAEELRR 773 (1007)
T ss_pred CCEEEEEeccccccccCCCCCCcEEEEeCCCCCCCchhHHHHHHHHHHHHHH
Confidence 468999999999999999999999999863211 11 2688888777665
No 59
>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=36.09 E-value=31 Score=26.32 Aligned_cols=31 Identities=19% Similarity=0.429 Sum_probs=24.8
Q ss_pred hHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 004736 35 NRELEKFLVEAGLYESKEEDEKREQVLGRIRQ 66 (732)
Q Consensus 35 s~eL~~~L~~~~l~pSeEE~~~R~~VL~~L~~ 66 (732)
+.+|.++|++.|+..++.. ..|+++|+.+++
T Consensus 6 ~~~L~~wL~~~gi~~~~~~-~~rd~Ll~~~k~ 36 (38)
T PF10281_consen 6 DSDLKSWLKSHGIPVPKSA-KTRDELLKLAKK 36 (38)
T ss_pred HHHHHHHHHHcCCCCCCCC-CCHHHHHHHHHH
Confidence 4689999999998876655 679999888764
No 60
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=35.75 E-value=1.3e+02 Score=38.43 Aligned_cols=48 Identities=13% Similarity=0.066 Sum_probs=36.7
Q ss_pred CCeEEEEeccccccCCCCCCCeeEEeecCCccCcc----chHHHHHHHHHHh
Q 004736 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSRE----EDFFFILHNILAE 136 (732)
Q Consensus 89 ~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~re----~dFF~~l~~~L~~ 136 (732)
.+.-|+.+|+|+-+=-.+.||||++++.+...... ..||..+.+.|..
T Consensus 214 ~~~aviamGklG~~EL~~~SDiDLi~ly~~~~~~~~~~~~~~~~rl~q~l~~ 265 (1007)
T PRK14109 214 VRLAVIAMGKCGARELNYVSDVDVIFVAEPAEGVDEAAALAVATRLASELMR 265 (1007)
T ss_pred CCeEEEEeccccccccCCccCCCEEEEeCCCCCcccccHHHHHHHHHHHHHH
Confidence 46799999999999999999999999986432111 3577777776665
No 61
>COG3541 Predicted nucleotidyltransferase [General function prediction only]
Probab=35.68 E-value=18 Score=38.80 Aligned_cols=21 Identities=33% Similarity=0.366 Sum_probs=18.1
Q ss_pred eccccccCCCCCCCeeEEeec
Q 004736 96 FGSYRLGVHGPGADIDALCVG 116 (732)
Q Consensus 96 FGSy~lGv~~p~SDIDll~v~ 116 (732)
=||+.-|+..|+||+|+=-|.
T Consensus 16 sGS~~yGf~spdSDyDvR~V~ 36 (248)
T COG3541 16 SGSHLYGFPSPDSDYDVRGVH 36 (248)
T ss_pred ccccccCCCCCCCccceeeEE
Confidence 499999999999999995543
No 62
>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=35.23 E-value=55 Score=32.51 Aligned_cols=77 Identities=19% Similarity=0.407 Sum_probs=39.2
Q ss_pred HHHHHHcCCCCCHHHHHHHHHH---HHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCC---CCeeE
Q 004736 39 EKFLVEAGLYESKEEDEKREQV---LGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPG---ADIDA 112 (732)
Q Consensus 39 ~~~L~~~~l~pSeEE~~~R~~V---L~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~---SDIDl 112 (732)
.+.|..+++..-.++...|..| +..+.+++++.+++ + +-.-..||||.+-+--|+ .|||+
T Consensus 10 ~~~l~s~~v~~~~~~~~grh~vS~lV~~V~klmeEyLrr----h----------Nk~CicYGSyslhllN~~I~YgDIDi 75 (149)
T PF03296_consen 10 SDYLNSYNVANPSGKVMGRHNVSDLVENVNKLMEEYLRR----H----------NKSCICYGSYSLHLLNPNIKYGDIDI 75 (149)
T ss_dssp HHHHHHH--S-------------THHHHHHHHHHHHHHH---------------TTTEEEESHHHHHTTSTTS--SS-EE
T ss_pred HHHHHHhcccccCccccccccCcHHHHHHHHHHHHHHHh----h----------CCCeEEeeeeeEEecCCCcccCcchh
Confidence 4667777777666677777664 55556666677654 1 234678999998777665 79999
Q ss_pred EeecCCccCccchHHHHHHHHHH
Q 004736 113 LCVGPSYVSREEDFFFILHNILA 135 (732)
Q Consensus 113 l~v~P~~v~re~dFF~~l~~~L~ 135 (732)
+=... ..|+-.++-++.
T Consensus 76 lqTNa------r~flI~laflI~ 92 (149)
T PF03296_consen 76 LQTNA------RTFLINLAFLIK 92 (149)
T ss_dssp EESTH------HHHHHHHHHHHH
T ss_pred hhccc------HHHHHHHHHHHh
Confidence 75443 256554544444
No 63
>PRK05092 PII uridylyl-transferase; Provisional
Probab=33.56 E-value=1.4e+02 Score=37.63 Aligned_cols=31 Identities=32% Similarity=0.542 Sum_probs=27.8
Q ss_pred CCeEEEEeccccccCCCCCCCeeEEeecCCc
Q 004736 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (732)
Q Consensus 89 ~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~ 119 (732)
.+.-|+..|.|+-|--.|.||||++++.+..
T Consensus 104 ~~~alvA~GgyGr~EL~p~SDiDLl~l~~~~ 134 (931)
T PRK05092 104 ERLAVLAVGGYGRGELAPGSDIDLLFLLPYK 134 (931)
T ss_pred CceEEEEecCcCCcccCCCCCceEEEEeCCC
Confidence 3578999999999999999999999998743
No 64
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=31.80 E-value=1e+02 Score=34.46 Aligned_cols=70 Identities=24% Similarity=0.224 Sum_probs=55.8
Q ss_pred eEEEEeccccccCCCCCCCeeEEeecCCccCccchHHHHHHHHHHhccCCceEEEeccCccceEEEEecCceeeEEeee
Q 004736 91 ALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYAS 169 (732)
Q Consensus 91 ~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~re~dFF~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~ 169 (732)
.++-.-||.|=|-.+ .+|||++|..... . . +.+.|.+++++.++..-.+.+|-++.--..|++||+-.+.
T Consensus 181 ~~~~~aGs~RR~ret-v~DiD~~~s~~~~-~---~----v~~~~~~~~~~~~vi~~G~~k~s~~~~~~~~~svD~r~v~ 250 (326)
T COG1796 181 IQASIAGSLRRGRET-VGDIDILISTSHP-E---S----VLEELLEMPNVQEVIAKGETKVSMLLILDEGTSVDFRVVP 250 (326)
T ss_pred heeeeccchhhcccc-ccceeeEeccCCc-H---H----HHHHHhcCCCcceeeecCCceeeEEEEecCCCeeEEEEcC
Confidence 566777999988776 6899998866421 1 1 5566777899999999999999988888899999998765
No 65
>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=28.67 E-value=24 Score=38.15 Aligned_cols=21 Identities=43% Similarity=0.680 Sum_probs=17.2
Q ss_pred eCChhhhhhhhhHHHHHHHHH
Q 004736 378 AANADDLLAWKGWVESRLRQL 398 (732)
Q Consensus 378 a~~~e~~~~w~GwVESRlR~L 398 (732)
-+|.-+...++||||||+-.+
T Consensus 95 DSn~~EGAVLKGWVESRFGL~ 115 (262)
T PF07357_consen 95 DSNSPEGAVLKGWVESRFGLL 115 (262)
T ss_pred CCCChhhhhhhhhhhhccCcC
Confidence 346778899999999999755
No 66
>PRK11072 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed
Probab=27.34 E-value=1.9e+02 Score=36.72 Aligned_cols=48 Identities=25% Similarity=0.287 Sum_probs=36.5
Q ss_pred CCeEEEEeccccccCCCCCCCeeEEeecCCc-cC----c---cchHHHHHHHHHHh
Q 004736 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSY-VS----R---EEDFFFILHNILAE 136 (732)
Q Consensus 89 ~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~-v~----r---e~dFF~~l~~~L~~ 136 (732)
.+.-|+..|-|+-+=-.+.||||++++.+.. .+ + ...||..+.+.|-.
T Consensus 153 ~~~aViamGKlG~~ELn~~SDIDLifly~~~~~~~~~~~~~~~~~~f~rl~q~li~ 208 (943)
T PRK11072 153 QPLLILGMGKLGGRELNFSSDIDLIFTYPEHGETQGGRRSIDNQQFFTRLGQRLIK 208 (943)
T ss_pred CCEEEEEeccccCccCCCccCCceEEEeCCCCCCCCCcccchHHHHHHHHHHHHHH
Confidence 4688999999999999999999999998743 11 1 13688888776654
No 67
>PHA02603 nrdC.11 hypothetical protein; Provisional
Probab=25.99 E-value=38 Score=37.87 Aligned_cols=25 Identities=28% Similarity=0.307 Sum_probs=21.5
Q ss_pred EEEEeccccccCCCCCCCeeEEeec
Q 004736 92 LIFTFGSYRLGVHGPGADIDALCVG 116 (732)
Q Consensus 92 kI~~FGSy~lGv~~p~SDIDll~v~ 116 (732)
-+-.+||...|+.+|+||+|.--|.
T Consensus 5 ~~~~~GShaYG~~tp~SD~D~rGV~ 29 (330)
T PHA02603 5 MKGLFGSHLYGTSTPESDVDYKGIF 29 (330)
T ss_pred EEEecccceeCCCCCCcccccceee
Confidence 4567999999999999999996654
No 68
>PRK11072 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed
Probab=22.80 E-value=2.5e+02 Score=35.67 Aligned_cols=60 Identities=12% Similarity=0.239 Sum_probs=41.1
Q ss_pred HhhcCCCccc-cccCCeEEEEeccccccCCCCCCCeeEEeecCCc----------cCccchHHHHHHHHHHh
Q 004736 76 TRLRGYSDQM-VEDANALIFTFGSYRLGVHGPGADIDALCVGPSY----------VSREEDFFFILHNILAE 136 (732)
Q Consensus 76 ~~~~g~~~~~-~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~----------v~re~dFF~~l~~~L~~ 136 (732)
+...|.+... ....+.-|+-+|-++-+=-+-+||||++.+.... .. ...||..+.+.|.+
T Consensus 666 ~~~~G~p~~~~~~~~~~aViamGKlGg~EL~y~SDlDlifvy~~~~~~~t~g~~~~~-~~~~~~rl~qrli~ 736 (943)
T PRK11072 666 VKRHGEPPHLEGRERGFAVIGYGKLGGKELGYASDLDLVFLHDCPEDAMTDGDKSID-GRQFYLRLAQRIIH 736 (943)
T ss_pred HHHhCCCCCccCCCCCEEEEeecCccCCccCCcccceEEEEeecCccccCCCCCccc-HHHHHHHHHHHHHH
Confidence 4456765321 1123578999998888888899999999998521 11 14689888887775
No 69
>PRK14108 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=22.69 E-value=4e+02 Score=34.14 Aligned_cols=48 Identities=19% Similarity=0.270 Sum_probs=36.2
Q ss_pred CCeEEEEeccccccCCCCCCCeeEEeecCCcc-C--cc---chHHHHHHHHHHh
Q 004736 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYV-S--RE---EDFFFILHNILAE 136 (732)
Q Consensus 89 ~~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v-~--re---~dFF~~l~~~L~~ 136 (732)
.+.-|+..|-|+-+=-.+.||||++++.+... + +. ..||..+.+.|-.
T Consensus 185 ~~~aViamGklGg~ELn~~SDiDLifly~~~~~~~~~~~~~~~~~~rl~q~li~ 238 (986)
T PRK14108 185 SGLIVLGMGKLGAGELNYSSDIDLIVFFDETAPILGDPIEAQPFFVRLTRRLVR 238 (986)
T ss_pred CCeEEEeeccccccccCCCCCCceEEEeCCCCCCccccchHHHHHHHHHHHHHH
Confidence 35789999999999999999999999987322 1 11 3688887776554
No 70
>KOG2708 consensus Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones]
Probab=21.42 E-value=7.7e+02 Score=26.97 Aligned_cols=83 Identities=19% Similarity=0.302 Sum_probs=52.1
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeccccccCCCCCCCeeEEeec--CCccCc
Q 004736 45 AGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVG--PSYVSR 122 (732)
Q Consensus 45 ~~l~pSeEE~~~R~~VL~~L~~iVk~wv~~v~~~~g~~~~~~~~~~~kI~~FGSy~lGv~~p~SDIDll~v~--P~~v~r 122 (732)
.|+.|.+....+|..+|..+++.+.+ ......|||++|.. |..-..
T Consensus 38 ~GFlP~~TA~HHr~~il~Lv~~al~e--------------------------------a~v~~~diD~icyTKGPGmgaP 85 (336)
T KOG2708|consen 38 EGFLPRDTARHHRAWILGLVKQALEE--------------------------------AGVTSDDIDCICYTKGPGMGAP 85 (336)
T ss_pred CCCCcchhHHHHHHHHHHHHHHHHHH--------------------------------cCCChhhCCEEEEcCCCCCCCc
Confidence 47889999999999999998887764 12336799999964 332211
Q ss_pred cchHHHHHHHHH---HhccC---------CceEEEeccCccceEEEEecC
Q 004736 123 EEDFFFILHNIL---AEMEE---------VTELQPVLDAHVPVMKFKFDG 160 (732)
Q Consensus 123 e~dFF~~l~~~L---~~~~~---------V~~l~~I~~ArVPIIKf~~~G 160 (732)
-.--..+++.| -+.|- |+-=+.|..|.-|++-..-.|
T Consensus 86 -L~~vaivaRtlsllw~kPlv~VNHCigHIEMGR~iTgA~nPvvLYvSGG 134 (336)
T KOG2708|consen 86 -LSVVAIVARTLSLLWNKPLVGVNHCIGHIEMGREITGAQNPVVLYVSGG 134 (336)
T ss_pred -hhhHHHHHHHHHHHhCCCcccchhhhhhhhhcceeccCCCCEEEEEeCC
Confidence 01112233333 33332 233367889999998777654
No 71
>COG1391 GlnE Glutamine synthetase adenylyltransferase [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms]
Probab=20.90 E-value=6.9e+02 Score=31.99 Aligned_cols=47 Identities=23% Similarity=0.294 Sum_probs=30.4
Q ss_pred CeEEEEeccccccCCCCCCCeeEEeecCCccCc------cchHHHHHHHHHHh
Q 004736 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVSR------EEDFFFILHNILAE 136 (732)
Q Consensus 90 ~~kI~~FGSy~lGv~~p~SDIDll~v~P~~v~r------e~dFF~~l~~~L~~ 136 (732)
+..|+--|-..-+=-.=.||||++++.|..-.. ..+||..+.+.|-+
T Consensus 173 ~l~VlgMGKlGa~ELNysSDIDlIf~y~~~~~t~g~~~dn~~fFtRl~qrLIr 225 (963)
T COG1391 173 GLLVLGMGKLGARELNYSSDIDLIFVYPESGPTQGGELDNAEFFTRLGQRLIR 225 (963)
T ss_pred ceEEEeccccCccccccccccceEEEeCCCCCccCCccchHHHHHHHHHHHHH
Confidence 455555554444333457999999998865433 13599888776664
Done!