Query 005429
Match_columns 697
No_of_seqs 253 out of 762
Neff 4.9
Searched_HMMs 46136
Date Thu Mar 28 23:18:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005429.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005429hhsearch_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 3E-142 6E-147 1150.6 41.3 491 1-500 1-501 (562)
2 PTZ00418 Poly(A) polymerase; P 100.0 9E-135 2E-139 1128.4 53.1 485 10-498 46-541 (593)
3 COG5186 PAP1 Poly(A) polymeras 100.0 3E-122 6E-127 963.5 33.4 478 13-495 4-525 (552)
4 PF04928 PAP_central: Poly(A) 100.0 1.9E-73 4.2E-78 587.1 21.2 254 13-362 1-254 (254)
5 COG5260 TRF4 DNA polymerase si 100.0 5.6E-31 1.2E-35 287.3 24.7 265 31-347 54-342 (482)
6 PF04926 PAP_RNA-bind: Poly(A) 100.0 4.2E-32 9.1E-37 261.0 9.2 135 363-498 1-156 (157)
7 KOG1906 DNA polymerase sigma [ 100.0 1.2E-28 2.6E-33 273.9 24.4 268 28-347 57-341 (514)
8 cd05402 NT_PAP_TUTase Nucleoti 99.8 7.1E-19 1.5E-23 159.5 13.4 110 56-210 1-113 (114)
9 KOG2277 S-M checkpoint control 99.8 6.6E-17 1.4E-21 184.0 22.7 253 47-348 125-431 (596)
10 TIGR03671 cca_archaeal CCA-add 99.6 1.3E-12 2.9E-17 143.3 34.7 343 39-461 3-364 (408)
11 PRK13300 tRNA CCA-pyrophosphor 99.6 1.7E-12 3.6E-17 144.3 31.6 346 38-461 3-367 (447)
12 COG1746 CCA1 tRNA nucleotidylt 99.2 1.5E-09 3.3E-14 118.8 23.0 346 36-461 5-368 (443)
13 PF03813 Nrap: Nrap protein; 99.2 9.8E-09 2.1E-13 124.4 29.3 341 98-460 1-425 (972)
14 KOG2054 Nucleolar RNA-associat 98.3 1.8E-05 3.8E-10 94.2 17.4 292 90-392 147-479 (1121)
15 smart00572 DZF domain in DSRM 98.3 3.9E-05 8.5E-10 80.0 17.0 213 93-346 5-230 (246)
16 cd05400 NT_2-5OAS_ClassI-CCAas 97.8 0.00019 4.1E-09 67.7 11.2 77 90-169 27-110 (143)
17 PF03828 PAP_assoc: Cid1 famil 97.6 3.7E-05 7.9E-10 62.7 2.6 56 261-319 1-59 (60)
18 cd05397 NT_Pol-beta-like Nucle 97.5 0.00012 2.7E-09 58.2 4.8 26 90-115 17-42 (49)
19 PF01909 NTP_transf_2: Nucleot 97.4 0.00022 4.8E-09 61.8 5.0 32 90-121 14-45 (93)
20 PF09249 tRNA_NucTransf2: tRNA 97.4 0.00058 1.3E-08 63.6 7.6 93 221-335 3-97 (114)
21 PF03813 Nrap: Nrap protein; 97.3 0.0021 4.5E-08 79.0 14.0 156 201-361 669-839 (972)
22 cd05403 NT_KNTase_like Nucleot 97.0 0.0012 2.7E-08 56.6 5.0 32 90-121 18-49 (93)
23 PF14091 DUF4269: Domain of un 96.1 0.058 1.3E-06 53.0 10.7 118 93-237 18-145 (152)
24 PF07528 DZF: DZF domain; Int 95.5 0.53 1.2E-05 49.7 16.0 207 96-345 2-231 (248)
25 COG1669 Predicted nucleotidylt 95.3 0.072 1.6E-06 48.7 7.7 46 58-119 8-53 (97)
26 COG1708 Predicted nucleotidylt 94.6 0.19 4.1E-06 45.3 8.4 28 90-117 26-53 (128)
27 PRK13746 aminoglycoside resist 94.3 0.084 1.8E-06 56.1 6.2 32 91-122 29-60 (262)
28 PF10421 OAS1_C: 2'-5'-oligoad 94.1 0.078 1.7E-06 53.9 5.3 47 214-260 41-88 (190)
29 cd00141 NT_POLXc Nucleotidyltr 92.9 1.4 3E-05 47.8 12.7 113 89-241 159-277 (307)
30 PRK02098 phosphoribosyl-dephos 91.6 0.36 7.7E-06 50.2 6.0 33 90-122 120-158 (221)
31 TIGR03135 malonate_mdcG holo-A 90.8 0.43 9.3E-06 48.9 5.7 33 90-122 108-146 (202)
32 PF14792 DNA_pol_B_palm: DNA p 88.6 1.9 4E-05 40.2 7.6 52 89-141 23-77 (112)
33 KOG2054 Nucleolar RNA-associat 88.1 2.9 6.2E-05 51.6 10.5 124 202-330 806-936 (1121)
34 cd05401 NT_GlnE_GlnD_like Nucl 87.6 2.8 6E-05 40.9 8.5 48 89-136 54-101 (172)
35 COG1665 Predicted nucleotidylt 84.3 0.18 3.8E-06 53.8 -1.8 26 94-119 125-150 (315)
36 PF03445 DUF294: Putative nucl 82.4 10 0.00022 36.4 9.5 49 88-136 47-96 (138)
37 KOG3793 Transcription factor N 79.3 33 0.00072 37.1 12.7 212 31-275 38-264 (362)
38 COG2844 GlnD UTP:GlnB (protein 71.7 15 0.00032 45.0 8.6 58 61-122 41-98 (867)
39 PF10620 MdcG: Phosphoribosyl- 69.2 8.5 0.00018 39.8 5.3 32 90-121 116-153 (213)
40 PF03281 Mab-21: Mab-21 protei 68.4 1.6E+02 0.0036 31.1 15.0 93 214-339 190-288 (292)
41 smart00483 POLXc DNA polymeras 68.1 66 0.0014 35.4 12.3 31 89-120 163-193 (334)
42 PRK05007 PII uridylyl-transfer 67.4 21 0.00045 44.4 9.0 56 60-119 54-109 (884)
43 PRK08609 hypothetical protein; 66.7 27 0.00058 41.3 9.4 108 90-241 175-283 (570)
44 PRK01759 glnD PII uridylyl-tra 61.7 29 0.00064 42.9 8.9 56 60-119 30-85 (854)
45 PF09970 DUF2204: Nucleotidyl 60.0 28 0.00061 35.0 7.0 80 90-176 16-100 (181)
46 PRK00227 glnD PII uridylyl-tra 57.4 32 0.00069 41.7 8.0 65 55-135 6-70 (693)
47 PRK01293 phosphoribosyl-dephos 57.2 20 0.00043 37.2 5.4 44 90-135 109-158 (207)
48 KOG2534 DNA polymerase IV (fam 56.0 48 0.001 36.7 8.2 49 88-137 169-217 (353)
49 PF03710 GlnE: Glutamate-ammon 55.9 36 0.00077 35.8 7.2 62 75-136 111-179 (247)
50 PF10127 Nuc-transf: Predicted 54.7 11 0.00025 39.1 3.3 27 91-117 21-47 (247)
51 PRK03059 PII uridylyl-transfer 49.8 56 0.0012 40.5 8.6 54 59-118 36-89 (856)
52 PRK00275 glnD PII uridylyl-tra 49.5 62 0.0013 40.4 8.9 57 60-120 52-108 (895)
53 PRK04374 PII uridylyl-transfer 47.3 68 0.0015 39.9 8.8 55 60-119 47-101 (869)
54 TIGR01693 UTase_glnD [Protein- 47.3 64 0.0014 39.8 8.6 31 89-119 42-72 (850)
55 PRK03381 PII uridylyl-transfer 46.5 67 0.0014 39.4 8.4 30 89-118 56-85 (774)
56 COG2413 Predicted nucleotidylt 44.7 40 0.00087 35.2 5.2 28 91-118 38-65 (228)
57 PF03296 Pox_polyA_pol: Poxvir 40.5 39 0.00084 33.2 4.2 78 38-135 9-92 (149)
58 PF10281 Ish1: Putative stress 39.4 26 0.00056 26.5 2.3 31 35-66 6-36 (38)
59 PRK14109 bifunctional glutamin 37.6 80 0.0017 40.0 7.4 48 89-136 722-773 (1007)
60 COG3541 Predicted nucleotidylt 37.1 16 0.00035 38.8 1.2 20 96-115 16-35 (248)
61 PRK14109 bifunctional glutamin 35.9 1.3E+02 0.0028 38.2 8.8 48 89-136 214-265 (1007)
62 COG1796 POL4 DNA polymerase IV 31.4 1E+02 0.0023 34.1 6.1 70 91-169 181-250 (326)
63 PF07357 DRAT: Dinitrogenase r 30.5 22 0.00047 38.2 0.8 21 378-398 95-115 (262)
64 PHA02603 nrdC.11 hypothetical 30.4 28 0.00061 38.6 1.7 25 92-116 5-29 (330)
65 PRK05092 PII uridylyl-transfer 29.8 1.8E+02 0.0039 36.5 8.6 30 89-118 104-133 (931)
66 PRK11072 bifunctional glutamin 24.7 2.2E+02 0.0049 35.9 8.2 48 89-136 153-208 (943)
67 COG1391 GlnE Glutamine synthet 23.0 6.3E+02 0.014 32.1 11.1 47 90-136 173-225 (963)
68 PRK11072 bifunctional glutamin 22.9 2.6E+02 0.0055 35.4 8.2 60 76-136 666-736 (943)
69 PRK14108 bifunctional glutamin 20.4 7.9E+02 0.017 31.4 11.7 48 89-136 185-238 (986)
No 1
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=100.00 E-value=3e-142 Score=1150.58 Aligned_cols=491 Identities=54% Similarity=0.942 Sum_probs=465.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCcCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 005429 1 MSSSERMSSPPPPKQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRG 80 (697)
Q Consensus 1 ~~~~~~~~s~~~~~~~Gvt~Pis~~~Pt~~D~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g 80 (697)
|.+.. +......+.||||+|||+++||++|+++|.+|+++|+++|+||++||..+|++||++|++||++|++++++++|
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 33333479999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccccCCeEEEEeeeccccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEecC
Q 005429 81 YSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDG 160 (697)
Q Consensus 81 ~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~G 160 (697)
+++++..+++++|+||||||||||+||||||+|||+|+|++|+ |||..|.++|+++++|++|++|++|+||||||+|+|
T Consensus 80 ~p~~~~~~aggkIftfGSYRLGVhg~GADIDtLcV~Prhv~R~-DFF~sf~~mL~~~~eVteL~~V~dAfVPiikfKf~G 158 (562)
T KOG2245|consen 80 LPDGMIENAGGKIFTFGSYRLGVHGPGADIDTLCVGPRHVSRS-DFFTSFYDMLKERPEVTELHAVEDAFVPIIKFKFDG 158 (562)
T ss_pred CChhhhhhcCceEEeccceeecccCCCCCcceeeeccccccHH-HHHHHHHHHHhcCccccccccccccccceEEEEecC
Confidence 9999999999999999999999999999999999999999996 999999999999999999999999999999999999
Q ss_pred eeeeEEeeeccccccccccccccccccCCCCcccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCc
Q 005429 161 LSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGF 240 (697)
Q Consensus 161 I~iDLsfa~l~~~~ip~~l~l~~d~~L~~lDe~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~ 240 (697)
|+|||+||+++.+.+|++|||.||++|+||||+|+||||||||||+||+|||+.+.||.+|||||+|||+||||+|.+||
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 005429 241 LGGVNWALLVARVCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCM 320 (697)
Q Consensus 241 LGG~swaLLVa~vcQl~Pn~s~~~LL~~FF~~Ys~wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~ 320 (697)
|||++|||||||+|||||||+++.||.+||.+|++|+||+||+|++++++.|++++|||+.|++||+|+||||||+||+|
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 005429 321 NSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTL 400 (697)
Q Consensus 321 Nsa~nVs~stlrvI~~EF~Ra~~Il~~i~~~~~~W~~Lf~p~~Ff~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~ 400 (697)
|++||||+||+++|.+||+||.+||++|+.++.+|++|||+++||.+|||||+|+++|.++|++.+|.||||||+|+|+.
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 HhhhcccCceeeccCCCCCCCCCCC----CceeEEEEeeeeCCCCccCCCceecchHHHHHHHHHHh----hccccCCc-
Q 005429 401 MIERDTYGKLQCHPYPHEYVDTSKP----CAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSIN----MYMFWKPG- 471 (697)
Q Consensus 401 ~LE~~~~~~l~ahp~P~~f~~~~~~----~~~~~ffIGL~~~~~~~~~~~~~~dl~~~v~eF~~~i~----~~~~~~~~- 471 (697)
+||+.. +++.|||+|+.|.++... .+...|||||.+.++ .++||+..+++|...++ ..+.+.+|
T Consensus 399 klE~~~-~i~~ahp~P~~f~~~~~~~~~~~~~~~~~igl~~~e~------~~~Dlt~~iq~f~~~v~~q~~~~~~~~~g~ 471 (562)
T KOG2245|consen 399 KLERNQ-VILIAHPNPKKFKDTYNCPLEEDPESLWFIGLEFDEN------VKIDLTKDIQSFKKNVERQAVNLTLIKAGC 471 (562)
T ss_pred HHHhhc-ceEEecCCcccccccccCCcccchhHhhhhccccccc------ccchhhhhHHHhhhhhhhcceeeeeeeccc
Confidence 999954 678899999999876532 346689999987754 34999999999999887 55677899
Q ss_pred -eEEEEEeeccCCCCCCcCCCCccccCCCc
Q 005429 472 -MEICVSHIRRKQIPPYVFPEGYKRTRHPR 500 (697)
Q Consensus 472 -m~i~v~~vkr~~LP~~v~~~g~~~~~~~~ 500 (697)
|.+.+.|+||++|+.+++++++++.|.-+
T Consensus 472 ~~~~~~~~~krr~l~~~~~~~~l~~~k~~~ 501 (562)
T KOG2245|consen 472 DVEIDFGHVKRRSLIQTITKEFLRLCKQYK 501 (562)
T ss_pred ccccccccccccccccccCHHHhhHHHhhc
Confidence 77778899999999999999887765543
No 2
>PTZ00418 Poly(A) polymerase; Provisional
Probab=100.00 E-value=9.2e-135 Score=1128.37 Aligned_cols=485 Identities=42% Similarity=0.786 Sum_probs=460.0
Q ss_pred CCCCCCCCCCCCCcCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccC
Q 005429 10 PPPPKQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDA 89 (697)
Q Consensus 10 ~~~~~~~Gvt~Pis~~~Pt~~D~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~ 89 (697)
..++++||||+|||+++||++|++.+.+|+++|+++|+|||+||.++|++||++|+++|++|+++++.++|++++++.++
T Consensus 46 ~~~~~~~Gvt~Pis~~~Pt~~d~~~s~~L~~~L~~~~~fes~ee~~kR~~vL~~L~~iv~~wv~~vs~~k~~~~~~~~~~ 125 (593)
T PTZ00418 46 IECALSYGVTDPISLNGPTEEDLKLSNELINLLKSYNLYETEEGKKKRERVLGSLNKLVREFVVEASIEQGINEEEASQI 125 (593)
T ss_pred cCcccccCCCCCccCCCCChHHHhhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhHHhcC
Confidence 34678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEEeeeccccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEecCeeeeEEeee
Q 005429 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYAS 169 (697)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~ 169 (697)
+++|+|||||+||||+|+||||+|||+|.|++|+ +||..|+++|++.++|++|++|++|+||||||+++||+|||+||+
T Consensus 126 ~g~I~tfGSYrLGV~~pgSDID~L~V~P~~vtre-dFF~~f~~~L~~~~~V~eL~~V~~A~VPiIk~~~~GI~iDL~fa~ 204 (593)
T PTZ00418 126 SGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRE-SFFSDFYAKLQQDPNITKLQPVPDAYTPVIKFVYDGIDIDLLFAN 204 (593)
T ss_pred CeEEEEeccccccCCCCCCcccEEEECCCCCCHH-HHHHHHHHHHhcCCCcceeeccCccccCeEEEEECCEEEeeeecc
Confidence 9999999999999999999999999999999996 999999999999999999999999999999999999999999999
Q ss_pred cccccccccccccccc-ccCCCCcccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHH
Q 005429 170 ISRLVVREDLDISDMS-VLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWAL 248 (697)
Q Consensus 170 l~~~~ip~~l~l~~d~-~L~~lDe~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaL 248 (697)
++...+|+++++.+|+ +|++||++++||||||||+|+|+++||+.+.||.+|||||+|||+||||+|++||||||+|||
T Consensus 205 l~~~~vp~~~~~l~d~~lL~nlde~s~rSLNG~Rvtd~Il~lVPn~~~Fr~aLR~IKlWAkrRGIYsNv~GflGGV~wAI 284 (593)
T PTZ00418 205 LPLPTIPDCLNSLDDDYILRNVDEKTVRSLNGCRVADLILASVPNKDYFRTTLRFIKLWAKRRGIYSNVLGYLGGVSWAI 284 (593)
T ss_pred cCCCCCCccccccCchhhhhcCCHHHhhhhccHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccccccccccchHHHHH
Confidence 9999999999988886 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHHhhcCCCCCceeeccccc-----ccCCcccccCCCCCCCCCCceEEeCCCCCCCCcc
Q 005429 249 LVARVCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDE-----AELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSS 323 (697)
Q Consensus 249 LVa~vcQl~Pn~s~~~LL~~FF~~Ys~wdW~~pV~l~~i~~-----g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa 323 (697)
||||+||+|||+++++||.+||.+|++|+||+||+|+++++ |.+++++|||+.|++|++|+||||||+||+||+|
T Consensus 285 LvARVCQLyPna~~s~Lv~~FF~iys~W~Wp~PV~L~~i~~~~~~~g~~~~~VWdPr~~~~dr~h~MPIITPayP~mNst 364 (593)
T PTZ00418 285 LTARICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKEVPNIPGLMNFKVWDPRVNPQDRAHLMPIITPAFPSMNST 364 (593)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCCCeEcccccccccCCcccCCcccCCCCCcccccccCCeecCCCCCcccc
Confidence 99999999999999999999999999999999999998875 6688999999999999999999999999999999
Q ss_pred CccCHhHHHHHHHHHHHHHHHHHHhhh-cCCCccccccccchhhhcccEEEEEEEeCChhhhhhhhhhhHhhHHHHHHHh
Q 005429 324 YNVSTSTLRVMMDQFQYGNTICEEVEL-NKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMI 402 (697)
Q Consensus 324 ~nVs~stlrvI~~EF~Ra~~Il~~i~~-~~~~W~~Lf~p~~Ff~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~L 402 (697)
||||.+|+++|++||+||++|++++.. ++.+|++||+|++||.+|++||+|++.+.+++++..|.||||||||.|+.+|
T Consensus 365 ~nVt~sT~~vI~~Ef~Ra~~i~~~i~~~~~~~W~~Lfep~~Ff~~Yk~yl~V~v~a~~~~~~~~w~G~VESRlR~Lv~~L 444 (593)
T PTZ00418 365 HNVTYTTKRVITEEFKRAHEIIKYIEKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKKL 444 (593)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHcCCcchhhhcceEEEEEEEECCHHHhhhhhhHHHHHHHHHHHHh
Confidence 999999999999999999999999988 8899999999999999999999999999999999999999999999999999
Q ss_pred hhcccCceeeccCCCCCCCCCC-CCceeEEEEeeeeCCCCccCCCceecchHHHHHHHHHHhhcc---ccCCceEEEEEe
Q 005429 403 ERDTYGKLQCHPYPHEYVDTSK-PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSINMYM---FWKPGMEICVSH 478 (697)
Q Consensus 403 E~~~~~~l~ahp~P~~f~~~~~-~~~~~~ffIGL~~~~~~~~~~~~~~dl~~~v~eF~~~i~~~~---~~~~~m~i~v~~ 478 (697)
|+. +.+.+||||++|.+... ..|.++|||||.++.+.. .+..++||+.++++|.+.|++|. .|.++|||+|+|
T Consensus 445 E~~--~~i~~~p~P~~f~~~~~~~~~~~~ffIGL~~~~~~~-~~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~~i~v~~ 521 (593)
T PTZ00418 445 ETL--NNLKIRPYPKFFKYQDDGWDYASSFFIGLVFFSKNV-YNNSTFDLRYAIRDFVDIINNWPEMEKYPDQIDINIKY 521 (593)
T ss_pred hcc--CCceEeecCcccccCCCCceeEEEEEEeEeeccCCC-CCCceEecHHHHHHHHHHHHhhhhcccCCCCceEEEEE
Confidence 974 34678999999988763 356789999999876543 23358999999999999999886 367889999999
Q ss_pred eccCCCCCCcCCCCccccCC
Q 005429 479 IRRKQIPPYVFPEGYKRTRH 498 (697)
Q Consensus 479 vkr~~LP~~v~~~g~~~~~~ 498 (697)
||+++||++||++|++|+..
T Consensus 522 Vk~~~Lp~~v~~~~~~~~~~ 541 (593)
T PTZ00418 522 LKKSQLPAFVLSQTPEEPVK 541 (593)
T ss_pred eehHhCCHhhccCCCcCCCc
Confidence 99999999999999877443
No 3
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=100.00 E-value=2.7e-122 Score=963.51 Aligned_cols=478 Identities=42% Similarity=0.755 Sum_probs=457.2
Q ss_pred CCCCCCCCCCcCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeE
Q 005429 13 PKQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANAL 92 (697)
Q Consensus 13 ~~~~Gvt~Pis~~~Pt~~D~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~ 92 (697)
.++||||+|||+.+.|+++.+++.+|+++|++.|+|+++.|.+.|.+||++|+.++++|+.++++.+|+.+.|+.+++++
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 EEEeeeccccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEecCeeeeEEeeeccc
Q 005429 93 IFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISR 172 (697)
Q Consensus 93 I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~ 172 (697)
|++|||||||||+||||||++||.|+|++|+ |||+.|..+|++.++++++.+|++|+||||||+|.||+|||.||+++.
T Consensus 84 IFTyGSYRLGVhgpGsDIDtLvvVPkHVsR~-dFFt~f~~~Lrer~ei~eva~vpDAfVPIIK~KF~GIsIDLifARLs~ 162 (552)
T COG5186 84 IFTYGSYRLGVHGPGSDIDTLVVVPKHVSRS-DFFTHFYEELRERPEIEEVAKVPDAFVPIIKLKFQGISIDLIFARLSI 162 (552)
T ss_pred eeeecceeeeccCCCCCcceEEEecccccHH-HHHHHHHHHhccCcchhhhccCCcccceeEEEEecCccceeeeeeccC
Confidence 9999999999999999999999999999996 999999999999999999999999999999999999999999999999
Q ss_pred cccccccccccccccCCCCcccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHH
Q 005429 173 LVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVAR 252 (697)
Q Consensus 173 ~~ip~~l~l~~d~~L~~lDe~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~ 252 (697)
+.+|..|+++|+++|++|||+|++||||.||+|+||++||+...|+.+||+||+||++|.||.|.+||.||++|+|||||
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 005429 253 VCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLR 332 (697)
Q Consensus 253 vcQl~Pn~s~~~LL~~FF~~Ys~wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~stlr 332 (697)
+||||||++...++.+||+++++|+||+||+|+||++|++..++|||+.|++|+.|.||||||+||+||.+||||.||..
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 005429 333 VMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQC 412 (697)
Q Consensus 333 vI~~EF~Ra~~Il~~i~~~~~~W~~Lf~p~~Ff~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~a 412 (697)
+|..||-||.+|+++|+.+..+|..||+..+||.+||+||.|++.+.++|++.+|.|+||||+|.|+.+||... +++.|
T Consensus 323 vIl~EfvRa~~I~~di~~n~~~w~~lFek~DFF~RYk~yleitA~s~~~E~~lKW~GlvESKiR~Lv~klE~vd-~i~~A 401 (552)
T COG5186 323 VILMEFVRAHKILSDIERNALDWRRLFEKSDFFSRYKLYLEITAMSSCEEDFLKWEGLVESKIRILVSKLEAVD-DILYA 401 (552)
T ss_pred hHHHHHHHHHHhhhhHhhccccHHHHHHhhhHHHHHhHhhhhhhhhcchhhhhhhhhHHHHHHHHHHHHHHHhh-hhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999754 56889
Q ss_pred ccCCCCCCCCC----------------------------------C---------CCceeEEEEeeeeCCCCccCCCcee
Q 005429 413 HPYPHEYVDTS----------------------------------K---------PCAHCAFFMGLQRKPGEVVQEGQQF 449 (697)
Q Consensus 413 hp~P~~f~~~~----------------------------------~---------~~~~~~ffIGL~~~~~~~~~~~~~~ 449 (697)
||||+.|...- . ..|-+.|||||+.... ..++++
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 235689
Q ss_pred cchHHHHHHHHHHhhcccc-CCceEEEEEeeccCCCCCCcCCCCccc
Q 005429 450 DIRGSVEEFKLSINMYMFW-KPGMEICVSHIRRKQIPPYVFPEGYKR 495 (697)
Q Consensus 450 dl~~~v~eF~~~i~~~~~~-~~~m~i~v~~vkr~~LP~~v~~~g~~~ 495 (697)
||..+++||.+.++.|+++ ..+|.|.|+.+|+++||+-||.+|+.|
T Consensus 479 di~~p~~EF~elcr~~d~gd~~~mni~v~~~K~~dlpdeVF~~geer 525 (552)
T COG5186 479 DIEQPVKEFIELCREYDEGDASGMNIEVNSLKRKDLPDEVFYPGEER 525 (552)
T ss_pred eeeccHHHHHHHHHHhhccccceeeeehhhccccCCchhhcCCCccC
Confidence 9999999999999999654 578999999999999999999988765
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=1.9e-73 Score=587.10 Aligned_cols=254 Identities=59% Similarity=1.048 Sum_probs=204.1
Q ss_pred CCCCCCCCCCcCCCCCHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeE
Q 005429 13 PKQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANAL 92 (697)
Q Consensus 13 ~~~~Gvt~Pis~~~Pt~~D~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~ 92 (697)
.++||||+|||+++||+.|++.+++|+++|++++++||+||.++|++||++|++++++|+++
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 37899999999999999999999999999999999999999999999999999999999863
Q ss_pred EEEeeeccccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEecCeeeeEEeeeccc
Q 005429 93 IFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISR 172 (697)
Q Consensus 93 I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~ 172 (697)
..
T Consensus 63 ------------------------------------------------------------------------------~~ 64 (254)
T PF04928_consen 63 ------------------------------------------------------------------------------AL 64 (254)
T ss_dssp ------------------------------------------------------------------------------SS
T ss_pred ------------------------------------------------------------------------------hh
Confidence 45
Q ss_pred cccccccccccccccCCCCcccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHH
Q 005429 173 LVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVAR 252 (697)
Q Consensus 173 ~~ip~~l~l~~d~~L~~lDe~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~ 252 (697)
..+|+++++.++++|++||++|++||||+||+++|+++||+.+.||.++|+||+|||+||||+|++||||||+||||||+
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 005429 253 VCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLR 332 (697)
Q Consensus 253 vcQl~Pn~s~~~LL~~FF~~Ys~wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~stlr 332 (697)
+||+|||+++++||.+||.+|++|+|++||+|+++.++.+++++|+|+.|++|++|+||||||+||+||+|+|||.+|++
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 99999999999999999999999999999999999988899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCcccccccc
Q 005429 333 VMMDQFQYGNTICEEVELNKAQWSALFEPY 362 (697)
Q Consensus 333 vI~~EF~Ra~~Il~~i~~~~~~W~~Lf~p~ 362 (697)
+|++||+||+++++++..++.+|++||+|+
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=5.6e-31 Score=287.30 Aligned_cols=265 Identities=21% Similarity=0.257 Sum_probs=211.3
Q ss_pred HHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCCCCe
Q 005429 31 DMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADI 110 (697)
Q Consensus 31 D~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDI 110 (697)
...++.+|.++.. .+.|+.+|.++|.+.|++|++++++- ++ .+.+++|||+.+|+++|+|||
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--YIAPSDEELKRRKALLEKLRTLLKKE--------------FP--DADLKVFGSTETGLALPKSDI 115 (482)
T ss_pred HHHHHHHHHHHHH--hhCCCHHHHHHHHHHHHHHHHHHHHh--------------CC--ccceeEecccccccccCcccc
Confidence 4466667777775 48899999999999999999999853 23 469999999999999999999
Q ss_pred eEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEe--cCeeeeEEeeeccccccccccccccccccC
Q 005429 111 DALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKF--DGLSIDLLYASISRLVVREDLDISDMSVLN 188 (697)
Q Consensus 111 D~l~v~P~~v~re~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~--~GI~iDLsfa~l~~~~ip~~l~l~~d~~L~ 188 (697)
|++++.+.....+..--..++..|.......++.+|..|+||||||.. .|+.|||+|++.
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 999999776665421112455555555567789999999999999998 699999999983
Q ss_pred CCCcccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHHHHhhCCC---------
Q 005429 189 DVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPN--------- 259 (697)
Q Consensus 189 ~lDe~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~vcQl~Pn--------- 259 (697)
+|++.|..++.++-.++++|+|+.+||+||++|.++++.+|+|+||++++||..++|++|.
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 6889999999999999999999999999999999999999999999999999999999971
Q ss_pred ---------CCHHHHHHHHHHHhh-cCCCCCceeecccccccCC--cccccCCCCCCCCCCceEEeCCC-CCCCCccCcc
Q 005429 260 ---------AVPSMLVSRFFRVYT-MWRWPNPVMLCAIDEAELG--FSVWDPRKNRRDKTHHMPIITPA-YPCMNSSYNV 326 (697)
Q Consensus 260 ---------~s~~~LL~~FF~~Ys-~wdW~~pV~l~~i~~g~lg--~~~W~p~~~~~dr~~~MpIiTP~-~P~~Nsa~nV 326 (697)
.+++.|+..||++|+ .|+|..-++...-++--+. .+.|--... ...++|++|. .+..++ ..
T Consensus 248 ~~l~~~~~~~~lgvLf~dFf~~yG~~f~Y~~~~~si~~g~~~~~K~e~g~~~~~~----p~~LsiqdP~td~n~~~--~a 321 (482)
T COG5260 248 SPLKYNKNIDNLGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPKYEKGWLKPSK----PNSLSIQDPGTDRNNDI--SA 321 (482)
T ss_pred chhhccccccccchHHHHHHHHhccccChhheEEEecCCceeeehhhcccccccC----CCcEeecCCCCCccccc--cc
Confidence 258999999999999 5999875554332211111 134432111 2679999999 554433 33
Q ss_pred CHhHHHHHHHHHHHHHHHHHH
Q 005429 327 STSTLRVMMDQFQYGNTICEE 347 (697)
Q Consensus 327 s~stlrvI~~EF~Ra~~Il~~ 347 (697)
..-+++.|+.+|.+|.+++.+
T Consensus 322 ~s~~ik~i~~~F~~aF~lls~ 342 (482)
T COG5260 322 VSFNIKDIKAAFIRAFELLSN 342 (482)
T ss_pred ccchHHHHHHHHHHHHHHHhh
Confidence 345799999999999999987
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=4.2e-32 Score=260.96 Aligned_cols=135 Identities=36% Similarity=0.714 Sum_probs=104.9
Q ss_pred chhhhcccEEEEEEEeCChhhhhhhhhhhHhhHHHHHHHhhhcccCceeeccCCCCCC------------------CCCC
Q 005429 363 LFFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYV------------------DTSK 424 (697)
Q Consensus 363 ~Ff~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~------------------~~~~ 424 (697)
+||.+|||||+|+|++.+++++.+|.||||||||.||.+||+.. ++..|||||++|. +...
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 005429 425 PCAHCAFFMGLQRKPGEVVQEGQQFDIRGSVEEFKLSINMYMF---WKPGMEICVSHIRRKQIPPYVFPEGYKRTRH 498 (697)
Q Consensus 425 ~~~~~~ffIGL~~~~~~~~~~~~~~dl~~~v~eF~~~i~~~~~---~~~~m~i~v~~vkr~~LP~~v~~~g~~~~~~ 498 (697)
..+.++|||||++........++++||+.++++|++.|++|.. +.++|+|+|+|||+++||++||++|.+|+++
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 3578899999999876543344679999999999999999754 6688999999999999999999999888654
No 7
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=99.96 E-value=1.2e-28 Score=273.95 Aligned_cols=268 Identities=22% Similarity=0.308 Sum_probs=211.6
Q ss_pred CHHHHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCC
Q 005429 28 TEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPG 107 (697)
Q Consensus 28 t~~D~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~ 107 (697)
.+.=..++++++.+++ .+.||.+|.+.|.+++++++..|++- + ..+.|++||||.+|+++|+
T Consensus 57 ~~~s~~l~~eI~~fv~--~l~pt~~e~~~R~~~~~~i~~~v~~~--------------~--~~a~v~~FGS~~tglyLP~ 118 (514)
T KOG1906|consen 57 NLVSERLRNEILDFVQ--YLIPTPEEIEVRSELVEKIRDVVKQK--------------W--PDASVYVFGSVPTGLYLPD 118 (514)
T ss_pred chhHHHHHHHHHHHHH--HhcCCchHHHHHHHHHHHHHHHHHHh--------------c--ccceeEEeeeeeccccccc
Confidence 4455566777888876 48999999999999999999988721 2 3699999999999999999
Q ss_pred CCeeEEeecCCccCchhhHHHHHHHHHHh--ccCCceEEEeccCccceEEEEe--cCeeeeEEeeecccccccccccccc
Q 005429 108 ADIDALCVGPSYVSREEDFFFILHNILAE--MEEVTELQPVLDAHVPVMKFKF--DGLSIDLLYASISRLVVREDLDISD 183 (697)
Q Consensus 108 SDID~l~v~P~~v~re~dFf~~l~~~L~~--~~~V~~l~~I~~ArVPIIKf~~--~GI~iDLsfa~l~~~~ip~~l~l~~ 183 (697)
||||+++..+....++ +.+..+.-++.. ...-..+..|..|+||||||+. .+|.|||+|++
T Consensus 119 sDIDl~v~~~~~~~~e-~~~~~~~l~~~~e~~~~~~~v~~v~karvpiik~~d~~s~i~vDISFn~-------------- 183 (514)
T KOG1906|consen 119 SDIDLVVLSKFLNDKE-DRAVKLELALELEEDNSAFHVKVVQKARVPIIKFKDPVSNIHVDISFNQ-------------- 183 (514)
T ss_pred cceEEEEecccccCch-hhHHHHHHHHhhhhccccceEEEeeeeeeeeEEeecCccceEEEeeecc--------------
Confidence 9999999999777664 555555444443 2233468889999999999996 79999999998
Q ss_pred ccccCCCCcccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHHHHhhCCCC---
Q 005429 184 MSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPNA--- 260 (697)
Q Consensus 184 d~~L~~lDe~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~vcQl~Pn~--- 260 (697)
.|||+.++.|..++-+.+.+|.++.++|+|...|++++..+|+++||++++||+.++|++|..
T Consensus 184 --------------~~G~~aa~~i~~~~~~~p~~~~lvlvlk~fl~~r~ln~v~tGgisSyal~~Lv~~fl~l~~~~~s~ 249 (514)
T KOG1906|consen 184 --------------TNGVKAAKFIKDFLRDHPFLRSLVLVLKQFLYERRLNGVHTGGISSYALELLVLSFLQLHPRSKSG 249 (514)
T ss_pred --------------cCchhHHHHHHHHHhcCccchhHHHHHHHHHHhhcccccccccchHHHHHHHHHHHHhhcccccCC
Confidence 478999999999999999999999999999999999999999999999999999999999864
Q ss_pred ------CHHHHHHHHHHHhh-cCCCCC-ceeecccccccCC--cccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhH
Q 005429 261 ------VPSMLVSRFFRVYT-MWRWPN-PVMLCAIDEAELG--FSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTST 330 (697)
Q Consensus 261 ------s~~~LL~~FF~~Ys-~wdW~~-pV~l~~i~~g~lg--~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~st 330 (697)
.++.||.+||++|+ +|.+.. -|.+....+ ..+ ...|- .+...+...+.|+||..|..+.++.- .+
T Consensus 250 ~~~~~~~~~vll~~f~e~yG~~f~~~k~~i~~~~~g~-~~~~~~~~~~--~~~~~~~~~LsieDP~~P~ndigr~s--~~ 324 (514)
T KOG1906|consen 250 RLAVLKNLGVLLIKFFELYGRNFGYDKLGISLSLGGE-YVSKELTGFF--NNSLERPGSLSIEDPVDPTNDIGRSS--FN 324 (514)
T ss_pred ccchhcccchHHHHHHHHhccccCchhhceeccCCcc-cccHHhhhhh--cccccCCCccccCCCCCccccccccc--cc
Confidence 37889999999999 566654 233222111 111 11121 12223456799999999976665322 46
Q ss_pred HHHHHHHHHHHHHHHHH
Q 005429 331 LRVMMDQFQYGNTICEE 347 (697)
Q Consensus 331 lrvI~~EF~Ra~~Il~~ 347 (697)
+..|+.+|..|+..+..
T Consensus 325 ~~~v~~~F~~af~~l~~ 341 (514)
T KOG1906|consen 325 FSQVKGAFAYAFKVLTN 341 (514)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 88999999999988765
No 8
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
Probab=99.80 E-value=7.1e-19 Score=159.55 Aligned_cols=110 Identities=39% Similarity=0.751 Sum_probs=97.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCCCCeeEEeecCCc-cCchhhHHHHHHHHH
Q 005429 56 KREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY-VSREEDFFFILHNIL 134 (697)
Q Consensus 56 ~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~-v~re~dFf~~l~~~L 134 (697)
.|++++++|++++++|. .++++++|||+++|+++|+||||+++..|.. ... ..++..+.+.|
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 3589999999999999999999999999986 333 58999999999
Q ss_pred HhccCCceEEEeccCccceEEEEec--CeeeeEEeeeccccccccccccccccccCCCCcccccccchhhHHHHHHHh
Q 005429 135 AEMEEVTELQPVLDAHVPVMKFKFD--GLSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKL 210 (697)
Q Consensus 135 ~~~~~V~~l~~I~~ArVPIIKf~~~--GI~iDLsfa~l~~~~ip~~l~l~~d~~L~~lDe~s~rSLNG~Rvtd~Il~l 210 (697)
++...+.++..|.+|+||||||.+. |++|||+|++ .||++++++|..+
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 9988788999999999999999997 9999999997 4788888887765
No 9
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=99.75 E-value=6.6e-17 Score=183.99 Aligned_cols=253 Identities=22% Similarity=0.297 Sum_probs=190.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCCCCeeEEeecCCc-cCc---
Q 005429 47 LYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY-VSR--- 122 (697)
Q Consensus 47 l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~-v~r--- 122 (697)
..+...+...|...+..++.++..-+ +.....+..|||..+|+....+|+|+++..... ..-
T Consensus 125 ~~~~~~~~~~~~~~~~~l~~~~~~~~--------------p~~~~~~~~~gs~~~~~~~~~~d~d~~~~~~~~~~~~~~~ 190 (596)
T KOG2277|consen 125 FKLPHSDVKTRKLILDKLRALASLLF--------------PDSILSLYLFGSSDLGLGERSSDLDLCVDFTSSFLSFEKI 190 (596)
T ss_pred cCCCccccchHHHHHHHHHHHHHHhc--------------CCCcceeeccCcccccccccccCcceeecccccccccchh
Confidence 33555666677777777777776432 222334789999999999999999943333222 110
Q ss_pred -hhhHHHHHHHHHHhccC--CceEEEeccCccceEEEEe--cCeeeeEEeeeccccccccccccccccccCCCCcccccc
Q 005429 123 -EEDFFFILHNILAEMEE--VTELQPVLDAHVPVMKFKF--DGLSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRS 197 (697)
Q Consensus 123 -e~dFf~~l~~~L~~~~~--V~~l~~I~~ArVPIIKf~~--~GI~iDLsfa~l~~~~ip~~l~l~~d~~L~~lDe~s~rS 197 (697)
...++..+.+.|....+ +..++.|..|+||||||.+ .++++|+++.+..
T Consensus 191 ~~~~~~~l~~~~~~~~~~~~~~~~~~i~~A~vPiik~~~~~~~~~~d~s~~n~~-------------------------- 244 (596)
T KOG2277|consen 191 KGLEILKLLAKCLASLLEEGVREVQQILSARVPIIKFNDSGSGLECDLSVNNSD-------------------------- 244 (596)
T ss_pred hhHHHHHHHHHHHHhccccccceeeeeeecCCCEEEecCCCCCCceeeeeccch--------------------------
Confidence 13456667777877543 7889999999999999965 5899999988632
Q ss_pred cchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccc-hHHHHHHHHHHHhhCCCC----------------
Q 005429 198 LNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLG-GVNWALLVARVCQLYPNA---------------- 260 (697)
Q Consensus 198 LNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LG-G~swaLLVa~vcQl~Pn~---------------- 260 (697)
|.+++..+..+...+.+|++|...||+||+++++++...|.+. +|++++||++++|.++..
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 3455666666666778999999999999999999999999998 699999999999986310
Q ss_pred ---------------------------CHHHHHHHHHHHhh-cCCCCCceeecccccccCCcccccCCCCCCCCCCceEE
Q 005429 261 ---------------------------VPSMLVSRFFRVYT-MWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPI 312 (697)
Q Consensus 261 ---------------------------s~~~LL~~FF~~Ys-~wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpI 312 (697)
+++.|+..||.||+ .|||++-++-...... +. ..|. ......+.|
T Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~f~~yy~~~Fdf~~~~I~~r~~~~-l~-~~~~-----~~~~~~l~i 395 (596)
T KOG2277|consen 323 KPVVKKKVLCSFLRVFQRNPSNSQNTGSLGELLLGFFSYYASLFDFRKNAISIRRGRA-LK-RAKK-----IKSKKFLCI 395 (596)
T ss_pred ccchhhhhhhccccccccccccccccchHHHHHHHHHHHHhhhcccccceeeeeeccc-cc-ccch-----hhhccceee
Confidence 25689999999999 7999986553322111 11 0011 112346899
Q ss_pred eCCCCCCCCccCccCHhHHHHHHHHHHHHHHHHHHh
Q 005429 313 ITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEV 348 (697)
Q Consensus 313 iTP~~P~~Nsa~nVs~stlrvI~~EF~Ra~~Il~~i 348 (697)
.+|+....|.+..++...+..|+.+|+....++...
T Consensus 396 ~dp~~~~~n~~~~~~~~~~~~i~~~~~~~~~~~~~~ 431 (596)
T KOG2277|consen 396 EDPFEVSHNADAGVTLKVLLLIQDEFQESRRVFKDV 431 (596)
T ss_pred ccccccccCccccchHHHHHHHHHHHHHHHHHhhhh
Confidence 999999999999999999999999999999998875
No 10
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=99.62 E-value=1.3e-12 Score=143.25 Aligned_cols=343 Identities=20% Similarity=0.247 Sum_probs=209.6
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCC-CCCeeEEeecC
Q 005429 39 EKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGP-GADIDALCVGP 117 (697)
Q Consensus 39 ~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p-~SDID~l~v~P 117 (697)
.+.|+. +-||+||.++-+.+.++|...+++++++. ...++++.|||++=|.+++ +||||++++.|
T Consensus 3 ~~vl~~--i~Ps~eE~~~~~~~~~~l~~~l~~~~~e~------------~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~ 68 (408)
T TIGR03671 3 EEVLER--IKPTEEEREKLKKVADELIARLEEIIEEL------------GVDAEVVLVGSYARGTWLKGDRDIDIFILFP 68 (408)
T ss_pred HHHhhh--cCCCHHHHHHHHHHHHHHHHHHHHHHHhc------------CCcceEEEEeeEecCCccCCCCceeEEEEeC
Confidence 445553 77999999999999999999888876531 1247999999999999999 99999999999
Q ss_pred CccCchhhHH---HHHHHHHHhc-cCCceEEEeccCccceEEEEecCeeeeEEeeeccccccccccccccc-cccCCCCc
Q 005429 118 SYVSREEDFF---FILHNILAEM-EEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDM-SVLNDVDE 192 (697)
Q Consensus 118 ~~v~re~dFf---~~l~~~L~~~-~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~~ip~~l~l~~d-~~L~~lDe 192 (697)
....++ ++= ..+...+.+. +... ..-|--|-++..+.|+++||.=|- ++.+. .+...+|-
T Consensus 69 ~~~~~e-~l~~~gl~i~~~~~~~~~~~~----~~yaeHpYv~~~~~G~~VDiVPcy----------~v~~g~~~~taVDR 133 (408)
T TIGR03671 69 KDTSRE-ELEEYGLEIGHEVLKRGGNYE----ERYAEHPYVSGEIEGFEVDVVPCY----------KVESGEEIISAVDR 133 (408)
T ss_pred CCCCHH-HHHHHHHHHHHHHHhhCCCHh----heeccCceEEEEEccEEEEEEeeE----------EccCcCeeeccccC
Confidence 887764 332 1222222221 1111 357778999999999999997442 22222 12222221
Q ss_pred ccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCC--ccCccchHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 005429 193 PTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSN--VTGFLGGVNWALLVARVCQLYPNAVPSMLVSRFF 270 (697)
Q Consensus 193 ~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn--~~G~LGG~swaLLVa~vcQl~Pn~s~~~LL~~FF 270 (697)
. ..-+++++.... +.|+..+|++|.|+|.-|+|++ +.++++||..-||++++ -+...++..
T Consensus 134 t-------p~H~~fv~~rl~--~~~~d~VRLlK~f~k~igvYGsE~~~~GFSGYl~ELLv~~y------G~F~~~l~~-- 196 (408)
T TIGR03671 134 T-------PFHTRYVLERLD--GKLRDDVRLLKQFLKGIGVYGSELKTRGFSGYLCELLVIHY------GSFENVLKA-- 196 (408)
T ss_pred c-------hHHHHHHHHhhh--hhHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHh------CCHHHHHHH--
Confidence 1 122466665543 3488999999999999999955 57889999999999995 122333322
Q ss_pred HHhhcCCCCCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHHHHHHHHHHHHHHhhh
Q 005429 271 RVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVEL 350 (697)
Q Consensus 271 ~~Ys~wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~stlrvI~~EF~Ra~~Il~~i~~ 350 (697)
.+ +|..++.+.....+ .. .-.+++.|+||.+|..|+|..+|..++..+...-+++. .+
T Consensus 197 --a~--~wk~~~~id~~~~~--------~~----~f~~PlvViDPvDp~RNVAaalS~~~~~~fv~aar~fl---~~--- 254 (408)
T TIGR03671 197 --AS--KWKPGVVIDIEEHG--------TK----KFDDPLVVIDPVDPKRNVAAALSLENLARFILAARMFL---KN--- 254 (408)
T ss_pred --HH--hcCCCeEEecCccc--------cc----cCCCCEEEeCCCCCcchHHHHcCHHHHHHHHHHHHHHH---HC---
Confidence 23 34556666332111 11 12468999999999999999999888877765443332 22
Q ss_pred cCCCcccccccc-----ch---hhhcc-cEEEEEEEeCChhhhhhhhhhhHhhHHHHHHHhhhcccCceeeccCCCCCCC
Q 005429 351 NKAQWSALFEPY-----LF---FESYR-NYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYVD 421 (697)
Q Consensus 351 ~~~~W~~Lf~p~-----~F---f~~Yk-~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~~ 421 (697)
+=..+|.|. ++ +.+-. +.+.|..-.++.-+= ..-|-++--.+.|...||+.....+....| .+
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 11 12222 334444433442222 334666666777777788765444444444 22
Q ss_pred CCCCCceeEEEEeeeeCCCC--ccCCCceecchHHHHHHHHH
Q 005429 422 TSKPCAHCAFFMGLQRKPGE--VVQEGQQFDIRGSVEEFKLS 461 (697)
Q Consensus 422 ~~~~~~~~~ffIGL~~~~~~--~~~~~~~~dl~~~v~eF~~~ 461 (697)
. -.|..++=|....-. ....|.++.-+.-...|.+.
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 124455555433211 11234456555667788863
No 11
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=99.59 E-value=1.7e-12 Score=144.27 Aligned_cols=346 Identities=20% Similarity=0.244 Sum_probs=207.4
Q ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCC-CCCeeEEeec
Q 005429 38 LEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGP-GADIDALCVG 116 (697)
Q Consensus 38 L~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p-~SDID~l~v~ 116 (697)
+.+.|+. +-||+||.++-.++.+.|...+++++.+ .+ ..++++.+|||+-|.|++ +||||++++.
T Consensus 3 ~~evl~~--i~Ps~eE~~~l~~~~~~l~~~L~~~~~~----~~--------~~~~V~l~GS~ArgT~L~GdsDIDIFv~f 68 (447)
T PRK13300 3 LEEVLER--IKPTEEEREKLKKVAEELIERLEEAIKE----LG--------LDAEVELVGSTARGTWLSGDRDIDIFVLF 68 (447)
T ss_pred HHHHHHh--cCCCHHHHHHHHHHHHHHHHHHHHHHHh----cC--------CceEEEEEeeecCCcccCCCCceeEEEEe
Confidence 3455554 7899999999999999998888887643 22 138999999999999999 7899999999
Q ss_pred CCccCchhhH----HHHHHHHHHhccCCceEEEeccCccceEEEEecCeeeeEEeeeccccccccccccccc-cccCCCC
Q 005429 117 PSYVSREEDF----FFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDM-SVLNDVD 191 (697)
Q Consensus 117 P~~v~re~dF----f~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~~ip~~l~l~~d-~~L~~lD 191 (697)
|....++ ++ .......++..-.-.+++ -|--|-++..+.|+++||.=|- ++.+. .+...+|
T Consensus 69 p~~~~~e-~L~~~gl~i~~~~~~~~~~~~~~~---yaeHpyv~~~~~G~~VDiVPcy----------~v~~~~~~~saVD 134 (447)
T PRK13300 69 PKDTSRE-ELEEKGLEIGKEVAKELLGDYEER---YAEHPYVTGEIDGFEVDIVPCY----------KVESGEEIISAVD 134 (447)
T ss_pred CCCCCHH-HHHHHHHHHHHHHHHhhCCcceee---eccCceEEEEECCEEEEEEeeE----------EccCcCccccccc
Confidence 9887764 22 112223333311112333 4888999999999999998542 22221 1222222
Q ss_pred cccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCC--ccCccchHHHHHHHHHHHhhCCCCCHHHHHHHH
Q 005429 192 EPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSN--VTGFLGGVNWALLVARVCQLYPNAVPSMLVSRF 269 (697)
Q Consensus 192 e~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn--~~G~LGG~swaLLVa~vcQl~Pn~s~~~LL~~F 269 (697)
-. ..-+++|+..+- +.++..+|++|.|+|.-|+|++ +.++++||..-||++++ -+-..++..+
T Consensus 135 Rt-------p~H~~fv~~rl~--~~~~d~VRLlK~f~k~~gvYGsE~k~~GFSGYl~ELLv~~y------G~F~~~l~~a 199 (447)
T PRK13300 135 RT-------PFHTKYVKERLK--GKLEDEVRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHY------GSFENVLKAA 199 (447)
T ss_pred Cc-------hHHHHHHHHhhh--hhHHHHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHh------CCHHHHHHHH
Confidence 11 123567766553 3488999999999999999955 57899999999999995 2233333332
Q ss_pred HHHhhcCCCCCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHHHHHHHHHHHHHHhh
Q 005429 270 FRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVE 349 (697)
Q Consensus 270 F~~Ys~wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~stlrvI~~EF~Ra~~Il~~i~ 349 (697)
++| .-++.+...+.+ .. ....+++.|+||.+|..|+|.++|..++..+... |..-+.+
T Consensus 200 ----~~w--~~~~~I~~~~~~--------~~---~~f~~PlvViDPvDp~RNVAaa~S~~~~~~fv~a---ar~fL~~-- 257 (447)
T PRK13300 200 ----SKW--KPPVKIDLEKHG--------KE---YKFDDPLVVIDPVDPNRNVAAALSLENLATFILA---AREFLKN-- 257 (447)
T ss_pred ----HhC--CCCceEeccccC--------cc---ccCCCCEEEeCCCCCcchHHHHcCHHHHHHHHHH---HHHHHhC--
Confidence 334 434554332111 00 0124689999999999999999998887766542 2223332
Q ss_pred hcCCCccccccccc-----h---hhh-cccEEEEEEEeCChhhhhhhhhhhHhhHHHHHHHhhhcccCceeeccCCCCCC
Q 005429 350 LNKAQWSALFEPYL-----F---FES-YRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEYV 420 (697)
Q Consensus 350 ~~~~~W~~Lf~p~~-----F---f~~-Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~ 420 (697)
+=..+|.|.+ + +.+ =.+.+.|..-.++.-+= ..-|-++--.+.|...||+.....+.... |.
T Consensus 258 ----Ps~~fF~~~~~~~~~~~~~l~~R~t~~~~v~f~~p~~v~D-il~pQl~r~~~~i~~~L~~~gF~v~~~~~----~~ 328 (447)
T PRK13300 258 ----PSLEFFFPSDLSPEEILEELERRGTTVLALEFPRPDIVED-ILYPQLERSLRSIVKLLEREGFEVLRSGA----WA 328 (447)
T ss_pred ----CCHHhcCCCCCChHHHHHHHhhcCceEEEEEeCCCCCCcc-chhHHHHHHHHHHHHHHHHCCCEEEEeee----ec
Confidence 1223333333 1 111 12444555544442222 33466666677777778876544343322 22
Q ss_pred CCCCCCceeEEEEeeeeCC--CCccCCCceecchHHHHHHHHH
Q 005429 421 DTSKPCAHCAFFMGLQRKP--GEVVQEGQQFDIRGSVEEFKLS 461 (697)
Q Consensus 421 ~~~~~~~~~~ffIGL~~~~--~~~~~~~~~~dl~~~v~eF~~~ 461 (697)
+ . -.|..++=|.... .-....|.++....-...|.+.
T Consensus 329 d-~---~~~~l~~el~~~~lp~~~~h~GPpv~~~~~a~~F~~k 367 (447)
T PRK13300 329 D-E---DRAYLLLELEVAELPNVKLHIGPPVWVREHAENFIEK 367 (447)
T ss_pred C-C---CeEEEEEEeecccCCCeeeeeCCCcCchhhHHHHHHH
Confidence 2 1 2344444444221 1111223445555557788763
No 12
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=99.22 E-value=1.5e-09 Score=118.75 Aligned_cols=346 Identities=19% Similarity=0.190 Sum_probs=204.0
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCC-CCCeeEEe
Q 005429 36 RELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGP-GADIDALC 114 (697)
Q Consensus 36 ~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p-~SDID~l~ 114 (697)
..|.+.|+. +.||+||.++=+++.+.|...+++.+ +++|+ .+.+..+||++=|.|++ +.|||+.|
T Consensus 5 ~~l~evl~~--i~P~~eE~~~~~~~~e~l~~~~~~~~----~e~~~--------~aev~lVGS~AkgTwL~gd~DIDvFi 70 (443)
T COG1746 5 EVLEEVLKR--IKPTEEERKKLKEVAEELRERINEII----EELGI--------DAEVVLVGSYAKGTWLRGDHDIDVFI 70 (443)
T ss_pred HHHHHHHHH--cCCCHHHHHHHHHHHHHHHHHHHHHH----HhcCC--------cceEEEEeecccCcccCCCcceeEEE
Confidence 345666664 67999999888888888877777654 34443 58899999999999999 67999999
Q ss_pred ecCCccCchhhH----HHHHHHHHHhccCCceEEEeccCccceEEEEecCeeeeEEeeeccccccccccccccccccCCC
Q 005429 115 VGPSYVSREEDF----FFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDMSVLNDV 190 (697)
Q Consensus 115 v~P~~v~re~dF----f~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~l~~~~ip~~l~l~~d~~L~~l 190 (697)
..|....++ .. +......|.+. =-.+.-|-=|-+.-.+.|+++|+.=|-... -+ ..+...+
T Consensus 71 ~Fp~d~~~e-el~~~GL~ig~~~l~~~-----~~~~~YAeHPYV~g~v~G~eVDvVPCy~v~--~~-------~~~~sAV 135 (443)
T COG1746 71 AFPKDTSEE-ELEEKGLEIGREVLKRG-----NYEERYAEHPYVTGEVDGYEVDVVPCYKVE--DG-------EKIISAV 135 (443)
T ss_pred ECCCCCCHH-HHHHHHHHHHHHHhcCC-----chhhhhccCCeeEEEEccEEEEEEeccccc--Cc-------ccccccc
Confidence 999987764 12 12223333320 112457777999999999999998554211 01 1122222
Q ss_pred CcccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCc--cCccchHHHHHHHHHHHhhCCCCCHHHHHHH
Q 005429 191 DEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNV--TGFLGGVNWALLVARVCQLYPNAVPSMLVSR 268 (697)
Q Consensus 191 De~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~--~G~LGG~swaLLVa~vcQl~Pn~s~~~LL~~ 268 (697)
| |+.- =+.++..-+-... +.=+|++|.+.|.=|+|++- .++++||.--||+++|= .
T Consensus 136 D----RTpl---Ht~yv~e~L~~~~--~deVrLLK~FlK~iGvYGaE~rt~GFSGYL~ELLII~yG-------------s 193 (443)
T COG1746 136 D----RTPL---HTRYVEEHLKGRQ--KDEVRLLKQFLKGIGVYGAELRTQGFSGYLCELLIIHYG-------------S 193 (443)
T ss_pred c----Ccch---hHHHHHHHhcccc--hhHHHHHHHHHhccCccceeeeeccchHHHHHHHHhhhc-------------c
Confidence 2 1111 1345555443321 23479999999999999975 78999999999999872 2
Q ss_pred HHHHhhcC-CCCCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHHHHHHHHHHHHHH
Q 005429 269 FFRVYTMW-RWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEE 347 (697)
Q Consensus 269 FF~~Ys~w-dW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~stlrvI~~EF~Ra~~Il~~ 347 (697)
|-..--.. +|.-+++|..- .|..... ...+|.|+||.+|..|+|.+||..++..+. -|.+..-+
T Consensus 194 Fe~vl~~a~~wrp~~~ID~~--------~~~~e~f---~d~PliVvDPVDP~RNVAAalSl~~la~f~----~aar~FL~ 258 (443)
T COG1746 194 FENVLKAASRWRPGKIIDLE--------GHKRERF---EDEPLIVVDPVDPKRNVAAALSLENLARFV----HAAREFLK 258 (443)
T ss_pred HHHHHHHHhccCCCeEEecc--------chhhhcc---CCCCeEecCCCCCccchhhhcCHHHHHHHH----HHHHHHhc
Confidence 33333322 38877777541 2211222 123899999999999999999987765543 33222211
Q ss_pred hhhcCCCcccccccc---c-----hhhhcccEEEEEEEeCChhhhhhhhhhhHhhHHHHHHHhhhcccCceeeccCCCCC
Q 005429 348 VELNKAQWSALFEPY---L-----FFESYRNYLQVDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEY 419 (697)
Q Consensus 348 i~~~~~~W~~Lf~p~---~-----Ff~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f 419 (697)
.+=.+.|.|. . ...+=.+-+.|.+-..+.-+ ...-|-++---+.|...||......+..+.|
T Consensus 259 -----~PS~efF~p~~~~~~~~~~~~~rgt~v~~l~~~~pd~vd-DilypQl~r~~~~l~r~Le~~gF~vl~~~~~---- 328 (443)
T COG1746 259 -----NPSPEFFFPRKPKPLLLSKLRRRGTHVLALVFPKPDLVD-DILYPQLERTARSLFRALEEEGFRVLRSGVW---- 328 (443)
T ss_pred -----CCChhhcCCCCcCcccccchhhcCceEEEEEeCCCCCCc-chhhHHHHHHHHHHHHHHHHcCCEEeeeeee----
Confidence 1222233221 1 11111233333333344322 2344777777778888888765444444333
Q ss_pred CCCCCCCceeEEEEeeeeCCCC--ccCCCceecchHHHHHHHHH
Q 005429 420 VDTSKPCAHCAFFMGLQRKPGE--VVQEGQQFDIRGSVEEFKLS 461 (697)
Q Consensus 420 ~~~~~~~~~~~ffIGL~~~~~~--~~~~~~~~dl~~~v~eF~~~ 461 (697)
.|... ++.-|+=+....-. ....+.++.-..+++ |.+.
T Consensus 329 ~D~~~---~~~v~~E~~~~~l~~i~~r~GPp~~~e~a~r-F~~k 368 (443)
T COG1746 329 SDESE---RIYVLLELESKELPRIELRVGPPVWTEHAVR-FIEK 368 (443)
T ss_pred ecCCc---ceEEEEEEecccccceeeecCCCccchhHHH-HHHh
Confidence 23221 34445555432211 011133344466766 7763
No 13
>PF03813 Nrap: Nrap protein; InterPro: IPR005554 Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus []. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [].
Probab=99.17 E-value=9.8e-09 Score=124.41 Aligned_cols=341 Identities=15% Similarity=0.223 Sum_probs=206.7
Q ss_pred eccccCcC---CCCCeeEEeecCCccCchhhH------------HHHHHHHH--HhccCCceEEEe---ccCccceEEEE
Q 005429 98 SYRLGVHG---PGADIDALCVGPSYVSREEDF------------FFILHNIL--AEMEEVTELQPV---LDAHVPVMKFK 157 (697)
Q Consensus 98 Sy~lGv~~---p~SDID~l~v~P~~v~re~dF------------f~~l~~~L--~~~~~V~~l~~I---~~ArVPIIKf~ 157 (697)
||.++... ++-.||+.+.-|..+-.++|| ...++..| .+...+.++... .+.+-|||.+.
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 56666555 466999999999866554443 23456667 223333344333 67888999999
Q ss_pred ec-----C------eeeeEEeeeccccccccc-c-----------------------ccccccccCCCCcccccccchhh
Q 005429 158 FD-----G------LSIDLLYASISRLVVRED-L-----------------------DISDMSVLNDVDEPTVRSLNGCR 202 (697)
Q Consensus 158 ~~-----G------I~iDLsfa~l~~~~ip~~-l-----------------------~l~~d~~L~~lDe~s~rSLNG~R 202 (697)
-. + +.|-|..+.... .+|.. | ...|..+|.++- -..
T Consensus 81 p~~~~~~~~~~~~~~~iRi~~~~~~~-~F~~~rl~P~rnnvR~~~~~~~~~~~~~pTP~YNssIL~D~~--------~~~ 151 (972)
T PF03813_consen 81 PKGKKDSDDFSKTKFRIRIIPSIPSD-TFPLSRLAPSRNNVRPSWFDEEDSSSLPPTPHYNSSILEDML--------MEE 151 (972)
T ss_pred ECCccccccccCCcEEEEEEecCCcc-cCCHHhcCCCCCccCcCcccccccCCCCCCCcchHHHHHHHh--------HHH
Confidence 42 2 445554443111 11110 0 011222222210 011
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCc-cCccchHHHHHHHHHHHhh---------CCCCCHHHHHHHHHHH
Q 005429 203 VADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNV-TGFLGGVNWALLVARVCQL---------YPNAVPSMLVSRFFRV 272 (697)
Q Consensus 203 vtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~-~G~LGG~swaLLVa~vcQl---------~Pn~s~~~LL~~FF~~ 272 (697)
-..++.+.....+.|+.+++++|.||++||+.+.. .|++||+-|+||+++.+|- .+..+.-+|+..+..|
T Consensus 152 ~l~~l~~~~~~~p~f~dA~iLlkvWl~QRg~~~~~~~~Gf~~f~~s~lla~Ll~~g~~~~~~~l~~~mSsyQlFr~~l~f 231 (972)
T PF03813_consen 152 HLKYLHEASKSSPAFRDACILLKVWLRQRGFGSGISQGGFGGFEWSMLLAYLLQGGGRNGKKKLSKSMSSYQLFRAVLQF 231 (972)
T ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHhcCCCCcccCCCCcchHHHHHHHHHHHcCCCccCCcccCCCCCHHHHHHHHHHH
Confidence 23344455556799999999999999999998875 5889999999999999986 3456788999999999
Q ss_pred hhcCCC-CCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHHHHHHHHHHHHHHhhhc
Q 005429 273 YTMWRW-PNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELN 351 (697)
Q Consensus 273 Ys~wdW-~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~stlrvI~~EF~Ra~~Il~~i~~~ 351 (697)
.+..|| .+|+.++...+.......|. ..+....++|. -.+|.+++++.++++.|+.|-+++.+++++-.
T Consensus 232 LA~~d~~~~~l~~~~~~~~~~~~~~~~-------~~~~~vf~D~s-g~~Nl~~~ms~~s~~~L~~eA~~tl~lL~~~~-- 301 (972)
T PF03813_consen 232 LATTDLSKKPLFFKSSSDSTESLEEFH-------SAFDPVFVDPS-GGLNLLAKMSPSSYEELQHEAKLTLELLDDSS-- 301 (972)
T ss_pred HhccccccCceEEecCCCccchhhhhh-------ccCCeEEEeCC-CCEEEEEcCCHHHHHHHHHHHHHHHHHhcccc--
Confidence 999999 66899876542111111111 23455666664 56899999999999999999999999998632
Q ss_pred CCCccccc-cc-cchhhhcccEEEEE---EEe----CChhhhhhhhhhhHhhHHHHHHH-hhhcccCceeeccC---CCC
Q 005429 352 KAQWSALF-EP-YLFFESYRNYLQVD---IVA----ANADDLLAWKGWVESRLRQLTLM-IERDTYGKLQCHPY---PHE 418 (697)
Q Consensus 352 ~~~W~~Lf-~p-~~Ff~~Yk~yl~I~---v~a----~~~e~~~~w~GwVESRlR~Lv~~-LE~~~~~~l~ahp~---P~~ 418 (697)
....+.+| .+ ..+..+|.+++.|. ... ....+...|...+..++-.|+.+ |..... .++++ +.+
T Consensus 302 ~d~F~~lFl~~~~~~~~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lL~raLgdR~~---~i~v~~~~~~~ 378 (972)
T PF03813_consen 302 DDGFDSLFLTKVDPPALRFDHVLRISPDSLLSSFSPDESLDFLSFSNYLLRKIYRLLKRALGDRAK---LIRVLRPSQPP 378 (972)
T ss_pred ccchhhhhcccCCcccccCCEEEEEcchhhcccccccccccccchhHHHHHHHHHHHHHHHHHHHH---eEEEeCCCCCC
Confidence 34577777 44 46778999999991 111 11233344444566677666643 543221 23333 122
Q ss_pred CCCCCC--CCceeEEEEeeeeCCCCc---cCCCceecchHHHHHHHH
Q 005429 419 YVDTSK--PCAHCAFFMGLQRKPGEV---VQEGQQFDIRGSVEEFKL 460 (697)
Q Consensus 419 f~~~~~--~~~~~~ffIGL~~~~~~~---~~~~~~~dl~~~v~eF~~ 460 (697)
+.-... ........|||..+.... ..-|-..|-.....+|++
T Consensus 379 w~i~~~~~~~~~~~l~vGl~ln~~~~~r~vd~GP~a~d~~ea~~FR~ 425 (972)
T PF03813_consen 379 WSISSKPPKSKPKTLTVGLILNPENAFRLVDRGPSAEDKEEAAAFRE 425 (972)
T ss_pred cccCCCCCCCCCceEEEEEEEchhhceeeeeeCcCCcCcHHHHHHHH
Confidence 211111 111226889998875211 001111233456677776
No 14
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=98.30 E-value=1.8e-05 Score=94.23 Aligned_cols=292 Identities=17% Similarity=0.199 Sum_probs=172.2
Q ss_pred CeEEE-EeeeccccC-cCCCCCeeEEeecCCccCchhhH------------HHHHHHHHHhccCCceEEEe---ccCccc
Q 005429 90 NALIF-TFGSYRLGV-HGPGADIDALCVGPSYVSREEDF------------FFILHNILAEMEEVTELQPV---LDAHVP 152 (697)
Q Consensus 90 ~~~I~-~FGSy~lGv-~~p~SDID~l~v~P~~v~re~dF------------f~~l~~~L~~~~~V~~l~~I---~~ArVP 152 (697)
.+++. ..||+.+|. ..|+.-+|+++..|+..-...|+ +..+...|.+.+....+... .+-.-|
T Consensus 147 p~~v~~vv~sal~~~~~~P~i~vDvll~mP~e~~~~kd~ln~Ryf~kra~yla~~~~hl~e~l~~~~~~f~~~n~d~~~p 226 (1121)
T KOG2054|consen 147 PAQVTKVVGSALLGTCLRPDISVDVLLTMPREILQQKDGLNQRYFRKRALYLAYLAHHLLEDLLFGSLEFSYTNGDHLKP 226 (1121)
T ss_pred ccccceeeeecccCcccCCcchhhhhhhhhHHhhcCcccccccccchHHHHHHHHHHHHHhccccceeeecccCCccccc
Confidence 34555 556666654 45789999999999754332233 33344444444433333332 234558
Q ss_pred eEEEEecCeeeeEEeeecccccccccccc-ccccccCCCC----------cccccccchh--------hHHHHHHHhCCC
Q 005429 153 VMKFKFDGLSIDLLYASISRLVVREDLDI-SDMSVLNDVD----------EPTVRSLNGC--------RVADQILKLVPN 213 (697)
Q Consensus 153 IIKf~~~GI~iDLsfa~l~~~~ip~~l~l-~~d~~L~~lD----------e~s~rSLNG~--------Rvtd~Il~lVP~ 213 (697)
|+.+...|-..|++-.+.+..-+|-.+.+ .++.+|-+.- +..---.|-. -...++.+....
T Consensus 227 il~i~~~~~~~~~~~~~~~~~li~~~~~~f~~~kllp~~~~ir~~~e~~e~ppTP~yN~svL~~~~le~~~q~L~K~~s~ 306 (1121)
T KOG2054|consen 227 ILLIRPRGKDERLVTVRPPDFLIPCRLLPFKNNKLLPWYNGIRPAGEGSEEPPTPRYNTSVLEDQVLEEYLQLLSKTLSS 306 (1121)
T ss_pred hhhccccCCccccccccCccccccccccccccccccchhcccCccccCCCCCCCCccchhHHHHHHHHHHHHHHHHHHhh
Confidence 88888766555554433221112211111 1111110000 0000001111 112233444555
Q ss_pred hhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHHHHh---hCCCCCHHHHHHHHHHHhhcCCCCC-ceeeccccc
Q 005429 214 VEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQ---LYPNAVPSMLVSRFFRVYTMWRWPN-PVMLCAIDE 289 (697)
Q Consensus 214 ~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~vcQ---l~Pn~s~~~LL~~FF~~Ys~wdW~~-pV~l~~i~~ 289 (697)
-+.|+.++.+.|.|+++|-. +-..|++||+-|++++++... ++.+.+..+++..-|+|.+.|||.. -+-+++-.
T Consensus 307 ~~~f~da~~Llk~WlrqRs~-~~~~~gfg~f~~s~lvv~L~s~~ki~~~~S~yqvfR~vl~flat~dlt~~~~~l~~~~- 384 (1121)
T KOG2054|consen 307 AKGFKDALALLKVWLRQRSL-DIGQGGFGGFLLSALVVYLVSTRKIHTTLSAYQVFRSVLQFLATTDLTVNGISLVPSS- 384 (1121)
T ss_pred hhhHHHHHHHHHHHHHhhhh-hcccCcchHHHHHHHHHHHHhcCchhhcchHHHHHHHHHHHHhhhhhhccceEeccCC-
Confidence 68999999999999999922 224689999999999998874 4566788999999999999999986 45554411
Q ss_pred ccCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHHHHHHHHHHHHHHhhhcCCCccccc-cccchhhhc
Q 005429 290 AELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALF-EPYLFFESY 368 (697)
Q Consensus 290 g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~stlrvI~~EF~Ra~~Il~~i~~~~~~W~~Lf-~p~~Ff~~Y 368 (697)
.. . |....-+..+....++ ..-..|...|++.++++.+++|.+-+..++.+.. ....+.+| ++.+.|..|
T Consensus 385 ~s--~----~~~~~f~e~~~~~f~D-~s~~~NLc~~mt~s~y~~~q~ea~ltl~lL~~~~--~~~F~~IFmtkip~~~~y 455 (1121)
T KOG2054|consen 385 PS--L----PALADFHEGQLVTFID-SSGHLNLCANMTASTYEQVQEEARLTLMLLDSRA--DDGFSLIFMTKIPVFRAY 455 (1121)
T ss_pred CC--c----hhhhhhhhcceeeEec-cCCcchhhhhccHHHHHHHHHHHHHHHHHHhhhh--hcCcceeeeecCCchhhh
Confidence 00 0 0000000112233333 2345789999999999999999999999999865 34678777 788999999
Q ss_pred ccEEEEEEEeCChhhhhhhhhhhH
Q 005429 369 RNYLQVDIVAANADDLLAWKGWVE 392 (697)
Q Consensus 369 k~yl~I~v~a~~~e~~~~w~GwVE 392 (697)
.|-+.+.--..-+.....-.||.|
T Consensus 456 Dh~l~l~~~~~l~~~~~~~~~~~~ 479 (1121)
T KOG2054|consen 456 DHVLHLSPLSRLQAAEHLLSGFCE 479 (1121)
T ss_pred heeeeccccchhhhHHhhcccchh
Confidence 998887654333334444444443
No 15
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=98.25 E-value=3.9e-05 Score=79.95 Aligned_cols=213 Identities=16% Similarity=0.150 Sum_probs=147.1
Q ss_pred EEEeeeccccCcCCCC-CeeEEeecCCccCchhhHHHHH----HHHHHhccCCceEEEeccCccceEEEEec----Ceee
Q 005429 93 IFTFGSYRLGVHGPGA-DIDALCVGPSYVSREEDFFFIL----HNILAEMEEVTELQPVLDAHVPVMKFKFD----GLSI 163 (697)
Q Consensus 93 I~~FGSy~lGv~~p~S-DID~l~v~P~~v~re~dFf~~l----~~~L~~~~~V~~l~~I~~ArVPIIKf~~~----GI~i 163 (697)
|.-.||+.-|+.+.|. +.|+++++....+.+ ....+ .+-|+...+=.....|..+.+|.++..+. -...
T Consensus 5 V~rVG~~aKG~ll~Gd~~~~lVv~c~~~PT~~--ll~~v~~~l~e~l~~~~~~e~~~~~~~~~~~~~~~~i~ltSp~~r~ 82 (246)
T smart00572 5 VMRVGSFAKGTLLKGDNVAELVLLCKEKPTSE--LVARLARKLPEQLKAVTEDEALIIVTSTKEPTMEVGILITSPLARV 82 (246)
T ss_pred eEEeeeeccCceecCCCceeEEEEecCCCcHH--HHHHHHHHHHHHHhhcCcccceeeeeccCCCceeEEEEEecccccc
Confidence 6678999999999977 889999998777753 44444 44444322112223456777788888762 2223
Q ss_pred eEEeeeccccccccccccccccccCCCC-cccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccc
Q 005429 164 DLLYASISRLVVREDLDISDMSVLNDVD-EPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLG 242 (697)
Q Consensus 164 DLsfa~l~~~~ip~~l~l~~d~~L~~lD-e~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LG 242 (697)
+...+. .|+++.-.+ +-.-+| ..|+.+|-.+|-+.+..........|+.++|++|-|.++..... -|.
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 333222 233332111 122334 35888899999999999888888899999999999999876543 389
Q ss_pred hHHHHHHHHHHHhhCC-CCCHHHHHHHHHHHhhc-CCCCCceeecccccccCCcccccCCCCCCCCCCceEEeCCCCC-C
Q 005429 243 GVNWALLVARVCQLYP-NAVPSMLVSRFFRVYTM-WRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYP-C 319 (697)
Q Consensus 243 G~swaLLVa~vcQl~P-n~s~~~LL~~FF~~Ys~-wdW~~pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P-~ 319 (697)
++.+-|++++.+-... ..++++-+.+||++.++ .-+|.- --|+||+.+ .
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 9999999999886332 23689999999999985 222210 136788886 7
Q ss_pred CCccCccCHhHHHHHHHHHHHHHHHHH
Q 005429 320 MNSSYNVSTSTLRVMMDQFQYGNTICE 346 (697)
Q Consensus 320 ~Nsa~nVs~stlrvI~~EF~Ra~~Il~ 346 (697)
.|++...|......|...-+.+.+++.
T Consensus 204 ~nv~~~lT~qqrd~It~sAQ~alRl~A 230 (246)
T smart00572 204 TDALTALTLQQREDVTASAQTALRLLA 230 (246)
T ss_pred ccHHHhcCHHHHHHHHHHHHHHHHHHH
Confidence 788888888888888888887777763
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=97.81 E-value=0.00019 Score=67.66 Aligned_cols=77 Identities=27% Similarity=0.317 Sum_probs=56.4
Q ss_pred CeEEEEeeeccccCcCC-CCCeeEEeecCCccC----chhhHHHHHHHHHHhccCCceEEEeccCccceEEEEec--Cee
Q 005429 90 NALIFTFGSYRLGVHGP-GADIDALCVGPSYVS----REEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFD--GLS 162 (697)
Q Consensus 90 ~~~I~~FGSy~lGv~~p-~SDID~l~v~P~~v~----re~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~--GI~ 162 (697)
...++.||||+.|...+ .||||++++.+.... ...+++..+.+.|.+...- -.. ....-|.|.+.+. +++
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 47899999999999987 899999999886643 1245677777778764321 111 2455578888886 899
Q ss_pred eeEEeee
Q 005429 163 IDLLYAS 169 (697)
Q Consensus 163 iDLsfa~ 169 (697)
|||+-+.
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=97.61 E-value=3.7e-05 Score=62.68 Aligned_cols=56 Identities=20% Similarity=0.317 Sum_probs=36.4
Q ss_pred CHHHHHHHHHHHhh-cCCCCCceeecccccccCC--cccccCCCCCCCCCCceEEeCCCCCC
Q 005429 261 VPSMLVSRFFRVYT-MWRWPNPVMLCAIDEAELG--FSVWDPRKNRRDKTHHMPIITPAYPC 319 (697)
Q Consensus 261 s~~~LL~~FF~~Ys-~wdW~~pV~l~~i~~g~lg--~~~W~p~~~~~dr~~~MpIiTP~~P~ 319 (697)
++++||..||+||+ .|||.+-|+.... .+.+. ...|.. ....+...|+|++|+.|.
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 47999999999999 8999997665432 11111 133431 112245789999999885
No 18
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=97.55 E-value=0.00012 Score=58.20 Aligned_cols=26 Identities=35% Similarity=0.532 Sum_probs=24.5
Q ss_pred CeEEEEeeeccccCcCCCCCeeEEee
Q 005429 90 NALIFTFGSYRLGVHGPGADIDALCV 115 (697)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v 115 (697)
..+++.||||+.|.+.+.||||++|+
T Consensus 17 ~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 17 GYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred CcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 57899999999999999999999987
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=97.40 E-value=0.00022 Score=61.84 Aligned_cols=32 Identities=34% Similarity=0.464 Sum_probs=29.6
Q ss_pred CeEEEEeeeccccCcCCCCCeeEEeecCCccC
Q 005429 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVS 121 (697)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~ 121 (697)
...|+.||||+.|.+.|+||||++++.+....
T Consensus 14 ~~~v~lfGS~a~g~~~~~SDIDl~i~~~~~~~ 45 (93)
T PF01909_consen 14 VAEVYLFGSYARGDATPDSDIDLLIILDEPED 45 (93)
T ss_dssp TEEEEEEHHHHHTSSCTTSCEEEEEEESSTSC
T ss_pred CCEEEEECCcccCcCCCCCCEEEEEEeCCccc
Confidence 58999999999999999999999999988764
No 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=97.38 E-value=0.00058 Score=63.62 Aligned_cols=93 Identities=24% Similarity=0.335 Sum_probs=60.0
Q ss_pred HHHHHHHHHHhCCCCCc--cCccchHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhhcCCCCCceeecccccccCCccccc
Q 005429 221 LRCLKFWAKRRGVYSNV--TGFLGGVNWALLVARVCQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWD 298 (697)
Q Consensus 221 lr~IK~WAK~RGIysn~--~G~LGG~swaLLVa~vcQl~Pn~s~~~LL~~FF~~Ys~wdW~~pV~l~~i~~g~lg~~~W~ 298 (697)
+|++|.++|.-|+|++- .++++||..-|||++|=- +....+.-+ +|..|+.|..-..+... +
T Consensus 3 VrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~yGs----------F~~~l~~a~--~W~~~~~Id~~~~~~~~-~--- 66 (114)
T PF09249_consen 3 VRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHYGS----------FENVLEAAA--KWKPPVVIDLEDHGEPS-K--- 66 (114)
T ss_dssp HHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHHHSS----------HHHHHHHHT--T--TTEEEETT-TTE---E---
T ss_pred hHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHHHCC----------HHHHHHHHH--hcCCCeEEccCccchhh-h---
Confidence 68999999999999875 689999999999998731 233333334 77778887653211100 1
Q ss_pred CCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHH
Q 005429 299 PRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMM 335 (697)
Q Consensus 299 p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~stlrvI~ 335 (697)
.-.+++.|+||.+|..|+|.+||..++..+.
T Consensus 67 ------~f~~PlvviDPvDp~RNVAAalS~~~~~~fv 97 (114)
T PF09249_consen 67 ------KFDDPLVVIDPVDPNRNVAAALSLENLAEFV 97 (114)
T ss_dssp ------EE-SS-EEEETTEEEEETTTTS-HHHHHHHH
T ss_pred ------hcCCCeEEcCCCCCCchHhHhcCHHHHHHHH
Confidence 1136899999999999999999987766544
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=97.34 E-value=0.0021 Score=78.97 Aligned_cols=156 Identities=23% Similarity=0.356 Sum_probs=109.2
Q ss_pred hhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHHHH-hhCC---CCCHHHHHHHHHHHhhcC
Q 005429 201 CRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVC-QLYP---NAVPSMLVSRFFRVYTMW 276 (697)
Q Consensus 201 ~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~vc-Ql~P---n~s~~~LL~~FF~~Ys~w 276 (697)
.+-+..|..+.-..+.|.+++|++|.|...+-+ .|++.--.+=||||++. +-+| ..++..=+.+|+++-+.|
T Consensus 669 p~h~~~i~~l~~~~p~fs~tvRL~KrW~~shlL----s~~i~~E~vELlva~vfl~~~p~~~P~S~~~GFlRfL~lLs~~ 744 (972)
T PF03813_consen 669 PKHTSAIHGLHTRFPSFSPTVRLAKRWLSSHLL----SGHISEEAVELLVASVFLSPAPWSPPSSPQTGFLRFLHLLSTW 744 (972)
T ss_pred HHHHHHHHHHHhhCCchhHHHHHHHHHHHhccC----cccCCHHHHHHHHHHHhcCCCCCCCCCCHhHHHHHHHHHHHhC
Confidence 344556666666778999999999999999977 46788889999999987 3344 345666677888888999
Q ss_pred CCCC-ceeeccccccc--------CCcccccCCCCCCCCCCceEEeCCCCCCCCc--cCccCHhHHHHHHHHHHHHHHHH
Q 005429 277 RWPN-PVMLCAIDEAE--------LGFSVWDPRKNRRDKTHHMPIITPAYPCMNS--SYNVSTSTLRVMMDQFQYGNTIC 345 (697)
Q Consensus 277 dW~~-pV~l~~i~~g~--------lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Ns--a~nVs~stlrvI~~EF~Ra~~Il 345 (697)
||.+ |++++..++-. ..|..|.. .++......|.|.||.+|.-.. ...-+..-+++|+.--+.+.+++
T Consensus 745 dW~~~PLiVd~~~~l~~~~~~~i~~~f~~~R~-~dp~~~~p~~~IaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~sl~~l 823 (972)
T PF03813_consen 745 DWREEPLIVDFNNELTEEDRAEIETNFDAWRK-IDPAMNLPAMFIATPYDPEGSLWTRNGPSKVVAKRLTALAKASLKLL 823 (972)
T ss_pred CCCcCCEEEECCCCCCHHHHHHHHHHHHHhhc-cCccccCCcEEEEeCCCCCCCEeECCCCCHHHHHHHHHHHHHHHHHH
Confidence 9995 88876532111 12334432 3444456789999999986321 12344556788887777788888
Q ss_pred HHhhhcCCCccccccc
Q 005429 346 EEVELNKAQWSALFEP 361 (697)
Q Consensus 346 ~~i~~~~~~W~~Lf~p 361 (697)
+.-..+..+|..||.|
T Consensus 824 ~~~~~~~~~~~~lF~~ 839 (972)
T PF03813_consen 824 EEQGLSDLDWKSLFRP 839 (972)
T ss_pred HhcCCCCCCHHHhcCC
Confidence 7433346799999976
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=96.96 E-value=0.0012 Score=56.57 Aligned_cols=32 Identities=31% Similarity=0.492 Sum_probs=28.8
Q ss_pred CeEEEEeeeccccCcCCCCCeeEEeecCCccC
Q 005429 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVS 121 (697)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~ 121 (697)
-..++.|||++.|-+.++||||++++++....
T Consensus 18 i~~i~LfGS~arg~~~~~SDiDl~vi~~~~~~ 49 (93)
T cd05403 18 VEKVYLFGSYARGDARPDSDIDLLVIFDDPLD 49 (93)
T ss_pred ccEEEEEeeeecCCCCCCCCeeEEEEeCCCCC
Confidence 37899999999999999999999999987654
No 23
>PF14091 DUF4269: Domain of unknown function (DUF4269)
Probab=96.06 E-value=0.058 Score=52.99 Aligned_cols=118 Identities=22% Similarity=0.354 Sum_probs=74.7
Q ss_pred EEEeeeccccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceE-EEeccCccceEEEEecCeeeeEEeeecc
Q 005429 93 IFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTEL-QPVLDAHVPVMKFKFDGLSIDLLYASIS 171 (697)
Q Consensus 93 I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~dFf~~l~~~L~~~~~V~~l-~~I~~ArVPIIKf~~~GI~iDLsfa~l~ 171 (697)
-...|.+.+|+..++||||++|.++.. +.|-..+.+...+.++.+-- ..|..-..=+..|.+.|..|-|- ++.
T Consensus 18 PiL~GTiPi~Idi~~SDLDIic~~~d~----~~F~~~l~~~f~~~~~f~~~~~~i~~~~~~~~~F~~~~~~~EiF-~Q~- 91 (152)
T PF14091_consen 18 PILVGTIPIGIDIPGSDLDIICEVPDP----EAFEQLLQSLFGQFEGFTIKEKTIRGEPSIVANFRYEGFPFEIF-GQP- 91 (152)
T ss_pred CEEecccccccCCCCCCccEEEEeCCH----HHHHHHHHHHhccCCCceeeeceeCCceeEEEEEEECCceEEEe-ecC-
Confidence 456799999999999999999999753 13333334444444443211 22344445567788889988874 431
Q ss_pred ccccccccccccccccCCCCcccccccchhhHHHHHHHhCCCh-hhHHHHHHHHH--------HHHHHhCCCCCc
Q 005429 172 RLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNV-EHFCTTLRCLK--------FWAKRRGVYSNV 237 (697)
Q Consensus 172 ~~~ip~~l~l~~d~~L~~lDe~s~rSLNG~Rvtd~Il~lVP~~-~~FR~llr~IK--------~WAK~RGIysn~ 237 (697)
..+..-||+|=...-.+++-.. +.||.-+|-+| +||+--||-++.
T Consensus 92 ---------------------~Pv~~QnayrHm~iE~rLL~~~g~~~r~~Ii~LK~~GlKTEPAFa~lLgL~GDP 145 (152)
T PF14091_consen 92 ---------------------IPVEEQNAYRHMLIEHRLLELHGPSFREEIIELKESGLKTEPAFAKLLGLEGDP 145 (152)
T ss_pred ---------------------CChhhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHcCCcchHHHHHHhCCCCCh
Confidence 1234568888543333444444 78999998888 477777766543
No 24
>PF07528 DZF: DZF domain; InterPro: IPR006561 This domain is found in proteins containing the double-stranded RNA-binding motif, DSRM (IPR001159 from INTERPRO), or the zinc finger domain C2H2 (IPR007087 from INTERPRO). This domain is found exclusively in the metazoa.
Probab=95.49 E-value=0.53 Score=49.71 Aligned_cols=207 Identities=14% Similarity=0.179 Sum_probs=131.6
Q ss_pred eeeccccCcCCCC-CeeEEeecCCccCchhhHHHHHHHHHH----hc-cCCceEEEe------ccCccceEEEEe--c--
Q 005429 96 FGSYRLGVHGPGA-DIDALCVGPSYVSREEDFFFILHNILA----EM-EEVTELQPV------LDAHVPVMKFKF--D-- 159 (697)
Q Consensus 96 FGSy~lGv~~p~S-DID~l~v~P~~v~re~dFf~~l~~~L~----~~-~~V~~l~~I------~~ArVPIIKf~~--~-- 159 (697)
.||+.-|+.+.|. +.|+|+++..-.+. +++..+.+.|. .. +. +-...+ ...+.|.+...+ .
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 5999999999887 89999999887775 46665554444 32 22 111112 222335555543 2
Q ss_pred CeeeeEEeeeccccccccccccccccccCCCCc-ccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCcc
Q 005429 160 GLSIDLLYASISRLVVREDLDISDMSVLNDVDE-PTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVT 238 (697)
Q Consensus 160 GI~iDLsfa~l~~~~ip~~l~l~~d~~L~~lDe-~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~ 238 (697)
.+.+.+.... .+++.. ..+.-..||. .|..+|-.+|-|.++.+........+.++|++|-...|--- +
T Consensus 79 ~~r~~~~~~~-----~~~~~~--~~dp~~~Ld~~~cl~aLaalRhakWFq~~a~~l~s~~~viRIlrDl~~R~p~----w 147 (248)
T PF07528_consen 79 VMRVRVLITT-----IPENLS--KLDPEDHLDRKKCLSALAALRHAKWFQARANGLQSCVIVIRILRDLRQRVPT----W 147 (248)
T ss_pred ceEEEEeccc-----cCcccc--ccChhhcCCHHHHHHHHHHHHHhHHHHHHhccCCCcceehhhHHHHHHhCCC----C
Confidence 2333333222 222221 1112223454 58888889999999998888888889999999999887533 5
Q ss_pred CccchHHHHHHHHHHHhhCCC---CCHHHHHHHHHHHhhc-CCCCC-ceeecccccccCCcccccCCCCCCCCCCceEEe
Q 005429 239 GFLGGVNWALLVARVCQLYPN---AVPSMLVSRFFRVYTM-WRWPN-PVMLCAIDEAELGFSVWDPRKNRRDKTHHMPII 313 (697)
Q Consensus 239 G~LGG~swaLLVa~vcQl~Pn---~s~~~LL~~FF~~Ys~-wdW~~-pV~l~~i~~g~lg~~~W~p~~~~~dr~~~MpIi 313 (697)
+.|+++.+=+|+-+..--.|+ .++++-+.+||+..|. +-.|. |- |.
T Consensus 148 ~~L~~W~leLL~~~~i~~~~~~~~l~~g~a~RRvle~lasGillp~~~g-----------------------------l~ 198 (248)
T PF07528_consen 148 QPLSSWALELLVEKAISNNSSRQPLSPGDAFRRVLECLASGILLPGSPG-----------------------------LR 198 (248)
T ss_pred CCCChhHHHHHHHHHeeeCCCCCCCChHHHHHHHHHHHhCceecCCCCC-----------------------------Cc
Confidence 668888888887776653333 4689999999999884 33332 11 33
Q ss_pred CCCC-CCCCccCccCHhHHHHHHHHHHHHHHHH
Q 005429 314 TPAY-PCMNSSYNVSTSTLRVMMDQFQYGNTIC 345 (697)
Q Consensus 314 TP~~-P~~Nsa~nVs~stlrvI~~EF~Ra~~Il 345 (697)
||+. ...++..+.|......|..--+.+.+++
T Consensus 199 DPcE~~~~~~~~~lt~qq~e~it~sAQ~~LRll 231 (248)
T PF07528_consen 199 DPCEKDPVDVLDTLTLQQREDITSSAQTALRLL 231 (248)
T ss_pred CCCCCCCceeeccCCHHHHHHHHHHHHHHHHHH
Confidence 5555 4456677777777777776666655554
No 25
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=95.32 E-value=0.072 Score=48.73 Aligned_cols=46 Identities=30% Similarity=0.420 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCCCCeeEEeecCCc
Q 005429 58 EQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (697)
Q Consensus 58 ~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (697)
+++++++...+++|. | -..+-.||||+=|=..|+||||+++-....
T Consensus 8 ~~~lr~~~~~l~~k~-------g---------v~~~~vFGS~aRgE~~~~SDIDILVef~~~ 53 (97)
T COG1669 8 KKILRKIKPELKEKY-------G---------VKRVAVFGSYARGEQKPDSDIDILVEFEPG 53 (97)
T ss_pred HHHHHHHHHHHHHHh-------C---------CceEEEeeeeecCCCCCCCCceeEEeecCC
Confidence 344556666666553 2 267999999999999999999999976544
No 26
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=94.56 E-value=0.19 Score=45.33 Aligned_cols=28 Identities=43% Similarity=0.630 Sum_probs=26.2
Q ss_pred CeEEEEeeeccccCcCCCCCeeEEeecC
Q 005429 90 NALIFTFGSYRLGVHGPGADIDALCVGP 117 (697)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v~P 117 (697)
...++.||||+-|=+.+.||||++++++
T Consensus 26 ~~~v~LfGS~arG~~~~~SDiDv~vv~~ 53 (128)
T COG1708 26 DLLIYLFGSYARGDFVKESDIDLLVVSD 53 (128)
T ss_pred CeEEEEEccCcccccccCCCeeEEEEcC
Confidence 5889999999999999999999999983
No 27
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=94.29 E-value=0.084 Score=56.10 Aligned_cols=32 Identities=28% Similarity=0.265 Sum_probs=28.4
Q ss_pred eEEEEeeeccccCcCCCCCeeEEeecCCccCc
Q 005429 91 ALIFTFGSYRLGVHGPGADIDALCVGPSYVSR 122 (697)
Q Consensus 91 ~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~r 122 (697)
.-|+.|||++.|-..|.||||++++.....+.
T Consensus 29 ~~vyLfGS~~~G~~~p~SDIDllvvv~~~l~~ 60 (262)
T PRK13746 29 LAIHLYGSAVDGGLKPHSDIDLLVTVAVPLDE 60 (262)
T ss_pred EEEEEECCcccCCCCCCCceeEEEEeCCCCCH
Confidence 46899999999999999999999999887653
No 28
>PF10421 OAS1_C: 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus ; InterPro: IPR018952 This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between residues 320 and 344 at the extreme C-terminal end []. Oligoadenylate synthetases are antiviral enzymes that counteract viral attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesise 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication []. This domain is often associated with IPR002934 from INTERPRO. ; PDB: 1PX5_B.
Probab=94.11 E-value=0.078 Score=53.86 Aligned_cols=47 Identities=13% Similarity=0.051 Sum_probs=33.1
Q ss_pred hhhHHHHHHHHHHHHHHhCCCCCcc-CccchHHHHHHHHHHHhhCCCC
Q 005429 214 VEHFCTTLRCLKFWAKRRGVYSNVT-GFLGGVNWALLVARVCQLYPNA 260 (697)
Q Consensus 214 ~~~FR~llr~IK~WAK~RGIysn~~-G~LGG~swaLLVa~vcQl~Pn~ 260 (697)
....+.|+|+||+|-+...-..... +.+.+|++-||+++.-..-.+.
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 3678999999999999876553333 4467999999999998765544
No 29
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=92.87 E-value=1.4 Score=47.76 Aligned_cols=113 Identities=24% Similarity=0.251 Sum_probs=71.6
Q ss_pred CCeEEEEeeeccccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEe------cCee
Q 005429 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKF------DGLS 162 (697)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~------~GI~ 162 (697)
...++.+-||||=|-.+ .+|||+|+..+.... ..++..+...|.+.+.+..+. ..-..-....+ .|+.
T Consensus 159 ~~~~v~i~GS~RRg~et-~gDiDilv~~~~~~~--~~~~~~v~~~l~~~~~~~~~~---~~g~~k~~~~~~~~~~~~~~r 232 (307)
T cd00141 159 PVLQVEIAGSYRRGKET-VGDIDILVTHPDATS--RGLLEKVVDALVELGFVTEVL---SKGDTKASGILKLPGGWKGRR 232 (307)
T ss_pred CceEEEEcccccCCCCc-cCCEEEEEecCCccc--cccHHHHHHHHHhCCCeehhh---hCCCceEEEEEecCCCCCceE
Confidence 46899999999998776 579999998876544 257777888888877654321 11111122222 2899
Q ss_pred eeEEeeeccccccccccccccccccCCCCcccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCcc
Q 005429 163 IDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFL 241 (697)
Q Consensus 163 iDLsfa~l~~~~ip~~l~l~~d~~L~~lDe~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~L 241 (697)
|||.++.... . .-.++-+-.+. . -.|-++.||++||..=+..|..
T Consensus 233 VDl~~~p~~~------~------------------------~~all~fTGs~-~---~nr~lR~~A~~~G~~L~~~GL~ 277 (307)
T cd00141 233 VDLRVVPPEE------F------------------------GAALLYFTGSK-Q---FNRALRRLAKEKGLKLNEYGLF 277 (307)
T ss_pred EEEEEeCHHH------H------------------------HHHHHHhhCCH-H---HHHHHHHHHHHcCCeeeccccc
Confidence 9999876311 0 11222222232 2 2466699999999887776664
No 30
>PRK02098 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=91.56 E-value=0.36 Score=50.23 Aligned_cols=33 Identities=24% Similarity=0.274 Sum_probs=28.0
Q ss_pred CeEEEEeeecc----ccC--cCCCCCeeEEeecCCccCc
Q 005429 90 NALIFTFGSYR----LGV--HGPGADIDALCVGPSYVSR 122 (697)
Q Consensus 90 ~~~I~~FGSy~----lGv--~~p~SDID~l~v~P~~v~r 122 (697)
+..+.+|||+. +|+ -.++||||+++-.|.....
T Consensus 120 g~~~gv~GS~a~qlaTG~~~l~~~SDLDLLi~~~~~~~~ 158 (221)
T PRK02098 120 GVDCRVFGSLAWQALTGLPYLSASSDLDLLWPLPAAAQI 158 (221)
T ss_pred CCcEEEeeehHHHHhhCCcccCCCCCeeEEEecCChhhH
Confidence 56899999999 999 7899999999988765443
No 31
>TIGR03135 malonate_mdcG holo-ACP synthase, malonate decarboxylase-specific. Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A. Members of this protein family are the phosphoribosyl-dephospho-CoA transferase specific to the malonate decarboxylase system. This enzyme can also be designated holo-ACP synthase (2.7.7.61). The corresponding component of the citrate lyase system, CitX, shows little or no sequence similarity to this family.
Probab=90.83 E-value=0.43 Score=48.92 Aligned_cols=33 Identities=27% Similarity=0.272 Sum_probs=28.2
Q ss_pred CeEEEEeeec----cccC--cCCCCCeeEEeecCCccCc
Q 005429 90 NALIFTFGSY----RLGV--HGPGADIDALCVGPSYVSR 122 (697)
Q Consensus 90 ~~~I~~FGSy----~lGv--~~p~SDID~l~v~P~~v~r 122 (697)
+..+.+|||+ .+|+ -.++||||+++-.|.....
T Consensus 108 ~~~~gv~GS~~~qlaTg~~~~~~~SDLDLLi~~~~~~~~ 146 (202)
T TIGR03135 108 GVPWGVYGSAGWQLLTGLPYLHASSDLDLLLRAPSPLSL 146 (202)
T ss_pred CCcEEEecchHHHHhcCCcccCCCCCeeEEEcCCChhhH
Confidence 5789999999 8999 7899999999988865544
No 32
>PF14792 DNA_pol_B_palm: DNA polymerase beta palm ; PDB: 1RZT_A 3PML_A 2PFN_A 3HX0_K 3HWT_A 2GWS_E 2BCQ_A 3UPQ_A 2BCS_A 3UQ2_A ....
Probab=88.64 E-value=1.9 Score=40.15 Aligned_cols=52 Identities=33% Similarity=0.319 Sum_probs=39.1
Q ss_pred CCeEEEEeeeccccCcCCCCCeeEEeecCCccCc---hhhHHHHHHHHHHhccCCc
Q 005429 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSR---EEDFFFILHNILAEMEEVT 141 (697)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~r---e~dFf~~l~~~L~~~~~V~ 141 (697)
.+..+..-||||=|-.+.+ |||+++..|..... ...++..+.+.|.+..-++
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 4699999999999988765 99999999876552 1368888999998754443
No 33
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=88.10 E-value=2.9 Score=51.60 Aligned_cols=124 Identities=18% Similarity=0.236 Sum_probs=72.8
Q ss_pred hHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHHHHhh-C---CCCCHHHHHHHHHHHhhcCC
Q 005429 202 RVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQL-Y---PNAVPSMLVSRFFRVYTMWR 277 (697)
Q Consensus 202 Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~vcQl-~---Pn~s~~~LL~~FF~~Ys~wd 277 (697)
|.+-.|-.+-..++.|-.++|+-|.|...+=+.+ |.+ ==++-||||...+. + |..++-.=+.+|..+-|+||
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 3444444455567889999999999998875543 222 45577888876643 3 34566666889999999999
Q ss_pred CCC-ceeecccccccCCc--ccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhH
Q 005429 278 WPN-PVMLCAIDEAELGF--SVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTST 330 (697)
Q Consensus 278 W~~-pV~l~~i~~g~lg~--~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~st 330 (697)
|.. |.+++-..+-+-.- ..-+.-...|.....|.|+||-+- .++.+.=+..+
T Consensus 882 W~~~PLIvd~nn~~~ed~~~e~~e~f~s~R~~lp~m~vit~yD~-~~~~~t~~~P~ 936 (1121)
T KOG2054|consen 882 WKFDPLIVDFNNGFPEDERSELEEKFISARKQLPPMVVITPYDH-LGSKFTRTSPN 936 (1121)
T ss_pred ccCCceEEEcCCCCcHHHHHHHHHHHhhhcccCCceEEeecccc-ccccccccCch
Confidence 986 77765321100000 000000112223448999999654 33434333344
No 34
>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=87.59 E-value=2.8 Score=40.95 Aligned_cols=48 Identities=23% Similarity=0.275 Sum_probs=36.8
Q ss_pred CCeEEEEeeeccccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHh
Q 005429 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAE 136 (697)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~dFf~~l~~~L~~ 136 (697)
...-++.+|||+-|=-.+.||||++++.+........+|..+.+.+.+
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 468999999999999999999999999875432123567666665554
No 35
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=84.30 E-value=0.18 Score=53.85 Aligned_cols=26 Identities=31% Similarity=0.395 Sum_probs=22.5
Q ss_pred EEeeeccccCcCCCCCeeEEeecCCc
Q 005429 94 FTFGSYRLGVHGPGADIDALCVGPSY 119 (697)
Q Consensus 94 ~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (697)
=.-||..+|++..+||||+++-|+.+
T Consensus 125 GVTGSiL~gl~~~nSDIDfVVYG~~~ 150 (315)
T COG1665 125 GVTGSILLGLYDENSDIDFVVYGQMW 150 (315)
T ss_pred cccccccccccCCCCCceEEEEcHHH
Confidence 34599999999999999999999544
No 36
>PF03445 DUF294: Putative nucleotidyltransferase DUF294; InterPro: IPR005105 This domain is found associated with an N-terminal cyclic nucleotide-binding domain (IPR000595 from INTERPRO) and two CBS domains (IPR000644 from INTERPRO). This domain, normally represents the C-terminal region, is uncharacterised; however, it seems to be similar to the nucleotidyltransferase domain (IPR002934 from INTERPRO), conserving the DXD motif, which strongly suggests that proteins containing this domain are also nucleotidyltransferases.; GO: 0008773 [protein-PII] uridylyltransferase activity
Probab=82.36 E-value=10 Score=36.41 Aligned_cols=49 Identities=20% Similarity=0.148 Sum_probs=38.0
Q ss_pred cCCeEEEEeeeccccCcCCCCCeeEEeecCCccCch-hhHHHHHHHHHHh
Q 005429 88 DANALIFTFGSYRLGVHGPGADIDALCVGPSYVSRE-EDFFFILHNILAE 136 (697)
Q Consensus 88 ~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re-~dFf~~l~~~L~~ 136 (697)
....-++.+||++=+=.++.||+|..+|.......+ ..+|..|.+.+..
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 357999999999999999999999999988732221 4677776666553
No 37
>KOG3793 consensus Transcription factor NFAT, subunit NF45 [Transcription]
Probab=79.34 E-value=33 Score=37.11 Aligned_cols=212 Identities=17% Similarity=0.193 Sum_probs=109.6
Q ss_pred HHHhhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCCCCe
Q 005429 31 DMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADI 110 (697)
Q Consensus 31 D~~~t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDI 110 (697)
|-..+++|.+- ..++.|+.+|...=...+.+++.++.+.+. .|+- .-.-..|--.|||..|..+.++|.
T Consensus 38 D~~f~~alLkR--nqdL~P~~~~q~~I~~~vtKV~~vLdn~~~-----~~L~----~~~ieevrqVGSF~k~T~~tg~~~ 106 (362)
T KOG3793|consen 38 DTSFSEALLKR--NQDLAPNSAEQASILSLVTKVNNVLDNLVA-----PGLF----EVQIEEVRQVGSFKKGTMTTGHNV 106 (362)
T ss_pred chHHHHHHHhh--hccCCCCHHHHHHHHHHHHHHHHHHHhhcc-----CCce----EeehhhhhhccceeccccccCCcc
Confidence 66666666542 357999999987777777777776665431 2222 111256778999999999999876
Q ss_pred -eEEeecCCccCch--hhHHHHHHHHHHh-cc-CCceEEEeccCccceEEEE--e--cCeeeeEEeeecccccccccccc
Q 005429 111 -DALCVGPSYVSRE--EDFFFILHNILAE-ME-EVTELQPVLDAHVPVMKFK--F--DGLSIDLLYASISRLVVREDLDI 181 (697)
Q Consensus 111 -D~l~v~P~~v~re--~dFf~~l~~~L~~-~~-~V~~l~~I~~ArVPIIKf~--~--~GI~iDLsfa~l~~~~ip~~l~l 181 (697)
|++++-.--.+.| ...=.++.+-|+- ++ +|-. |=+.+-- + ..-.+-|+++. +|+++.
T Consensus 107 advVViLkTLPt~EaV~aLg~Kv~e~lka~d~~Evlt--------vl~~e~G~~I~s~~~~VRiLIt~-----iP~n~~- 172 (362)
T KOG3793|consen 107 ADLVVILKTLPTLEAVAALGNKVVESLRAQDPSEVLT--------VLTNETGFEISSSDATVRILITT-----VPPNLR- 172 (362)
T ss_pred cceEEEeecCCcHHHHHHHHHHHHHHhhhcChHHHHH--------HHhhccceeeecccceEEEEEee-----cCchhc-
Confidence 6666554333332 0111223333332 11 1111 1111111 1 12233344443 343322
Q ss_pred ccccccCCCCcccc-cccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHH-HHHHHHhhC-C
Q 005429 182 SDMSVLNDVDEPTV-RSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWAL-LVARVCQLY-P 258 (697)
Q Consensus 182 ~~d~~L~~lDe~s~-rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaL-LVa~vcQl~-P 258 (697)
.-+++-.||-+-+ ..+-.+|-+.++-+. ......+.++|++|---.+ +.||--=-.|+| |++++|-+. |
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 1122233343211 223334444333322 2234567788888865443 235533334665 777888653 4
Q ss_pred C---CCHHHHHHHHHHHhhc
Q 005429 259 N---AVPSMLVSRFFRVYTM 275 (697)
Q Consensus 259 n---~s~~~LL~~FF~~Ys~ 275 (697)
+ +.++.-+.+||++.+.
T Consensus 245 ~RQ~l~ln~Afrr~~qilaA 264 (362)
T KOG3793|consen 245 TRQPLALNVAYRRCLQILAA 264 (362)
T ss_pred ccccchhhHHHHHHHHHHHh
Confidence 4 3577889999999985
No 38
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=71.74 E-value=15 Score=45.03 Aligned_cols=58 Identities=21% Similarity=0.354 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCCCCeeEEeecCCccCc
Q 005429 61 LGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSR 122 (697)
Q Consensus 61 L~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~r 122 (697)
+.....++..|..++-...|+++ ..+.-|..+|.|+=|--.|.||||++++.|.-.+.
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 33444555566666666677764 34689999999999999999999999999987653
No 39
>PF10620 MdcG: Phosphoribosyl-dephospho-CoA transferase MdcG; InterPro: IPR017557 Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A. Members of this protein family are the phosphoribosyl-dephospho-CoA transferase specific to the malonate decarboxylase system. This enzyme can also be designated holo-ACP synthase (2.7.7.61 from EC). The corresponding component of the citrate lyase system, CitX, shows little or no sequence similarity to this family.; GO: 0016779 nucleotidyltransferase activity
Probab=69.15 E-value=8.5 Score=39.80 Aligned_cols=32 Identities=25% Similarity=0.290 Sum_probs=25.0
Q ss_pred CeEEEEeeeccc----cC--cCCCCCeeEEeecCCccC
Q 005429 90 NALIFTFGSYRL----GV--HGPGADIDALCVGPSYVS 121 (697)
Q Consensus 90 ~~~I~~FGSy~l----Gv--~~p~SDID~l~v~P~~v~ 121 (697)
+...-+|||+.. |+ -.++||||+++-.+....
T Consensus 116 ~~~~gv~GS~g~qlaTGl~~l~~~SDLDLli~~~~~~~ 153 (213)
T PF10620_consen 116 GLRWGVYGSLGFQLATGLPYLHADSDLDLLIRPPSPSQ 153 (213)
T ss_pred CCCEEEehhHHHHHHhCccccCCCCCceEEEeCCChhH
Confidence 678999999854 33 348999999998887653
No 40
>PF03281 Mab-21: Mab-21 protein
Probab=68.40 E-value=1.6e+02 Score=31.08 Aligned_cols=93 Identities=15% Similarity=0.127 Sum_probs=62.9
Q ss_pred hhhHHHHHHHHHHHHHHhCCCCCccCccchHHHHHHHHHHHhhCCCC------CHHHHHHHHHHHhhcCCCCCceeeccc
Q 005429 214 VEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPNA------VPSMLVSRFFRVYTMWRWPNPVMLCAI 287 (697)
Q Consensus 214 ~~~FR~llr~IK~WAK~RGIysn~~G~LGG~swaLLVa~vcQl~Pn~------s~~~LL~~FF~~Ys~wdW~~pV~l~~i 287 (697)
....+.+++++|....... ...+.|++|++-.++.+.|..+|.. .+++.+.+++...-. -.
T Consensus 190 ~~~~~~~l~llk~l~~~~~---~~~~~l~syhLkt~ll~~~~~~p~~~~W~~~~l~~~l~~~l~~L~~----------~L 256 (292)
T PF03281_consen 190 NGCRKKCLRLLKALRDRHL---TNLSGLSSYHLKTVLLWLCEKHPSSSDWSEENLGERLLDLLDFLIK----------CL 256 (292)
T ss_pred cccHHHHHHHHHHHHHhcc---ccCCCccHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHHHHH----------HH
Confidence 4567889999999977766 5678899999999999999999876 244444444433321 11
Q ss_pred ccccCCcccccCCCCCCCCCCceEEeCCCCCCCCccCccCHhHHHHHHHHHH
Q 005429 288 DEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSYNVSTSTLRVMMDQFQ 339 (697)
Q Consensus 288 ~~g~lg~~~W~p~~~~~dr~~~MpIiTP~~P~~Nsa~nVs~stlrvI~~EF~ 339 (697)
.++.+ + .-+.|.+|.=.+.+..++..+..++.
T Consensus 257 ~~~~L----------p----------hff~~~~NLf~~~~~~~~~~~~~~~~ 288 (292)
T PF03281_consen 257 QEGRL----------P----------HFFIPNLNLFQHLSPEELDELARKLE 288 (292)
T ss_pred hcCCC----------C----------ccCCCCcccCCCCCHHHHHHHHHHHH
Confidence 11111 1 12567888888888777777766654
No 41
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=68.11 E-value=66 Score=35.43 Aligned_cols=31 Identities=32% Similarity=0.532 Sum_probs=25.2
Q ss_pred CCeEEEEeeeccccCcCCCCCeeEEeecCCcc
Q 005429 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYV 120 (697)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v 120 (697)
....+.+-||||=|-.+ ..|||+|+..+...
T Consensus 163 ~~~~v~i~GSyRRgket-~gDIDili~~~~~~ 193 (334)
T smart00483 163 PDAIVTLTGSFRRGKET-GHDVDFLITSPHPA 193 (334)
T ss_pred CCcEEEEecccccCCCc-CCCeeEEEecCCcc
Confidence 35789999999998776 57999999877643
No 42
>PRK05007 PII uridylyl-transferase; Provisional
Probab=67.41 E-value=21 Score=44.35 Aligned_cols=56 Identities=18% Similarity=0.271 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCCCCeeEEeecCCc
Q 005429 60 VLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (697)
Q Consensus 60 VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (697)
++.....++.++++.+-...+.+. ..+.-|...|+|+=|=-.|.||||++++.+..
T Consensus 54 ~~~~~s~~~D~~l~~l~~~~~~~~----~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~ 109 (884)
T PRK05007 54 LVEARTEFIDQLLQRLWIEAGFDQ----IPDLALVAVGGYGRGELHPLSDIDLLILSRKK 109 (884)
T ss_pred HHHHHHHHHHHHHHHHHHHccCCC----cCceEEEecCCCCCcccCCcccceEEEEeCCC
Confidence 555555666666655544444431 24689999999999999999999999998744
No 43
>PRK08609 hypothetical protein; Provisional
Probab=66.74 E-value=27 Score=41.27 Aligned_cols=108 Identities=16% Similarity=0.160 Sum_probs=61.4
Q ss_pred CeEEEEeeeccccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEe-cCeeeeEEee
Q 005429 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKF-DGLSIDLLYA 168 (697)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~-~GI~iDLsfa 168 (697)
..++..-||||=|--+ ..|||+|+..+... .+.+.|.+.+.|.++..-...+.-+ .+.. .|+.|||-++
T Consensus 175 ~~~v~~~GS~RR~~et-~gDiDili~~~~~~--------~~~~~l~~~~~v~~~~~~g~~~~~~-~~~~~~~~~vDl~~v 244 (570)
T PRK08609 175 IIRFSRAGSLRRARET-VKDLDFIIATDEPE--------AVREQLLQLPNIVEVIAAGDTKVSV-ELEYEYTISVDFRLV 244 (570)
T ss_pred ccEEEeccchhccccc-cCCeeEEEecCCHH--------HHHHHHHcCccHHHHHhcCCceEEE-EEecCCCeEEEEEEe
Confidence 5789999999998776 56999999775421 1223333344443321111111111 2332 4999999987
Q ss_pred eccccccccccccccccccCCCCcccccccchhhHHHHHHHhCCChhhHHHHHHHHHHHHHHhCCCCCccCcc
Q 005429 169 SISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFL 241 (697)
Q Consensus 169 ~l~~~~ip~~l~l~~d~~L~~lDe~s~rSLNG~Rvtd~Il~lVP~~~~FR~llr~IK~WAK~RGIysn~~G~L 241 (697)
.... ++ -.++-+-.. ..| .|-++.||+++|+.=|-+|..
T Consensus 245 ~~~~--~~----------------------------~aL~yfTGS-~~h---n~~lr~~A~~~g~~l~e~gl~ 283 (570)
T PRK08609 245 EPEA--FA----------------------------TTLHHFTGS-KDH---NVRMRQLAKERGEKISEYGVE 283 (570)
T ss_pred CHHH--HH----------------------------HHHHHHhcc-HHH---HHHHHHHHHHcCCcccccccc
Confidence 6311 00 112222222 222 355689999999988888874
No 44
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=61.72 E-value=29 Score=42.87 Aligned_cols=56 Identities=14% Similarity=0.199 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCCCCeeEEeecCCc
Q 005429 60 VLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (697)
Q Consensus 60 VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (697)
++.....++..+++.+-...+.+. ..+.-|...|+|+=|=-.|.||||++++.+..
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 666666666666665543333221 13589999999999999999999999998743
No 45
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=60.03 E-value=28 Score=35.05 Aligned_cols=80 Identities=21% Similarity=0.192 Sum_probs=46.5
Q ss_pred CeEEEEeeeccc----cCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhcc-CCceEEEeccCccceEEEEecCeeee
Q 005429 90 NALIFTFGSYRL----GVHGPGADIDALCVGPSYVSREEDFFFILHNILAEME-EVTELQPVLDAHVPVMKFKFDGLSID 164 (697)
Q Consensus 90 ~~~I~~FGSy~l----Gv~~p~SDID~l~v~P~~v~re~dFf~~l~~~L~~~~-~V~~l~~I~~ArVPIIKf~~~GI~iD 164 (697)
+.+.+..|++++ |.--...|||+.+..+.... +.++|..+..... .+ +-+.+ ...-.++++...++.||
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 55667899999887664432 2344444432211 11 11111 22334566666899999
Q ss_pred EEeeeccccccc
Q 005429 165 LLYASISRLVVR 176 (697)
Q Consensus 165 Lsfa~l~~~~ip 176 (697)
| +.++....+|
T Consensus 90 l-~~ni~~~~v~ 100 (181)
T PF09970_consen 90 L-LENIGDFYVP 100 (181)
T ss_pred c-hhccCCcccC
Confidence 9 6665555454
No 46
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=57.41 E-value=32 Score=41.69 Aligned_cols=65 Identities=15% Similarity=0.081 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCCCCeeEEeecCCccCchhhHHHHHHHHH
Q 005429 55 EKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNIL 134 (697)
Q Consensus 55 ~~R~~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~dFf~~l~~~L 134 (697)
+.|+++.+.-..+++.+ +++ .+.-|...|+|+=|=-.|.||||++++.+.... +++...|...|
T Consensus 6 ~~~~~~~~~~~~~~~~~--------~~~------~~~aLvAvGGYGR~EL~P~SDIDLLiL~~~~~~--~~~i~~~~~~L 69 (693)
T PRK00227 6 QLREDAEASALALLGSL--------QLP------PGTALAATGSLARREMTPYSDLDLILLHPPGAT--PDGVEDLWYPI 69 (693)
T ss_pred HHHHHHHHHHHHHHHhc--------CCC------CCeEEEEeccccccCcCCCcCceEEEEeCCccc--HHHHHHHHHHH
Confidence 45666666666666643 333 257899999999999999999999999974332 24444444444
Q ss_pred H
Q 005429 135 A 135 (697)
Q Consensus 135 ~ 135 (697)
=
T Consensus 70 W 70 (693)
T PRK00227 70 W 70 (693)
T ss_pred H
Confidence 3
No 47
>PRK01293 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=57.19 E-value=20 Score=37.19 Aligned_cols=44 Identities=25% Similarity=0.192 Sum_probs=30.0
Q ss_pred CeEEEEeeecccc------CcCCCCCeeEEeecCCccCchhhHHHHHHHHHH
Q 005429 90 NALIFTFGSYRLG------VHGPGADIDALCVGPSYVSREEDFFFILHNILA 135 (697)
Q Consensus 90 ~~~I~~FGSy~lG------v~~p~SDID~l~v~P~~v~re~dFf~~l~~~L~ 135 (697)
+...-+|||...- .-.++||||+++..|..... +-+..+.+.+.
T Consensus 109 ~~~wgv~GS~g~qlaTGl~~l~~~SDLDLlir~~~~l~~--~~~~~ll~~l~ 158 (207)
T PRK01293 109 GLAWGVTGSAGFELATGIPVLHADSDLDLLIRAPQPLAR--DQARELLQLLD 158 (207)
T ss_pred CCceeeehhHHHHHhhCCccccCCCCccEeecCCCcccH--HHHHHHHHHHh
Confidence 5677899997643 33589999999999876654 33444444444
No 48
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=56.05 E-value=48 Score=36.73 Aligned_cols=49 Identities=31% Similarity=0.482 Sum_probs=38.3
Q ss_pred cCCeEEEEeeeccccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhc
Q 005429 88 DANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEM 137 (697)
Q Consensus 88 ~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~dFf~~l~~~L~~~ 137 (697)
++++.+..-|||+=| ...+.|||+|+-.|..-+.+...+..+...|.+.
T Consensus 169 ~p~~~vt~~GsfRRG-k~~ggDvD~LithP~~~s~~~~~~~~l~~~le~~ 217 (353)
T KOG2534|consen 169 DPEAFVTVTGSFRRG-KKMGGDVDFLITHPGSTSTEAKLLQLLMILLEKK 217 (353)
T ss_pred CCCcEEEEeccccCC-cccCCCeeEEEeCCCCCchhhhHHHHHHHHHHhc
Confidence 457899999999998 4568899999998876553446777777777764
No 49
>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=55.88 E-value=36 Score=35.79 Aligned_cols=62 Identities=21% Similarity=0.168 Sum_probs=34.9
Q ss_pred HHhhcCCCccc-cccCCeEEEEeeeccccCcCCCCCeeEEeecCCccCc------hhhHHHHHHHHHHh
Q 005429 75 LTRLRGYSDQM-VEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSR------EEDFFFILHNILAE 136 (697)
Q Consensus 75 v~~~~g~~~~~-~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~r------e~dFf~~l~~~L~~ 136 (697)
+....|.+... ....+..|.-.|-+.-+=-..+||||++++.+..-.. ...||..+.+.|.+
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 44455655321 1223688999999998888999999999998643221 13688888777665
No 50
>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=54.66 E-value=11 Score=39.13 Aligned_cols=27 Identities=26% Similarity=0.214 Sum_probs=23.0
Q ss_pred eEEEEeeeccccCcCCCCCeeEEeecC
Q 005429 91 ALIFTFGSYRLGVHGPGADIDALCVGP 117 (697)
Q Consensus 91 ~~I~~FGSy~lGv~~p~SDID~l~v~P 117 (697)
.-...+||.+-|+.+|+||.|+-.|.-
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 455678999999999999999987653
No 51
>PRK03059 PII uridylyl-transferase; Provisional
Probab=49.84 E-value=56 Score=40.51 Aligned_cols=54 Identities=24% Similarity=0.369 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCCCCeeEEeecCC
Q 005429 59 QVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPS 118 (697)
Q Consensus 59 ~VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~ 118 (697)
+++..+..++..+++..-...+.+ .+.-|...|+|+=|--.|.||||++++.+.
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 366666666766666543332222 357899999999999999999999999863
No 52
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=49.55 E-value=62 Score=40.39 Aligned_cols=57 Identities=21% Similarity=0.243 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCCCCeeEEeecCCcc
Q 005429 60 VLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYV 120 (697)
Q Consensus 60 VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v 120 (697)
++..+..++...++.+-.....+ ...+.-|...|.|+=|--.|.||||++++.+...
T Consensus 52 ~~~~~s~~~d~~l~~~~~~~~~~----~~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~ 108 (895)
T PRK00275 52 LIEDRAWFVDQILQQAWHQFDWS----DDADIALVAVGGYGRGELHPYSDIDLLILLDSAD 108 (895)
T ss_pred HHHHHHHHHHHHHHHHHHHhccC----CCCCEEEEEcCCccccCcCCCCCceEEEEecCCC
Confidence 44444445544444433332221 1235899999999999999999999999987543
No 53
>PRK04374 PII uridylyl-transferase; Provisional
Probab=47.35 E-value=68 Score=39.92 Aligned_cols=55 Identities=18% Similarity=0.245 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCCCCeeEEeecCCc
Q 005429 60 VLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (697)
Q Consensus 60 VL~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (697)
++..+..++..+++.+-.... + ...+.-|...|+|+=|=-.|.||||++++.+..
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 444444455555554333222 1 113488999999999999999999999998743
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=47.32 E-value=64 Score=39.82 Aligned_cols=31 Identities=26% Similarity=0.389 Sum_probs=27.7
Q ss_pred CCeEEEEeeeccccCcCCCCCeeEEeecCCc
Q 005429 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSY 119 (697)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~ 119 (697)
.+.-|...|||+=|=-.|.||||++++.+..
T Consensus 42 ~~~aliA~GgyGR~El~p~SDiDll~l~~~~ 72 (850)
T TIGR01693 42 SGIALVAVGGYGRGELAPYSDIDLLFLHDGK 72 (850)
T ss_pred CCeEEEEeCCccccCcCCCCCCeEEEEeCCC
Confidence 4688999999999999999999999998743
No 55
>PRK03381 PII uridylyl-transferase; Provisional
Probab=46.50 E-value=67 Score=39.41 Aligned_cols=30 Identities=13% Similarity=0.165 Sum_probs=27.3
Q ss_pred CCeEEEEeeeccccCcCCCCCeeEEeecCC
Q 005429 89 ANALIFTFGSYRLGVHGPGADIDALCVGPS 118 (697)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~ 118 (697)
...-|...|+|+-|--.|.||||++++.+.
T Consensus 56 ~~~alvAvg~~gr~el~p~SD~Dll~l~~~ 85 (774)
T PRK03381 56 SGVALVAVGGLGRRELLPYSDLDLVLLHDG 85 (774)
T ss_pred CCeEEEEeCCcCCcCcCCCCCCeEEEEeCC
Confidence 458999999999999999999999999873
No 56
>COG2413 Predicted nucleotidyltransferase [General function prediction only]
Probab=44.68 E-value=40 Score=35.16 Aligned_cols=28 Identities=29% Similarity=0.430 Sum_probs=23.3
Q ss_pred eEEEEeeeccccCcCCCCCeeEEeecCC
Q 005429 91 ALIFTFGSYRLGVHGPGADIDALCVGPS 118 (697)
Q Consensus 91 ~~I~~FGSy~lGv~~p~SDID~l~v~P~ 118 (697)
..-+.+||.+.|=--|+||+|+.+.-|-
T Consensus 38 ie~~v~gSvarGDV~p~SDvDV~I~~~v 65 (228)
T COG2413 38 IEAVVYGSVARGDVRPGSDVDVAIPEPV 65 (228)
T ss_pred chhEEEeeeeccCcCCCCCceEEEecCC
Confidence 3456789999998889999999997743
No 57
>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=40.49 E-value=39 Score=33.24 Aligned_cols=78 Identities=19% Similarity=0.397 Sum_probs=38.1
Q ss_pred HHHHHHHcCCCCCHHHHHHHHHH---HHHHHHHHHHHHHHHHhhcCCCccccccCCeEEEEeeeccccCcCCC---CCee
Q 005429 38 LEKFLVEAGLYESKEEDEKREQV---LGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPG---ADID 111 (697)
Q Consensus 38 L~~~L~~~~l~pS~EE~~~R~~V---L~~L~~iv~~wv~~v~~~~g~~~~~~~~~~~~I~~FGSy~lGv~~p~---SDID 111 (697)
..+.|..+++..-.++...|..| +..+..++++.+++ + +-....||||.+-+--|+ .|||
T Consensus 9 a~~~l~s~~v~~~~~~~~grh~vS~lV~~V~klmeEyLrr----h----------Nk~CicYGSyslhllN~~I~YgDID 74 (149)
T PF03296_consen 9 ASDYLNSYNVANPSGKVMGRHNVSDLVENVNKLMEEYLRR----H----------NKSCICYGSYSLHLLNPNIKYGDID 74 (149)
T ss_dssp HHHHHHHH--S-------------THHHHHHHHHHHHHHH---------------TTTEEEESHHHHHTTSTTS--SS-E
T ss_pred HHHHHHHhcccccCccccccccCcHHHHHHHHHHHHHHHh----h----------CCCeEEeeeeeEEecCCCcccCcch
Confidence 34566777777666777777765 44555566666654 2 234788999988776665 7999
Q ss_pred EEeecCCccCchhhHHHHHHHHHH
Q 005429 112 ALCVGPSYVSREEDFFFILHNILA 135 (697)
Q Consensus 112 ~l~v~P~~v~re~dFf~~l~~~L~ 135 (697)
++=... ..|+-.|.-++.
T Consensus 75 ilqTNa------r~flI~laflI~ 92 (149)
T PF03296_consen 75 ILQTNA------RTFLINLAFLIK 92 (149)
T ss_dssp EEESTH------HHHHHHHHHHHH
T ss_pred hhhccc------HHHHHHHHHHHh
Confidence 964432 255554444444
No 58
>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=39.40 E-value=26 Score=26.50 Aligned_cols=31 Identities=19% Similarity=0.429 Sum_probs=24.6
Q ss_pred hHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 005429 35 NRELEKFLVEAGLYESKEEDEKREQVLGRIRQ 66 (697)
Q Consensus 35 t~eL~~~L~~~~l~pS~EE~~~R~~VL~~L~~ 66 (697)
+.+|.++|++.|+..++.. ..|+++|..++.
T Consensus 6 ~~~L~~wL~~~gi~~~~~~-~~rd~Ll~~~k~ 36 (38)
T PF10281_consen 6 DSDLKSWLKSHGIPVPKSA-KTRDELLKLAKK 36 (38)
T ss_pred HHHHHHHHHHcCCCCCCCC-CCHHHHHHHHHH
Confidence 4689999999998766554 679998887764
No 59
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=37.57 E-value=80 Score=39.96 Aligned_cols=48 Identities=17% Similarity=0.144 Sum_probs=37.3
Q ss_pred CCeEEEEeeeccccCcCCCCCeeEEeecCCccC-c---hhhHHHHHHHHHHh
Q 005429 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVS-R---EEDFFFILHNILAE 136 (697)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~-r---e~dFf~~l~~~L~~ 136 (697)
.+.-|..+|+|+=+=-.+.||||++++...... . ...||..+.+.+..
T Consensus 722 ~~~avia~Gk~Gr~EL~~~SDlDl~fl~~~~~~~~~~~~~~~~~rlaq~l~~ 773 (1007)
T PRK14109 722 ARIAVIGMGRLGGRELGYGSDADVMFVHEPAPGADEAEAVRWATAVAEELRR 773 (1007)
T ss_pred CCEEEEEeccccccccCCCCCCcEEEEeCCCCCCCchhHHHHHHHHHHHHHH
Confidence 468999999999999999999999999863211 1 02688888777765
No 60
>COG3541 Predicted nucleotidyltransferase [General function prediction only]
Probab=37.14 E-value=16 Score=38.81 Aligned_cols=20 Identities=35% Similarity=0.408 Sum_probs=17.6
Q ss_pred eeeccccCcCCCCCeeEEee
Q 005429 96 FGSYRLGVHGPGADIDALCV 115 (697)
Q Consensus 96 FGSy~lGv~~p~SDID~l~v 115 (697)
-||+.-|+..|+||+|+=-|
T Consensus 16 sGS~~yGf~spdSDyDvR~V 35 (248)
T COG3541 16 SGSHLYGFPSPDSDYDVRGV 35 (248)
T ss_pred ccccccCCCCCCCccceeeE
Confidence 49999999999999998544
No 61
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=35.92 E-value=1.3e+02 Score=38.22 Aligned_cols=48 Identities=13% Similarity=0.066 Sum_probs=36.7
Q ss_pred CCeEEEEeeeccccCcCCCCCeeEEeecCCccCch----hhHHHHHHHHHHh
Q 005429 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYVSRE----EDFFFILHNILAE 136 (697)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re----~dFf~~l~~~L~~ 136 (697)
.+.-|..+|+|+-+=-.++||||++++.+.....+ ..||..+.+.|..
T Consensus 214 ~~~aviamGklG~~EL~~~SDiDLi~ly~~~~~~~~~~~~~~~~rl~q~l~~ 265 (1007)
T PRK14109 214 VRLAVIAMGKCGARELNYVSDVDVIFVAEPAEGVDEAAALAVATRLASELMR 265 (1007)
T ss_pred CCeEEEEeccccccccCCccCCCEEEEeCCCCCcccccHHHHHHHHHHHHHH
Confidence 46899999999999999999999999986432110 2577777777665
No 62
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=31.36 E-value=1e+02 Score=34.14 Aligned_cols=70 Identities=24% Similarity=0.220 Sum_probs=55.1
Q ss_pred eEEEEeeeccccCcCCCCCeeEEeecCCccCchhhHHHHHHHHHHhccCCceEEEeccCccceEEEEecCeeeeEEeee
Q 005429 91 ALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYAS 169 (697)
Q Consensus 91 ~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~re~dFf~~l~~~L~~~~~V~~l~~I~~ArVPIIKf~~~GI~iDLsfa~ 169 (697)
.++-.-||.|=|-.+ .+|||++|... +.. . +.+.|.+++.+.++..-.+.+|-++.--..|++||+-++.
T Consensus 181 ~~~~~aGs~RR~ret-v~DiD~~~s~~-~~~---~----v~~~~~~~~~~~~vi~~G~~k~s~~~~~~~~~svD~r~v~ 250 (326)
T COG1796 181 IQASIAGSLRRGRET-VGDIDILISTS-HPE---S----VLEELLEMPNVQEVIAKGETKVSMLLILDEGTSVDFRVVP 250 (326)
T ss_pred heeeeccchhhcccc-ccceeeEeccC-CcH---H----HHHHHhcCCCcceeeecCCceeeEEEEecCCCeeEEEEcC
Confidence 566777999988776 68999977653 221 1 5566777889999988899999988888899999998765
No 63
>PF07357 DRAT: Dinitrogenase reductase ADP-ribosyltransferase (DRAT); InterPro: IPR009953 This family consists of several bacterial dinitrogenase reductase ADP-ribosyltransferase (DRAT) proteins. Members of this family seem to be specific to Rhodospirillum, Rhodobacter and Azospirillum species. Dinitrogenase reductase ADP-ribosyl transferase (DRAT) carries out the transfer of the ADP-ribose from NAD to the Arg-101 residue of one subunit of the dinitrogenase reductase homodimer, resulting in inactivation of that enzyme. Dinitrogenase reductase-activating glycohydrolase (DRAG) removes the ADP-ribose group attached to dinitrogenase reductase, thus restoring nitrogenase activity. The DRAT-DRAG system negatively regulates nitrogenase activity in response to exogenous NH4+ or energy limitation in the form of a shift to darkness or to anaerobic conditions [].
Probab=30.50 E-value=22 Score=38.17 Aligned_cols=21 Identities=43% Similarity=0.680 Sum_probs=17.2
Q ss_pred eCChhhhhhhhhhhHhhHHHH
Q 005429 378 AANADDLLAWKGWVESRLRQL 398 (697)
Q Consensus 378 a~~~e~~~~w~GwVESRlR~L 398 (697)
-+|.-+...++||||||+-.+
T Consensus 95 DSn~~EGAVLKGWVESRFGL~ 115 (262)
T PF07357_consen 95 DSNSPEGAVLKGWVESRFGLL 115 (262)
T ss_pred CCCChhhhhhhhhhhhccCcC
Confidence 356678899999999999755
No 64
>PHA02603 nrdC.11 hypothetical protein; Provisional
Probab=30.36 E-value=28 Score=38.56 Aligned_cols=25 Identities=28% Similarity=0.307 Sum_probs=21.6
Q ss_pred EEEEeeeccccCcCCCCCeeEEeec
Q 005429 92 LIFTFGSYRLGVHGPGADIDALCVG 116 (697)
Q Consensus 92 ~I~~FGSy~lGv~~p~SDID~l~v~ 116 (697)
-+..+||...|+.+|+||+|.--|+
T Consensus 5 ~~~~~GShaYG~~tp~SD~D~rGV~ 29 (330)
T PHA02603 5 MKGLFGSHLYGTSTPESDVDYKGIF 29 (330)
T ss_pred EEEecccceeCCCCCCcccccceee
Confidence 3567999999999999999997655
No 65
>PRK05092 PII uridylyl-transferase; Provisional
Probab=29.82 E-value=1.8e+02 Score=36.54 Aligned_cols=30 Identities=33% Similarity=0.583 Sum_probs=27.4
Q ss_pred CCeEEEEeeeccccCcCCCCCeeEEeecCC
Q 005429 89 ANALIFTFGSYRLGVHGPGADIDALCVGPS 118 (697)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~ 118 (697)
.+.-|...|.|+-|--.|.||||++++.+.
T Consensus 104 ~~~alvA~GgyGr~EL~p~SDiDLl~l~~~ 133 (931)
T PRK05092 104 ERLAVLAVGGYGRGELAPGSDIDLLFLLPY 133 (931)
T ss_pred CceEEEEecCcCCcccCCCCCceEEEEeCC
Confidence 357899999999999999999999999874
No 66
>PRK11072 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed
Probab=24.68 E-value=2.2e+02 Score=35.91 Aligned_cols=48 Identities=25% Similarity=0.287 Sum_probs=36.2
Q ss_pred CCeEEEEeeeccccCcCCCCCeeEEeecCCc-cC----c---hhhHHHHHHHHHHh
Q 005429 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSY-VS----R---EEDFFFILHNILAE 136 (697)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~-v~----r---e~dFf~~l~~~L~~ 136 (697)
.+..|+-.|-|.-+=-.+.||||++++.+.. .+ + ...||..+.+.|-.
T Consensus 153 ~~~aViamGKlG~~ELn~~SDIDLifly~~~~~~~~~~~~~~~~~~f~rl~q~li~ 208 (943)
T PRK11072 153 QPLLILGMGKLGGRELNFSSDIDLIFTYPEHGETQGGRRSIDNQQFFTRLGQRLIK 208 (943)
T ss_pred CCEEEEEeccccCccCCCccCCceEEEeCCCCCCCCCcccchHHHHHHHHHHHHHH
Confidence 4678999999998888999999999998732 11 1 13688888776654
No 67
>COG1391 GlnE Glutamine synthetase adenylyltransferase [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms]
Probab=23.03 E-value=6.3e+02 Score=32.12 Aligned_cols=47 Identities=23% Similarity=0.294 Sum_probs=28.9
Q ss_pred CeEEEEeeeccccCcCCCCCeeEEeecCCccCc------hhhHHHHHHHHHHh
Q 005429 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVSR------EEDFFFILHNILAE 136 (697)
Q Consensus 90 ~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v~r------e~dFf~~l~~~L~~ 136 (697)
+..|.--|-..-+==.=+||||++.+.|..-.. ..+||+.+.+.|-+
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 444444443333333358999999998865433 13599888776654
No 68
>PRK11072 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed
Probab=22.90 E-value=2.6e+02 Score=35.43 Aligned_cols=60 Identities=12% Similarity=0.245 Sum_probs=40.7
Q ss_pred HhhcCCCccc-cccCCeEEEEeeeccccCcCCCCCeeEEeecCC----------ccCchhhHHHHHHHHHHh
Q 005429 76 TRLRGYSDQM-VEDANALIFTFGSYRLGVHGPGADIDALCVGPS----------YVSREEDFFFILHNILAE 136 (697)
Q Consensus 76 ~~~~g~~~~~-~~~~~~~I~~FGSy~lGv~~p~SDID~l~v~P~----------~v~re~dFf~~l~~~L~~ 136 (697)
+...|.+... ....+..|.-+|-+.-+=-+-+||||++.+... ...- ..||..+.+.|.+
T Consensus 666 ~~~~G~p~~~~~~~~~~aViamGKlGg~EL~y~SDlDlifvy~~~~~~~t~g~~~~~~-~~~~~rl~qrli~ 736 (943)
T PRK11072 666 VKRHGEPPHLEGRERGFAVIGYGKLGGKELGYASDLDLVFLHDCPEDAMTDGDKSIDG-RQFYLRLAQRIIH 736 (943)
T ss_pred HHHhCCCCCccCCCCCEEEEeecCccCCccCCcccceEEEEeecCccccCCCCCcccH-HHHHHHHHHHHHH
Confidence 4456765321 112357888888888887888999999999852 1111 4689988887775
No 69
>PRK14108 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=20.45 E-value=7.9e+02 Score=31.38 Aligned_cols=48 Identities=19% Similarity=0.273 Sum_probs=35.9
Q ss_pred CCeEEEEeeeccccCcCCCCCeeEEeecCCcc-C--c---hhhHHHHHHHHHHh
Q 005429 89 ANALIFTFGSYRLGVHGPGADIDALCVGPSYV-S--R---EEDFFFILHNILAE 136 (697)
Q Consensus 89 ~~~~I~~FGSy~lGv~~p~SDID~l~v~P~~v-~--r---e~dFf~~l~~~L~~ 136 (697)
.+.-|.-.|-|.-+==.++||||++++.+... + + ...||..+.+.|-.
T Consensus 185 ~~~aViamGklGg~ELn~~SDiDLifly~~~~~~~~~~~~~~~~~~rl~q~li~ 238 (986)
T PRK14108 185 SGLIVLGMGKLGAGELNYSSDIDLIVFFDETAPILGDPIEAQPFFVRLTRRLVR 238 (986)
T ss_pred CCeEEEeeccccccccCCCCCCceEEEeCCCCCCccccchHHHHHHHHHHHHHH
Confidence 35789999999999999999999999987321 1 1 03588887776654
Done!