Query 006232
Match_columns 655
No_of_seqs 216 out of 642
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 20:18:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006232.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006232hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2245 Poly(A) polymerase and 100.0 1E-130 2E-135 1054.0 30.4 405 4-418 87-502 (562)
2 PTZ00418 Poly(A) polymerase; P 100.0 5E-124 1E-128 1033.9 42.5 437 4-449 124-572 (593)
3 COG5186 PAP1 Poly(A) polymeras 100.0 5E-112 1E-116 882.2 28.1 410 1-417 76-531 (552)
4 PF04928 PAP_central: Poly(A) 100.0 9.8E-63 2.1E-67 503.1 14.1 192 87-280 63-254 (254)
5 PF04926 PAP_RNA-bind: Poly(A) 100.0 3.9E-32 8.5E-37 258.3 9.1 134 281-415 1-156 (157)
6 COG5260 TRF4 DNA polymerase si 99.9 1.8E-24 3.8E-29 235.0 18.9 224 4-263 93-342 (482)
7 KOG1906 DNA polymerase sigma [ 99.9 7.6E-23 1.7E-27 226.0 19.2 226 3-263 98-341 (514)
8 cd05402 NT_PAP_TUTase Nucleoti 99.7 1E-16 2.2E-21 143.8 11.5 81 4-85 17-100 (114)
9 KOG2277 S-M checkpoint control 99.6 1.5E-14 3.2E-19 162.7 17.7 220 9-264 157-431 (596)
10 TIGR03671 cca_archaeal CCA-add 99.2 8.1E-09 1.8E-13 112.9 29.3 307 4-377 38-363 (408)
11 PRK13300 tRNA CCA-pyrophosphor 99.2 3.6E-09 7.9E-14 116.9 24.3 308 6-377 41-366 (447)
12 PF03813 Nrap: Nrap protein; 99.0 5.5E-08 1.2E-12 116.8 27.2 288 14-321 1-363 (972)
13 COG1746 CCA1 tRNA nucleotidylt 98.5 1.9E-05 4.1E-10 86.7 21.2 308 5-377 44-367 (443)
14 KOG2054 Nucleolar RNA-associat 98.1 1.6E-05 3.5E-10 94.0 12.6 271 4-295 145-464 (1121)
15 smart00572 DZF domain in DSRM 98.1 0.00017 3.7E-09 74.7 18.0 213 9-262 5-230 (246)
16 cd05400 NT_2-5OAS_ClassI-CCAas 97.6 0.00026 5.7E-09 66.0 9.0 78 5-85 26-110 (143)
17 PF01909 NTP_transf_2: Nucleot 97.1 0.00033 7.2E-09 60.0 2.6 34 4-37 12-45 (93)
18 PF03828 PAP_assoc: Cid1 famil 97.1 0.00046 9.9E-09 55.7 3.1 55 177-235 1-59 (60)
19 cd05397 NT_Pol-beta-like Nucle 97.0 0.00074 1.6E-08 53.4 3.9 28 4-31 15-42 (49)
20 cd05403 NT_KNTase_like Nucleot 96.3 0.013 2.9E-07 49.6 6.7 33 6-38 18-50 (93)
21 PF14091 DUF4269: Domain of un 96.2 0.055 1.2E-06 52.8 11.1 117 10-153 19-145 (152)
22 PF09249 tRNA_NucTransf2: tRNA 96.0 0.03 6.5E-07 52.2 7.9 93 137-251 3-97 (114)
23 PF03813 Nrap: Nrap protein; 95.9 0.071 1.5E-06 65.2 13.0 157 116-279 668-839 (972)
24 COG1708 Predicted nucleotidylt 93.7 0.13 2.9E-06 45.8 5.5 29 5-33 25-53 (128)
25 cd00141 NT_POLXc Nucleotidyltr 93.2 0.73 1.6E-05 49.4 11.0 113 5-157 159-277 (307)
26 PF07528 DZF: DZF domain; Int 93.1 4.2 9.1E-05 42.7 16.1 209 12-261 2-231 (248)
27 PRK13746 aminoglycoside resist 92.1 0.22 4.7E-06 52.6 5.2 31 8-38 30-60 (262)
28 COG1669 Predicted nucleotidylt 91.0 0.38 8.2E-06 43.9 4.8 32 4-35 22-53 (97)
29 COG1665 Predicted nucleotidylt 86.5 0.15 3.2E-06 54.1 -1.1 26 10-35 125-150 (315)
30 PRK02098 phosphoribosyl-dephos 85.9 0.96 2.1E-05 46.7 4.4 45 6-52 120-170 (221)
31 TIGR03135 malonate_mdcG holo-A 84.5 1.1 2.5E-05 45.5 4.1 45 6-52 108-158 (202)
32 cd05401 NT_GlnE_GlnD_like Nucl 83.5 2.1 4.6E-05 41.3 5.4 48 5-52 54-101 (172)
33 PF10421 OAS1_C: 2'-5'-oligoad 82.7 2.9 6.4E-05 42.4 6.1 47 130-176 41-88 (190)
34 PF14792 DNA_pol_B_palm: DNA p 79.6 2.9 6.3E-05 38.6 4.6 54 4-58 22-78 (112)
35 PRK08609 hypothetical protein; 71.9 14 0.00031 43.0 8.6 109 5-157 174-283 (570)
36 KOG2054 Nucleolar RNA-associat 65.1 36 0.00078 42.4 10.0 80 118-201 806-890 (1121)
37 smart00483 POLXc DNA polymeras 62.9 48 0.001 36.2 9.9 31 4-35 162-192 (334)
38 PF03445 DUF294: Putative nucl 61.5 15 0.00033 34.9 5.1 49 4-52 47-96 (138)
39 PF10620 MdcG: Phosphoribosyl- 53.7 22 0.00048 36.4 5.1 43 5-48 115-163 (213)
40 PRK05007 PII uridylyl-transfer 50.0 26 0.00057 43.0 5.8 34 4-37 78-111 (884)
41 PRK00227 glnD PII uridylyl-tra 48.1 30 0.00064 41.6 5.7 45 5-51 26-70 (693)
42 PF09970 DUF2204: Nucleotidyl 47.0 36 0.00079 34.0 5.3 81 6-92 16-100 (181)
43 COG2844 GlnD UTP:GlnB (protein 46.9 32 0.00069 42.0 5.6 35 4-38 64-98 (867)
44 PRK01293 phosphoribosyl-dephos 46.8 27 0.00058 36.0 4.4 44 6-51 109-158 (207)
45 PHA02603 nrdC.11 hypothetical 46.0 13 0.00029 40.7 2.2 24 8-31 5-28 (330)
46 PF12633 Adenyl_cycl_N: Adenyl 45.1 25 0.00054 36.2 3.9 30 8-38 99-129 (204)
47 PF03710 GlnE: Glutamate-ammon 40.9 28 0.00061 36.2 3.6 48 5-52 126-179 (247)
48 PF03281 Mab-21: Mab-21 protei 39.9 4.6E+02 0.01 27.4 13.9 97 130-256 190-289 (292)
49 COG3541 Predicted nucleotidylt 37.4 16 0.00035 38.6 1.2 20 11-30 15-34 (248)
50 PRK01759 glnD PII uridylyl-tra 36.6 50 0.0011 40.6 5.3 30 6-35 56-85 (854)
51 PF15431 TMEM190: Transmembran 36.0 23 0.00049 33.5 1.8 30 133-162 73-104 (134)
52 TIGR01693 UTase_glnD [Protein- 34.1 62 0.0014 39.5 5.6 31 5-35 42-72 (850)
53 PF07357 DRAT: Dinitrogenase r 33.7 16 0.00035 38.8 0.5 21 296-316 95-115 (262)
54 PRK00275 glnD PII uridylyl-tra 32.2 63 0.0014 39.9 5.2 32 6-37 78-109 (895)
55 COG1796 POL4 DNA polymerase IV 30.6 86 0.0019 34.6 5.3 69 8-85 182-250 (326)
56 PF10127 Nuc-transf: Predicted 29.9 26 0.00056 36.1 1.3 25 9-33 23-47 (247)
57 KOG2534 DNA polymerase IV (fam 28.7 1E+02 0.0022 34.2 5.4 50 4-54 169-218 (353)
58 PRK14109 bifunctional glutamin 28.0 70 0.0015 40.1 4.6 47 6-52 723-773 (1007)
59 PRK05092 PII uridylyl-transfer 27.8 89 0.0019 38.7 5.5 31 5-35 104-134 (931)
60 PRK14109 bifunctional glutamin 27.8 82 0.0018 39.5 5.2 47 6-52 215-265 (1007)
61 PRK04374 PII uridylyl-transfer 25.3 1.1E+02 0.0024 37.8 5.6 30 6-35 72-101 (869)
62 PRK03381 PII uridylyl-transfer 23.7 1.1E+02 0.0024 37.3 5.1 30 5-34 56-85 (774)
63 PRK03059 PII uridylyl-transfer 22.4 1.2E+02 0.0025 37.5 5.1 29 6-34 61-89 (856)
64 PRK14108 bifunctional glutamin 20.1 1.3E+02 0.0028 37.8 4.8 47 6-52 186-238 (986)
No 1
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=100.00 E-value=1.1e-130 Score=1054.03 Aligned_cols=405 Identities=57% Similarity=1.009 Sum_probs=386.9
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhcCCCceeEeeecCCCcceEEEEEcCeeeeEEe
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLY 83 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~ArVPIIKf~~~GI~IDL~f 83 (655)
--+++||||||||||||+||||||+|||+|+|++|+ |||..|+++|+++++|++|++|++|+||||||+|+||+|||+|
T Consensus 87 ~aggkIftfGSYRLGVhg~GADIDtLcV~Prhv~R~-DFF~sf~~mL~~~~eVteL~~V~dAfVPiikfKf~GI~IDllf 165 (562)
T KOG2245|consen 87 NAGGKIFTFGSYRLGVHGPGADIDTLCVGPRHVSRS-DFFTSFYDMLKERPEVTELHAVEDAFVPIIKFKFDGIEIDLLF 165 (562)
T ss_pred hcCceEEeccceeecccCCCCCcceeeeccccccHH-HHHHHHHHHHhcCccccccccccccccceEEEEecCeeeeeee
Confidence 357899999999999999999999999999999996 9999999999999999999999999999999999999999999
Q ss_pred eeccccccCCCCCCChhhhhccchhhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCcccchHHHH
Q 006232 84 ARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWA 163 (655)
Q Consensus 84 a~l~~~~ipe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfLGGiswA 163 (655)
|+|++++||+++||+||++|+++||+|+||||||||||+||+|||+.+.||.+|||||+|||+||||||.+||||||+||
T Consensus 166 ArL~l~~VP~dldl~ddslLknlDe~~vrSLNGcRVtdqiL~LVPn~~~F~~tLRaiKlWAKrrgVYsN~~GF~GGV~wA 245 (562)
T KOG2245|consen 166 ARLALPVVPEDLDLSDDSLLKNLDERCVRSLNGCRVTDQILKLVPNQENFRITLRAIKLWAKRRGVYSNVMGFLGGVAWA 245 (562)
T ss_pred hhcccccCCCcccccchHhhhcccHHHHHHhcCcCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcccccccccccchHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCCceeecccccCCCcccccCCCCCCCCCCCceeeeCCCCCCCCcccccC
Q 006232 164 LLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVS 243 (655)
Q Consensus 164 ILVArvcQlyPnas~s~LL~~FF~~Ys~WdWp~PV~L~~i~~g~lg~~vWdP~~~~~dr~hlMpIiTPa~P~~Nsa~NVs 243 (655)
|||||+|||||||+++.||.+||.+|++|+||+||+|+.+++|.++++||||+.|+.||||+|||||||||+||+|||||
T Consensus 246 ~LVARiCQLYPNA~~s~Lv~kfF~ifs~W~WP~PVlL~~ie~~~L~~~VWdPr~n~~DryHlMPIITPAyP~~nsthNVS 325 (562)
T KOG2245|consen 246 MLVARICQLYPNASPSTLVAKFFRVFSQWNWPNPVLLKPIEEGNLNLPVWDPRVNPSDRYHLMPIITPAYPQMNSTHNVS 325 (562)
T ss_pred HHHHHHHccCCCcchHHHHHHHHHHHhhccCCCceEeccccccccCccccCCCCCCCCcceecccccCCccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHhccCCCCCccccCccchhhhcccEEEEEEEecChhhhcchhhhhHHHHHHHHHHHhhc
Q 006232 244 TSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERH 323 (655)
Q Consensus 244 ~STl~vI~~EF~RA~~Il~~i~~~~~~~~W~~Lfep~~FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~ 323 (655)
+||+++|++||+||++||++|+.++. +|.+|||+++||.+|||||+|+++|.++|++.+|.||||||+|.|+.+||++
T Consensus 326 ~ST~~Vi~~Ef~~g~~I~~~i~~~k~--~W~~LFE~~~FF~rYk~yl~i~~~A~~~ed~l~w~G~vESriR~Lv~klE~~ 403 (562)
T KOG2245|consen 326 RSTLKVITEEFKRGLEICDDIELNKL--DWSDLFELYNFFSRYKHYLQITASAATEEDLLKWVGWVESRIRQLVLKLERN 403 (562)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccc--cHHHHhhhhHHHHHHhhHheeeeeccChHHHhhhhhHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999998 9999999999999999999999999999999999999999999999999996
Q ss_pred cccceeeccCCCCCCCCCC-----CcEEEEEEeeeeccCCCCCCCceechHHHHHHHHHHHH----hhccCCCC--cEEE
Q 006232 324 TYNMLQCHPHPGDFSDKSK-----PLYCSYFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVS----MYTLRKPG--MQIS 392 (655)
Q Consensus 324 ~~~~l~ahp~P~~f~~~~~-----~~~~~yfIGL~~~~~~~~~~~~~~DL~~~v~eF~~~v~----~~~~~~~g--m~i~ 392 (655)
. .++.|||+|+.|.++.. .|...|||||.+..+ .++||+..+++|+..|+ +++.++.| |++.
T Consensus 404 ~-~i~~ahp~P~~f~~~~~~~~~~~~~~~~~igl~~~e~------~~~Dlt~~iq~f~~~v~~q~~~~~~~~~g~~~~~~ 476 (562)
T KOG2245|consen 404 Q-VILIAHPNPKKFKDTYNCPLEEDPESLWFIGLEFDEN------VKIDLTKDIQSFKKNVERQAVNLTLIKAGCDVEID 476 (562)
T ss_pred c-ceEEecCCcccccccccCCcccchhHhhhhccccccc------ccchhhhhHHHhhhhhhhcceeeeeeecccccccc
Confidence 4 67899999999997642 456789999987653 34999999999999998 67888899 7788
Q ss_pred EEEecCCCCCCCcCCCCCCCCCCCCC
Q 006232 393 VAHVTRRNLPNFVFPGGVRPSRPSKG 418 (655)
Q Consensus 393 v~~Vkr~~LP~~v~~~~~~~~~~~k~ 418 (655)
+.|+||++|+.++++.+.|..|..|.
T Consensus 477 ~~~~krr~l~~~~~~~~l~~~k~~~~ 502 (562)
T KOG2245|consen 477 FGHVKRRSLIQTITKEFLRLCKQYKK 502 (562)
T ss_pred cccccccccccccCHHHhhHHHhhcc
Confidence 88999999999999999887765553
No 2
>PTZ00418 Poly(A) polymerase; Provisional
Probab=100.00 E-value=4.9e-124 Score=1033.86 Aligned_cols=437 Identities=43% Similarity=0.817 Sum_probs=397.3
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhcCCCceeEeeecCCCcceEEEEEcCeeeeEEe
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLY 83 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~ArVPIIKf~~~GI~IDL~f 83 (655)
-..++|+||||||||||+|+||||+|||+|+|++|+ +||..|+++|++.++|++|++|++|+||||||+|+||+|||+|
T Consensus 124 ~~~g~I~tfGSYrLGV~~pgSDID~L~V~P~~vtre-dFF~~f~~~L~~~~~V~eL~~V~~A~VPiIk~~~~GI~iDL~f 202 (593)
T PTZ00418 124 QISGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRE-SFFSDFYAKLQQDPNITKLQPVPDAYTPVIKFVYDGIDIDLLF 202 (593)
T ss_pred cCCeEEEEeccccccCCCCCCcccEEEECCCCCCHH-HHHHHHHHHHhcCCCcceeeccCccccCeEEEEECCEEEeeee
Confidence 467999999999999999999999999999999995 9999999999999999999999999999999999999999999
Q ss_pred eeccccccCCCCCCChhh-hhccchhhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCcccchHHH
Q 006232 84 ARLSLWVIPEDLDISQDS-ILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINW 162 (655)
Q Consensus 84 a~l~~~~ipe~ldl~~d~-lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfLGGisw 162 (655)
|+++...||+++++.+|+ +|++||++++|||||+||+|+|+++||+.++||.+|||||+|||+||||||++||||||+|
T Consensus 203 a~l~~~~vp~~~~~l~d~~lL~nlde~s~rSLNG~Rvtd~Il~lVPn~~~Fr~aLR~IKlWAkrRGIYsNv~GflGGV~w 282 (593)
T PTZ00418 203 ANLPLPTIPDCLNSLDDDYILRNVDEKTVRSLNGCRVADLILASVPNKDYFRTTLRFIKLWAKRRGIYSNVLGYLGGVSW 282 (593)
T ss_pred cccCCCCCCccccccCchhhhhcCCHHHhhhhccHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccccccccccchHHH
Confidence 999999999999988876 9999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCCceeeccccc-----CCCcccccCCCCCCCCCCCceeeeCCCCCCCC
Q 006232 163 ALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEE-----GSLGLQVWDPRRNPKDKYHLMPIITPAYPCMN 237 (655)
Q Consensus 163 AILVArvcQlyPnas~s~LL~~FF~~Ys~WdWp~PV~L~~i~~-----g~lg~~vWdP~~~~~dr~hlMpIiTPa~P~~N 237 (655)
||||||+||+|||+++++||.+||.+|++|+||+||+|++|++ |.++++||||+.|++|++|+||||||+||+||
T Consensus 283 AILvARVCQLyPna~~s~Lv~~FF~iys~W~Wp~PV~L~~i~~~~~~~g~~~~~VWdPr~~~~dr~h~MPIITPayP~mN 362 (593)
T PTZ00418 283 AILTARICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKEVPNIPGLMNFKVWDPRVNPQDRAHLMPIITPAFPSMN 362 (593)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCCCeEcccccccccCCcccCCcccCCCCCcccccccCCeecCCCCCcc
Confidence 9999999999999999999999999999999999999999875 77899999999999999999999999999999
Q ss_pred cccccChhhHHHHHHHHHHHHHHHHHHHh-ccCCCCCccccCccchhhhcccEEEEEEEecChhhhcchhhhhHHHHHHH
Q 006232 238 SSYNVSTSTLRIMMDEFQRGHEICEAMEK-NEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQL 316 (655)
Q Consensus 238 sa~NVs~STl~vI~~EF~RA~~Il~~i~~-~~~~~~W~~Lfep~~FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~L 316 (655)
+|||||.+|+++|++||+||++||+++.. ++. +|++||+|++||.+|++||+|++.+.+++++..|.||||||||.|
T Consensus 363 st~nVt~sT~~vI~~Ef~Ra~~i~~~i~~~~~~--~W~~Lfep~~Ff~~Yk~yl~V~v~a~~~~~~~~w~G~VESRlR~L 440 (593)
T PTZ00418 363 STHNVTYTTKRVITEEFKRAHEIIKYIEKNSEN--TWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFL 440 (593)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHhcCCC--CHHHHcCCcchhhhcceEEEEEEEECCHHHhhhhhhHHHHHHHHH
Confidence 99999999999999999999999999887 666 999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccccceeeccCCCCCCCCC--CCcEEEEEEeeeeccCCCCCCCceechHHHHHHHHHHHHhhc---cCCCCcEE
Q 006232 317 TLKIERHTYNMLQCHPHPGDFSDKS--KPLYCSYFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYT---LRKPGMQI 391 (655)
Q Consensus 317 v~~LE~~~~~~l~ahp~P~~f~~~~--~~~~~~yfIGL~~~~~~~~~~~~~~DL~~~v~eF~~~v~~~~---~~~~gm~i 391 (655)
+.+||+.. .+++||||++|.+.. ..|+++|||||+++.+... +.+++||+.++++|++.|++|. .|+++|+|
T Consensus 441 v~~LE~~~--~i~~~p~P~~f~~~~~~~~~~~~ffIGL~~~~~~~~-~~~~~Dl~~~~~~F~~~i~~~~~~~~~~~~~~i 517 (593)
T PTZ00418 441 IKKLETLN--NLKIRPYPKFFKYQDDGWDYASSFFIGLVFFSKNVY-NNSTFDLRYAIRDFVDIINNWPEMEKYPDQIDI 517 (593)
T ss_pred HHHhhccC--CceEeecCcccccCCCCceeEEEEEEeEeeccCCCC-CCceEecHHHHHHHHHHHHhhhhcccCCCCceE
Confidence 99999853 468999999998765 4588999999998765432 3458999999999999999886 46889999
Q ss_pred EEEEecCCCCCCCcCCCCCCCCCCCCCcccccccccccCCCCCCCCCCCccccccccc
Q 006232 392 SVAHVTRRNLPNFVFPGGVRPSRPSKGTWDSRRALERKVSSHTKPGADDGRKRKQTDD 449 (655)
Q Consensus 392 ~v~~Vkr~~LP~~v~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~ 449 (655)
+|+|||+++||+|||+.|.++.+.+|...+... .+...++|.|.....+.++.++
T Consensus 518 ~v~~Vk~~~Lp~~v~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~ 572 (593)
T PTZ00418 518 NIKYLKKSQLPAFVLSQTPEEPVKTKANTKTNT---SSATTSGQSGSSGSTSNSNSNE 572 (593)
T ss_pred EEEEeehHhCCHhhccCCCcCCCcccccccccc---ccccccccccccCcccCCCCCc
Confidence 999999999999999998877666663333322 2223344444444444444443
No 3
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=100.00 E-value=4.8e-112 Score=882.21 Aligned_cols=410 Identities=45% Similarity=0.838 Sum_probs=387.8
Q ss_pred CCCCCCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhcCCCceeEeeecCCCcceEEEEEcCeeee
Q 006232 1 MPRYLPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSID 80 (655)
Q Consensus 1 ~~r~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~ArVPIIKf~~~GI~ID 80 (655)
|-|-.+.+||||||||||||+||||||+|||.|.|++|+ |||+.|..+|++.++++++.+|++|+||||||+|+||+||
T Consensus 76 mar~aGGKIFTyGSYRLGVhgpGsDIDtLvvVPkHVsR~-dFFt~f~~~Lrer~ei~eva~vpDAfVPIIK~KF~GIsID 154 (552)
T COG5186 76 MARPAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVSRS-DFFTHFYEELRERPEIEEVAKVPDAFVPIIKLKFQGISID 154 (552)
T ss_pred ccccCCceeeeecceeeeccCCCCCcceEEEecccccHH-HHHHHHHHHhccCcchhhhccCCcccceeEEEEecCccce
Confidence 678889999999999999999999999999999999995 9999999999999999999999999999999999999999
Q ss_pred EEeeeccccccCCCCCCChhhhhccchhhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCcccchH
Q 006232 81 LLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGI 160 (655)
Q Consensus 81 L~fa~l~~~~ipe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfLGGi 160 (655)
|.||+|..+++|..++++|+++|++|||+|++||||.||||+||+|||+...|+.+|||||+||+||.||.|.+||.||+
T Consensus 155 LifARLs~P~Vp~~l~Lsd~nLLk~~dEkcilsLNGtRVTDeiL~LVP~~~vF~~ALRaIK~WAqRRavYaN~~GfpGGV 234 (552)
T COG5186 155 LIFARLSIPVVPDGLNLSDDNLLKSMDEKCILSLNGTRVTDEILNLVPSVKVFHSALRAIKYWAQRRAVYANPYGFPGGV 234 (552)
T ss_pred eeeeeccCCcCCCcccccchhhhhcchHHHHHhhcCceehHHHHHhCCchHHHHHHHHHHHHHHHhhhhhccccCCcchH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCCceeecccccCCCcccccCCCCCCCCCCCceeeeCCCCCCCCccc
Q 006232 161 NWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSY 240 (655)
Q Consensus 161 swAILVArvcQlyPnas~s~LL~~FF~~Ys~WdWp~PV~L~~i~~g~lg~~vWdP~~~~~dr~hlMpIiTPa~P~~Nsa~ 240 (655)
+||||||||||||||++...|+.+||.++++|+||+||+|++|++|.++.++|||+.|+.|++|.||||||+||+||.||
T Consensus 235 Awam~VARiCQLYPNA~S~vIv~kFF~ils~WnWPqPviLkPieDgplqvrvWnPKvYpsDk~HRMPvITPAYPSMCATH 314 (552)
T COG5186 235 AWAMCVARICQLYPNASSFVIVCKFFEILSSWNWPQPVILKPIEDGPLQVRVWNPKVYPSDKYHRMPVITPAYPSMCATH 314 (552)
T ss_pred HHHHHHHHHHhhccCcchHhHHHHHHHHHHhcCCCCCeEeeeccCCCeeEEeeCCccCcccccccCccccCCchhhhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccChhhHHHHHHHHHHHHHHHHHHHhccCCCCCccccCccchhhhcccEEEEEEEecChhhhcchhhhhHHHHHHHHHHH
Q 006232 241 NVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKI 320 (655)
Q Consensus 241 NVs~STl~vI~~EF~RA~~Il~~i~~~~~~~~W~~Lfep~~FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~L 320 (655)
|||.||..+|..||.||++|+.+|+.+.. +|..||+..|||.+||+||.|++.+.++|++.+|.|+||||+|.|+.+|
T Consensus 315 Nit~STq~vIl~EfvRa~~I~~di~~n~~--~w~~lFek~DFF~RYk~yleitA~s~~~E~~lKW~GlvESKiR~Lv~kl 392 (552)
T COG5186 315 NITNSTQHVILMEFVRAHKILSDIERNAL--DWRRLFEKSDFFSRYKLYLEITAMSSCEEDFLKWEGLVESKIRILVSKL 392 (552)
T ss_pred cccchhhhhHHHHHHHHHHhhhhHhhccc--cHHHHHHhhhHHHHHhHhhhhhhhhcchhhhhhhhhHHHHHHHHHHHHH
Confidence 99999999999999999999999998777 9999999999999999999999999999999999999999999999999
Q ss_pred hhccccceeeccCCCCCCC------------------------------------C--------CCCcEEEEEEeeeecc
Q 006232 321 ERHTYNMLQCHPHPGDFSD------------------------------------K--------SKPLYCSYFMGLQRKQ 356 (655)
Q Consensus 321 E~~~~~~l~ahp~P~~f~~------------------------------------~--------~~~~~~~yfIGL~~~~ 356 (655)
|-.. +++.|||||+.|.. + ...|++.|||||+...
T Consensus 393 E~vd-~i~~AhPF~K~F~~~y~c~~Ee~~e~i~~~~~~~~a~~s~d~~kl~~d~~~eees~~d~~k~y~tt~yIgld~~~ 471 (552)
T COG5186 393 EAVD-DILYAHPFPKAFRKVYNCVAEESIEKIGSGVTLEVAYESTDHEKLANDTVPEEESMEDGMKVYCTTFYIGLDVIP 471 (552)
T ss_pred HHhh-hhhhcCcCChhhhhhcCCccHHHHHHHhcccceeehhhccchhhhccccCchhhhhccccceeeeEEEEEEEeee
Confidence 9764 67889999999861 0 0127788999999764
Q ss_pred CCCCCCCceechHHHHHHHHHHHHhhccCC-CCcEEEEEEecCCCCCCCcCC-CCCCCCCCCC
Q 006232 357 GVPVGEGEQFDIRLTVKEFKQAVSMYTLRK-PGMQISVAHVTRRNLPNFVFP-GGVRPSRPSK 417 (655)
Q Consensus 357 ~~~~~~~~~~DL~~~v~eF~~~v~~~~~~~-~gm~i~v~~Vkr~~LP~~v~~-~~~~~~~~~k 417 (655)
. ..++++|+...+++|.+.|+.|++++ .+|.|.+..+|+++||+-||. ++.||+..+|
T Consensus 472 ~---~~~kkvdi~~p~~EF~elcr~~d~gd~~~mni~v~~~K~~dlpdeVF~~geerPs~~sK 531 (552)
T COG5186 472 V---KPGKKVDIEQPVKEFIELCREYDEGDASGMNIEVNSLKRKDLPDEVFYPGEERPSNSSK 531 (552)
T ss_pred c---CCCceeeeeccHHHHHHHHHHhhccccceeeeehhhccccCCchhhcCCCccCcccccc
Confidence 3 34678999999999999999997775 479999999999999999995 7777765333
No 4
>PF04928 PAP_central: Poly(A) polymerase central domain; InterPro: IPR007012 In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolutio has been determined []. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta-sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.; GO: 0004652 polynucleotide adenylyltransferase activity, 0006351 transcription, DNA-dependent; PDB: 1Q79_A 1Q78_A 1F5A_A 2O1P_A 2HHP_A 3C66_B 1FA0_A 2Q66_A.
Probab=100.00 E-value=9.8e-63 Score=503.14 Aligned_cols=192 Identities=64% Similarity=1.162 Sum_probs=155.1
Q ss_pred cccccCCCCCCChhhhhccchhhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCcccchHHHHHHH
Q 006232 87 SLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLV 166 (655)
Q Consensus 87 ~~~~ipe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfLGGiswAILV 166 (655)
....+|+++++.++++|++||++|++||||+||+++|+++||+.+.||.+|||||+|||+||||||++||||||+|||||
T Consensus 63 ~~~~~p~~l~~~~~~~l~~ld~~s~~sLnG~Rv~~~il~~Vp~~~~Fr~~lR~IK~WAk~RGIYsn~~GylGGI~waILv 142 (254)
T PF04928_consen 63 ALPRVPEDLDLLDDDPLRNLDEASVRSLNGVRVTDYILRLVPNQETFRTALRFIKLWAKRRGIYSNVFGYLGGIHWAILV 142 (254)
T ss_dssp SSSSB-TT--TT-GGGGTT--HHHHHHHHHHHHHHHHHCTSS-HHHHHHHHHHHHHHHHHTT-B-CCCTSB-HHHHHHHH
T ss_pred hhcCCCcccccCCchhhhCCCHhhccCcccccHHHHHHHHCCCHHHHHHHHHHHHHHHHHccccchhhccchHHHHHHHH
Confidence 56678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhCCCCCHHHHHHHHHHhhccCCCCCceeecccccCCCcccccCCCCCCCCCCCceeeeCCCCCCCCcccccChhh
Q 006232 167 ARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTST 246 (655)
Q Consensus 167 ArvcQlyPnas~s~LL~~FF~~Ys~WdWp~PV~L~~i~~g~lg~~vWdP~~~~~dr~hlMpIiTPa~P~~Nsa~NVs~ST 246 (655)
||+||+|||+++++||.+||.+|++|+||+||+|+.+.++.+++++|+|+.+.+|+.|+||||||+||+||+|+|||++|
T Consensus 143 Arvcql~Pn~~~~~ll~~FF~~ys~W~W~~PV~l~~~~~~~~~~~~w~p~~~~~~~~~~MpIiTP~yP~~Nst~nVt~st 222 (254)
T PF04928_consen 143 ARVCQLYPNASPSTLLSRFFQIYSQWDWPNPVVLDPIEDGPLGFKVWNPRLYPRDRRHLMPIITPAYPSMNSTYNVTRST 222 (254)
T ss_dssp HHHHHHSTT--HHHHHHHHHHHHHCS-TTS-EESS-----SSSCGS--TTT-HHHHC-SS-EE-SSSS--BTTTT--HHH
T ss_pred HHHHHHCccccccchHHHHHHHhcCCCCCCceeecccccCcccccCCCCCCCCCCcccceeEccCCCCccccccccCHHH
Confidence 99999999999999999999999999999999999999999999999999888999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCCCCCccccCcc
Q 006232 247 LRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPF 280 (655)
Q Consensus 247 l~vI~~EF~RA~~Il~~i~~~~~~~~W~~Lfep~ 280 (655)
+++|++||+||++|++++..++. +|++||+|+
T Consensus 223 ~~~i~~Ef~ra~~i~~~~~~~~~--~W~~L~e~~ 254 (254)
T PF04928_consen 223 LRIIREEFQRAHEILSEILKGGA--SWSDLFEPH 254 (254)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTSS---HHHCT---
T ss_pred HHHHHHHHHHHHHHHHHHHcCCC--CHHHHcCCC
Confidence 99999999999999999987776 999999985
No 5
>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=3.9e-32 Score=258.33 Aligned_cols=134 Identities=40% Similarity=0.767 Sum_probs=105.5
Q ss_pred chhhhcccEEEEEEEecChhhhcchhhhhHHHHHHHHHHHhhccccceeeccCCCCCC-------------------CCC
Q 006232 281 TFFEAYKNYLRIDISAENADDLRNWKGWVESRLRQLTLKIERHTYNMLQCHPHPGDFS-------------------DKS 341 (655)
Q Consensus 281 ~FF~~Yk~yl~I~v~a~~~e~~~~w~GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~-------------------~~~ 341 (655)
+||.+|||||+|+|+|.+++++.+|.||||||||.|+.+||+.. .+..|||||+.|. +..
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 69999999999999999999999999999999999999999975 4778999999998 122
Q ss_pred CCcEEEEEEeeeeccCCCCCCCceechHHHHHHHHHHHHhhcc---CCCCcEEEEEEecCCCCCCCcCCCCCCCCCC
Q 006232 342 KPLYCSYFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYTL---RKPGMQISVAHVTRRNLPNFVFPGGVRPSRP 415 (655)
Q Consensus 342 ~~~~~~yfIGL~~~~~~~~~~~~~~DL~~~v~eF~~~v~~~~~---~~~gm~i~v~~Vkr~~LP~~v~~~~~~~~~~ 415 (655)
..++++|||||++........++++||+.++++|++.|++|.+ +.++|+|+|+||||++||++||++|.++.++
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 4588999999999876543334679999999999999999877 5678999999999999999999998876543
No 6
>COG5260 TRF4 DNA polymerase sigma [DNA replication, recombination, and repair]
Probab=99.92 E-value=1.8e-24 Score=234.98 Aligned_cols=224 Identities=21% Similarity=0.300 Sum_probs=180.1
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhcCCCceeEeeecCCCcceEEEEE--cCeeeeE
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKF--SGVSIDL 81 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~ArVPIIKf~~--~GI~IDL 81 (655)
||++.+++||||-.|+++|+||||++++.+....++..=-..++..|....+..++.+|..|+||||||.. .|+.|||
T Consensus 93 ~pda~l~vFGS~~t~L~l~~SDiDl~I~s~~~~~~et~~~~~l~~~l~~~~~~~~~~~v~tarVPIIKl~d~~s~l~~Di 172 (482)
T COG5260 93 FPDADLKVFGSTETGLALPKSDIDLCIISDPRGYKETRNAGSLASHLFKKNLAKEVVVVSTARVPIIKLVDPQSGLHCDI 172 (482)
T ss_pred CCccceeEecccccccccCcccccEEEecCCccccccccHHHHHHHHHHhccCeeeEEEEecccceEEEecCccceEEEe
Confidence 89999999999999999999999999999776655421112455566666778899999999999999998 5999999
Q ss_pred EeeeccccccCCCCCCChhhhhccchhhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCcccchHH
Q 006232 82 LYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGIN 161 (655)
Q Consensus 82 ~fa~l~~~~ipe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfLGGis 161 (655)
+|++. +|++.|..|+.++-..+++|.++..||+||++|.+++...|+|+|++
T Consensus 173 sfn~~----------------------------~~~~~akl~~~~~~~~P~lrpLvliIKhwl~~R~ln~~~~GtL~sy~ 224 (482)
T COG5260 173 SFNNT----------------------------NGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVATGTLSSYT 224 (482)
T ss_pred ecCch----------------------------hHHHHHHHHHHHHhcCcccchHHHHHHHHHHHHhhcccccCcchhhh
Confidence 99984 47788899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhCCC------------------CCHHHHHHHHHHhhc-cCCCCCceeecccccC-CC-cc--cccCCCCC
Q 006232 162 WALLVARICQLYPN------------------AVPSMLVSRFFRVYT-QWRWPNPVLLCAIEEG-SL-GL--QVWDPRRN 218 (655)
Q Consensus 162 wAILVArvcQlyPn------------------as~s~LL~~FF~~Ys-~WdWp~PV~L~~i~~g-~l-g~--~vWdP~~~ 218 (655)
+.+||..++|++|. ..++.|+.+||++|+ .|+|..-++ .+..| .+ .. ..|=-..
T Consensus 225 i~cmV~sfLq~~~~~~~~~~~~~~~l~~~~~~~~lgvLf~dFf~~yG~~f~Y~~~~~--si~~g~~~~~K~e~g~~~~~- 301 (482)
T COG5260 225 ISCMVLSFLQMHPPFLFFDNGLLSPLKYNKNIDNLGVLFDDFFELYGKSFNYSLVVL--SINSGDFYLPKYEKGWLKPS- 301 (482)
T ss_pred hHHHHHHHHHhCCccccccccccchhhccccccccchHHHHHHHHhccccChhheEE--EecCCceeeehhhccccccc-
Confidence 99999999999981 257899999999999 688887543 23344 11 11 2332111
Q ss_pred CCCCCCceeeeCCC-CCCCCcccccChhhHHHHHHHHHHHHHHHHH
Q 006232 219 PKDKYHLMPIITPA-YPCMNSSYNVSTSTLRIMMDEFQRGHEICEA 263 (655)
Q Consensus 219 ~~dr~hlMpIiTPa-~P~~Nsa~NVs~STl~vI~~EF~RA~~Il~~ 263 (655)
+...+.|++|. .+..+++ ...-|...|+.+|.+|.+++.+
T Consensus 302 ---~p~~LsiqdP~td~n~~~~--a~s~~ik~i~~~F~~aF~lls~ 342 (482)
T COG5260 302 ---KPNSLSIQDPGTDRNNDIS--AVSFNIKDIKAAFIRAFELLSN 342 (482)
T ss_pred ---CCCcEeecCCCCCcccccc--cccchHHHHHHHHHHHHHHHhh
Confidence 12679999999 4444333 3445789999999999998864
No 7
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=99.90 E-value=7.6e-23 Score=226.01 Aligned_cols=226 Identities=19% Similarity=0.273 Sum_probs=180.4
Q ss_pred CCCCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhc--CCCceeEeeecCCCcceEEEEE--cCee
Q 006232 3 RYLPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTE--MPEVTELHPVPDAHVPVMKFKF--SGVS 78 (655)
Q Consensus 3 r~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~--~~~V~~l~~V~~ArVPIIKf~~--~GI~ 78 (655)
+||.+.|..||||.+|+++|+||||+++..+.+..++ +.+..+.-++.. ...-..+..|..|+||||||+. .+|.
T Consensus 98 ~~~~a~v~~FGS~~tglyLP~sDIDl~v~~~~~~~~e-~~~~~~~l~~~~e~~~~~~~v~~v~karvpiik~~d~~s~i~ 176 (514)
T KOG1906|consen 98 KWPDASVYVFGSVPTGLYLPDSDIDLVVLSKFLNDKE-DRAVKLELALELEEDNSAFHVKVVQKARVPIIKFKDPVSNIH 176 (514)
T ss_pred hcccceeEEeeeeeccccccccceEEEEecccccCch-hhHHHHHHHHhhhhccccceEEEeeeeeeeeEEeecCccceE
Confidence 5999999999999999999999999999999777664 566555555444 3344568899999999999996 7999
Q ss_pred eeEEeeeccccccCCCCCCChhhhhccchhhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCcccc
Q 006232 79 IDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLG 158 (655)
Q Consensus 79 IDL~fa~l~~~~ipe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfLG 158 (655)
|||+|++. ||||.++.|...+-+...+|.++..+|.|...|++++...|.++
T Consensus 177 vDISFn~~----------------------------~G~~aa~~i~~~~~~~p~~~~lvlvlk~fl~~r~ln~v~tGgis 228 (514)
T KOG1906|consen 177 VDISFNQT----------------------------NGVKAAKFIKDFLRDHPFLRSLVLVLKQFLYERRLNGVHTGGIS 228 (514)
T ss_pred EEeeeccc----------------------------CchhHHHHHHHHHhcCccchhHHHHHHHHHHhhcccccccccch
Confidence 99999984 68999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHhhCCCC---------CHHHHHHHHHHhhc-cCCCCC-ceeecccccCC-Cc--ccccCCCCCCCCCCC
Q 006232 159 GINWALLVARICQLYPNA---------VPSMLVSRFFRVYT-QWRWPN-PVLLCAIEEGS-LG--LQVWDPRRNPKDKYH 224 (655)
Q Consensus 159 GiswAILVArvcQlyPna---------s~s~LL~~FF~~Ys-~WdWp~-PV~L~~i~~g~-lg--~~vWdP~~~~~dr~h 224 (655)
+|++++||..+.|++|.. ..+.|+.+||++|+ +|++.. -|.+.. .|. .+ ...|- .+...+..
T Consensus 229 Syal~~Lv~~fl~l~~~~~s~~~~~~~~~~vll~~f~e~yG~~f~~~k~~i~~~~--~g~~~~~~~~~~~--~~~~~~~~ 304 (514)
T KOG1906|consen 229 SYALELLVLSFLQLHPRSKSGRLAVLKNLGVLLIKFFELYGRNFGYDKLGISLSL--GGEYVSKELTGFF--NNSLERPG 304 (514)
T ss_pred HHHHHHHHHHHHhhcccccCCccchhcccchHHHHHHHHhccccCchhhceeccC--CcccccHHhhhhh--cccccCCC
Confidence 999999999999999863 35689999999999 677665 343321 111 11 01111 12224456
Q ss_pred ceeeeCCCCCCCCcccccChhhHHHHHHHHHHHHHHHHH
Q 006232 225 LMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEA 263 (655)
Q Consensus 225 lMpIiTPa~P~~Nsa~NVs~STl~vI~~EF~RA~~Il~~ 263 (655)
.+.|++|..|..+.++. ...+..|+.+|..|+.++..
T Consensus 305 ~LsieDP~~P~ndigr~--s~~~~~v~~~F~~af~~l~~ 341 (514)
T KOG1906|consen 305 SLSIEDPVDPTNDIGRS--SFNFSQVKGAFAYAFKVLTN 341 (514)
T ss_pred ccccCCCCCcccccccc--cccHHHHHHHHHHHHHHHhh
Confidence 79999999997666522 24577899999999998753
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=99.70 E-value=1e-16 Score=143.77 Aligned_cols=81 Identities=33% Similarity=0.600 Sum_probs=75.4
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEEcCCC-CCchhhHHHHHHHHHhcCCCceeEeeecCCCcceEEEEEc--Ceeee
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCVGPRH-ATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFS--GVSID 80 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~-vtr~edFF~~l~~~L~~~~~V~~l~~V~~ArVPIIKf~~~--GI~ID 80 (655)
||++++++|||+++|+++|+||||+++..|.. ... ..++..+...|++...+.++..|..|+||||||.+. |++||
T Consensus 17 ~~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~~~~~-~~~l~~l~~~l~~~~~~~~~~~i~~ArVPiik~~~~~~~i~~D 95 (114)
T cd05402 17 FPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDR-EDFLRKLAKLLKKSGEVVEVEPIINARVPIIKFVDKPTGIEVD 95 (114)
T ss_pred CCCCEEEEecccccCCCCCCCCeeEEEEeCCCCccH-HHHHHHHHHHHHhCCCceeeEEeccCCCCEEEEEEcCCCeEEE
Confidence 79999999999999999999999999999986 333 489999999999988889999999999999999998 99999
Q ss_pred EEeee
Q 006232 81 LLYAR 85 (655)
Q Consensus 81 L~fa~ 85 (655)
|+|++
T Consensus 96 is~~~ 100 (114)
T cd05402 96 ISFNN 100 (114)
T ss_pred EEccc
Confidence 99997
No 9
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=99.60 E-value=1.5e-14 Score=162.68 Aligned_cols=220 Identities=21% Similarity=0.310 Sum_probs=168.4
Q ss_pred EEEeeccccCCcCCCCCeeEEEEcCCCC--C---c-hhhHHHHHHHHHhcCCC--ceeEeeecCCCcceEEEEE--cCee
Q 006232 9 LIGLGYDKYSVHGPGADIDTLCVGPRHA--T---R-EEDFFGELHQMLTEMPE--VTELHPVPDAHVPVMKFKF--SGVS 78 (655)
Q Consensus 9 L~~FGSyrLGV~~p~SDID~lcv~P~~v--t---r-~edFF~~l~~~L~~~~~--V~~l~~V~~ArVPIIKf~~--~GI~ 78 (655)
+..|||..+|+....+|+| +|+.-... . . ...++..+.++|....+ +..+..|..|+||||||.. .|++
T Consensus 157 ~~~~gs~~~~~~~~~~d~d-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i~~A~vPiik~~~~~~~~~ 235 (596)
T KOG2277|consen 157 LYLFGSSDLGLGERSSDLD-LCVDFTSSFLSFEKIKGLEILKLLAKCLASLLEEGVREVQQILSARVPIIKFNDSGSGLE 235 (596)
T ss_pred eeccCcccccccccccCcc-eeecccccccccchhhhHHHHHHHHHHHHhccccccceeeeeeecCCCEEEecCCCCCCc
Confidence 4599999999999999999 66543221 1 1 13566778888887553 8899999999999999965 5899
Q ss_pred eeEEeeeccccccCCCCCCChhhhhccchhhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCcccc
Q 006232 79 IDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLG 158 (655)
Q Consensus 79 IDL~fa~l~~~~ipe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfLG 158 (655)
+|+++.+.. |.+.+..+..+.....+||.+...||.||+++++++...|.+.
T Consensus 236 ~d~s~~n~~----------------------------~~~nS~ll~~~~~~d~r~~~L~~~vk~wa~~~~~~d~~~g~~~ 287 (596)
T KOG2277|consen 236 CDLSVNNSD----------------------------AILNSQLLRNYSEIDPRVRPLVLLVKHWAKEKGLNDAKPGGLN 287 (596)
T ss_pred eeeeeccch----------------------------hhhhhHHHHHhHhcCCCcchHhHHHHHHHHhccCCCCCCCcee
Confidence 999988642 2333444444455566999999999999999999999999988
Q ss_pred -hHHHHHHHHHHHhhCCC-------------------------------------------CCHHHHHHHHHHhhc-cCC
Q 006232 159 -GINWALLVARICQLYPN-------------------------------------------AVPSMLVSRFFRVYT-QWR 193 (655)
Q Consensus 159 -GiswAILVArvcQlyPn-------------------------------------------as~s~LL~~FF~~Ys-~Wd 193 (655)
.|++.+||++++|.++. .++..|+..||.||+ .|+
T Consensus 288 s~ysl~lmvi~fLq~~~~~ilp~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~f~~yy~~~Fd 367 (596)
T KOG2277|consen 288 SSYSLTLMVIHFLQTLSPPILPPLSKLLPESDSNDKPVVKKKVLCSFLRVFQRNPSNSQNTGSLGELLLGFFSYYASLFD 367 (596)
T ss_pred ccccHHHHHHHHHHhcCCcCCCchhhhchhcccccccchhhhhhhccccccccccccccccchHHHHHHHHHHHHhhhcc
Confidence 69999999999997631 024588899999999 899
Q ss_pred CCCceeecccccCCCcccccCCCCCCCCCCCceeeeCCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHH
Q 006232 194 WPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAM 264 (655)
Q Consensus 194 Wp~PV~L~~i~~g~lg~~vWdP~~~~~dr~hlMpIiTPa~P~~Nsa~NVs~STl~vI~~EF~RA~~Il~~i 264 (655)
|++-++ .+..|......|.. ...-.+.|.+|+....|.+..++.....+|+.+|+....++...
T Consensus 368 f~~~~I--~~r~~~~l~~~~~~-----~~~~~l~i~dp~~~~~n~~~~~~~~~~~~i~~~~~~~~~~~~~~ 431 (596)
T KOG2277|consen 368 FRKNAI--SIRRGRALKRAKKI-----KSKKFLCIEDPFEVSHNADAGVTLKVLLLIQDEFQESRRVFKDV 431 (596)
T ss_pred ccccee--eeeecccccccchh-----hhccceeeccccccccCccccchHHHHHHHHHHHHHHHHHhhhh
Confidence 998643 22222211100111 11246999999999999999999999999999999999998754
No 10
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=99.23 E-value=8.1e-09 Score=112.93 Aligned_cols=307 Identities=19% Similarity=0.210 Sum_probs=183.7
Q ss_pred CCCcEEEEeeccccCCcCC-CCCeeEEEEcCCCCCchhhHH---HHHHHHHhcC-CCceeEeeecCCCcceEEEEEcCee
Q 006232 4 YLPLVLIGLGYDKYSVHGP-GADIDTLCVGPRHATREEDFF---GELHQMLTEM-PEVTELHPVPDAHVPVMKFKFSGVS 78 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p-~SDID~lcv~P~~vtr~edFF---~~l~~~L~~~-~~V~~l~~V~~ArVPIIKf~~~GI~ 78 (655)
.+.++++.||||+=|.+++ +||||++++.|....++ ++= ..+...+.+. +.. -..-|-=|-++..+.|++
T Consensus 38 ~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~~~~~~e-~l~~~gl~i~~~~~~~~~~~----~~~yaeHpYv~~~~~G~~ 112 (408)
T TIGR03671 38 GVDAEVVLVGSYARGTWLKGDRDIDIFILFPKDTSRE-ELEEYGLEIGHEVLKRGGNY----EERYAEHPYVSGEIEGFE 112 (408)
T ss_pred CCcceEEEEeeEecCCccCCCCceeEEEEeCCCCCHH-HHHHHHHHHHHHHHhhCCCH----hheeccCceEEEEEccEE
Confidence 4668999999999999999 99999999999888774 322 2223323221 211 145688899999999999
Q ss_pred eeEEeeeccccccCCCCCCChh-hhhccchhhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCC--Cc
Q 006232 79 IDLLYARLSLWVIPEDLDISQD-SILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNV--AG 155 (655)
Q Consensus 79 IDL~fa~l~~~~ipe~ldl~~d-~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~--~G 155 (655)
|||.=|-- +.+- .+...+|-. ..=+++++.-. .+.++..+|.+|.|.|.-|+|++- .+
T Consensus 113 VDiVPcy~----------v~~g~~~~taVDRt-------p~H~~fv~~rl--~~~~~d~VRLlK~f~k~igvYGsE~~~~ 173 (408)
T TIGR03671 113 VDVVPCYK----------VESGEEIISAVDRT-------PFHTRYVLERL--DGKLRDDVRLLKQFLKGIGVYGSELKTR 173 (408)
T ss_pred EEEEeeEE----------ccCcCeeeccccCc-------hHHHHHHHHhh--hhhHHHHHHHHHHHHHhCCccchhhccC
Confidence 99985521 1111 111122211 11134444443 234889999999999999999664 57
Q ss_pred ccchHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCCceeecccccCCCcccccCCCCCCCCCCCceeeeCCCCCC
Q 006232 156 FLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPC 235 (655)
Q Consensus 156 fLGGiswAILVArvcQlyPnas~s~LL~~FF~~Ys~WdWp~PV~L~~i~~g~lg~~vWdP~~~~~dr~hlMpIiTPa~P~ 235 (655)
.++||.+=|||+++ .+-..++..+ +.| ..++.+ ++... ... .-...+.|++|..|.
T Consensus 174 GFSGYl~ELLv~~y------G~F~~~l~~a----~~w--k~~~~i-d~~~~-------~~~----~f~~PlvViDPvDp~ 229 (408)
T TIGR03671 174 GFSGYLCELLVIHY------GSFENVLKAA----SKW--KPGVVI-DIEEH-------GTK----KFDDPLVVIDPVDPK 229 (408)
T ss_pred CccHHHHHHHHHHh------CCHHHHHHHH----Hhc--CCCeEE-ecCcc-------ccc----cCCCCEEEeCCCCCc
Confidence 79999999999994 3444555443 334 445654 32211 100 012579999999999
Q ss_pred CCcccccChhhHHHHHHHHHHHHHHHHHHHhccCCCCCccccCcc-----ch---hhhcc-cEEEEEEEecChhhhcchh
Q 006232 236 MNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPF-----TF---FEAYK-NYLRIDISAENADDLRNWK 306 (655)
Q Consensus 236 ~Nsa~NVs~STl~vI~~EF~RA~~Il~~i~~~~~~~~W~~Lfep~-----~F---F~~Yk-~yl~I~v~a~~~e~~~~w~ 306 (655)
.|+|.++|..++..+...-+++++ .. =..+|.|. ++ +.+-. +.+.|....++.-+= ..-
T Consensus 230 RNVAaalS~~~~~~fv~aar~fl~-------~P----s~~fF~p~~~~~~~~~~~l~~r~t~~~~~~f~~p~~v~D-il~ 297 (408)
T TIGR03671 230 RNVAAALSLENLARFILAARMFLK-------NP----SLEFFFPPEIEPEEFLERLERRGTTLLAIVFRTPDVVDD-ILY 297 (408)
T ss_pred chHHHHcCHHHHHHHHHHHHHHHH-------CC----CHHHcCCCCCChHHHHHHHhhcCcEEEEEEeCCCCCCcc-chh
Confidence 999999999888877765554443 22 22455442 11 12222 333444444433222 234
Q ss_pred hhhHHHHHHHHHHHhhccccceeeccCCCCCCCCCCCcEEEEEEeeeeccC--CCCCCCceechHHHHHHHHH
Q 006232 307 GWVESRLRQLTLKIERHTYNMLQCHPHPGDFSDKSKPLYCSYFMGLQRKQG--VPVGEGEQFDIRLTVKEFKQ 377 (655)
Q Consensus 307 GwVESRlR~Lv~~LE~~~~~~l~ahp~P~~f~~~~~~~~~~yfIGL~~~~~--~~~~~~~~~DL~~~v~eF~~ 377 (655)
|-++--.+.|...||++...++....|- +.. .|+.++=|...+- .....|-.+.-+.....|.+
T Consensus 298 pQl~r~~~~i~~~L~~~gF~v~r~~~~~----~~~---~~~l~~el~~~~lp~~~~h~GPpv~~~~~a~~F~~ 363 (408)
T TIGR03671 298 PQLERSGRSLVKLLEREGFEVLRYGVWA----DEN---TCYLLLELESAELPRVKLHVGPPVWVRDHAEKFIE 363 (408)
T ss_pred HHHHHHHHHHHHHHHHCCCEEEEeeeec----CCC---eEEEEEEeeccccCCceeeeCCCccchhHHHHHHH
Confidence 6666666677777887766666666552 222 2455555543211 11122334555456777876
No 11
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=99.19 E-value=3.6e-09 Score=116.95 Aligned_cols=308 Identities=18% Similarity=0.202 Sum_probs=178.3
Q ss_pred CcEEEEeeccccCCcCC-CCCeeEEEEcCCCCCch---hhHHHHHHHHHhcCCCceeEeeecCCCcceEEEEEcCeeeeE
Q 006232 6 PLVLIGLGYDKYSVHGP-GADIDTLCVGPRHATRE---EDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDL 81 (655)
Q Consensus 6 ~~~L~~FGSyrLGV~~p-~SDID~lcv~P~~vtr~---edFF~~l~~~L~~~~~V~~l~~V~~ArVPIIKf~~~GI~IDL 81 (655)
+++++.+|||+=|.|++ ++|||++++.|....++ +.........++..-+-.+++ -|-=|-++..++|++|||
T Consensus 41 ~~~V~l~GS~ArgT~L~GdsDIDIFv~fp~~~~~e~L~~~gl~i~~~~~~~~~~~~~~~---yaeHpyv~~~~~G~~VDi 117 (447)
T PRK13300 41 DAEVELVGSTARGTWLSGDRDIDIFVLFPKDTSREELEEKGLEIGKEVAKELLGDYEER---YAEHPYVTGEIDGFEVDI 117 (447)
T ss_pred ceEEEEEeeecCCcccCCCCceeEEEEeCCCCCHHHHHHHHHHHHHHHHHhhCCcceee---eccCceEEEEECCEEEEE
Confidence 38999999999999999 77999999999888764 111222233333311112333 488899999999999999
Q ss_pred Eee-eccccccCCCCCCChhhhhccchhhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCC--Ccccc
Q 006232 82 LYA-RLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNV--AGFLG 158 (655)
Q Consensus 82 ~fa-~l~~~~ipe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~--~GfLG 158 (655)
+=| .+... ..+...+|-. ..=+++|+.-. .+.++..+|.+|.|.|.-|+|++- .+.++
T Consensus 118 VPcy~v~~~----------~~~~saVDRt-------p~H~~fv~~rl--~~~~~d~VRLlK~f~k~~gvYGsE~k~~GFS 178 (447)
T PRK13300 118 VPCYKVESG----------EEIISAVDRT-------PFHTKYVKERL--KGKLEDEVRLLKQFLKGIGVYGSELKTRGFS 178 (447)
T ss_pred EeeEEccCc----------CcccccccCc-------hHHHHHHHHhh--hhhHHHHHHHHHHHHHhCCccchhhccCCcc
Confidence 866 22110 1111222211 11234555443 234889999999999999999664 57899
Q ss_pred hHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCCceeecccccCCCcccccCCCCCCCCCCCceeeeCCCCCCCCc
Q 006232 159 GINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNS 238 (655)
Q Consensus 159 GiswAILVArvcQlyPnas~s~LL~~FF~~Ys~WdWp~PV~L~~i~~g~lg~~vWdP~~~~~dr~hlMpIiTPa~P~~Ns 238 (655)
||.+=|||+++ .+-..+|..+ +.|.- ++.|...+.+.. . .-...+.|++|..|..|+
T Consensus 179 GYl~ELLv~~y------G~F~~~l~~a----~~w~~--~~~I~~~~~~~~--------~---~f~~PlvViDPvDp~RNV 235 (447)
T PRK13300 179 GYLCELLIIHY------GSFENVLKAA----SKWKP--PVKIDLEKHGKE--------Y---KFDDPLVVIDPVDPNRNV 235 (447)
T ss_pred HHHHHHHHHHh------CCHHHHHHHH----HhCCC--CceEeccccCcc--------c---cCCCCEEEeCCCCCcchH
Confidence 99999999994 3445555554 34533 343321111100 0 113579999999999999
Q ss_pred ccccChhhHHHHHHHHHHHHHHHHHHHhccCCCCCccccCccc--------hhhh-cccEEEEEEEecChhhhcchhhhh
Q 006232 239 SYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFT--------FFEA-YKNYLRIDISAENADDLRNWKGWV 309 (655)
Q Consensus 239 a~NVs~STl~vI~~EF~RA~~Il~~i~~~~~~~~W~~Lfep~~--------FF~~-Yk~yl~I~v~a~~~e~~~~w~GwV 309 (655)
|.++|..++..+...-+ +.+ +.. =..+|.|.+ -+.+ =.+.+.|....++.-+=. .-|-+
T Consensus 236 Aaa~S~~~~~~fv~aar---~fL----~~P----s~~fF~~~~~~~~~~~~~l~~R~t~~~~v~f~~p~~v~Di-l~pQl 303 (447)
T PRK13300 236 AAALSLENLATFILAAR---EFL----KNP----SLEFFFPSDLSPEEILEELERRGTTVLALEFPRPDIVEDI-LYPQL 303 (447)
T ss_pred HHHcCHHHHHHHHHHHH---HHH----hCC----CHHhcCCCCCChHHHHHHHhhcCceEEEEEeCCCCCCccc-hhHHH
Confidence 99999888776654222 222 222 233444433 1111 124444554444432222 34566
Q ss_pred HHHHHHHHHHHhhccccceeeccCCCCCCCCCCCcEEEEEEeeeecc--CCCCCCCceechHHHHHHHHH
Q 006232 310 ESRLRQLTLKIERHTYNMLQCHPHPGDFSDKSKPLYCSYFMGLQRKQ--GVPVGEGEQFDIRLTVKEFKQ 377 (655)
Q Consensus 310 ESRlR~Lv~~LE~~~~~~l~ahp~P~~f~~~~~~~~~~yfIGL~~~~--~~~~~~~~~~DL~~~v~eF~~ 377 (655)
+--.+.|...||+....++....| .+.+ .|+.++=|...+ ......|-.+--+.-.+.|.+
T Consensus 304 ~r~~~~i~~~L~~~gF~v~~~~~~----~d~~---~~~l~~el~~~~lp~~~~h~GPpv~~~~~a~~F~~ 366 (447)
T PRK13300 304 ERSLRSIVKLLEREGFEVLRSGAW----ADED---RAYLLLELEVAELPNVKLHIGPPVWVREHAENFIE 366 (447)
T ss_pred HHHHHHHHHHHHHCCCEEEEeeee----cCCC---eEEEEEEeecccCCCeeeeeCCCcCchhhHHHHHH
Confidence 666666777788776655555444 3321 244444443221 111112333444444677875
No 12
>PF03813 Nrap: Nrap protein; InterPro: IPR005554 Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus []. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [].
Probab=99.04 E-value=5.5e-08 Score=116.78 Aligned_cols=288 Identities=15% Similarity=0.228 Sum_probs=185.9
Q ss_pred ccccCCcC---CCCCeeEEEEcCCCCCchhhHH------------HHHHHHH--hcCCCceeE---eeecCCCcceEEEE
Q 006232 14 YDKYSVHG---PGADIDTLCVGPRHATREEDFF------------GELHQML--TEMPEVTEL---HPVPDAHVPVMKFK 73 (655)
Q Consensus 14 SyrLGV~~---p~SDID~lcv~P~~vtr~edFF------------~~l~~~L--~~~~~V~~l---~~V~~ArVPIIKf~ 73 (655)
||.|+... ++-.||+.+.-|..+-.++||. ..++..| ++...+.++ -.=.+.+-|||.+.
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 67666655 4779999999997665443433 3466667 223333333 23457888999988
Q ss_pred Ec-----C------eeeeEEeeeccc-c---c-cCC------------------CCCCChhhhhccchhhhhhhccchhh
Q 006232 74 FS-----G------VSIDLLYARLSL-W---V-IPE------------------DLDISQDSILQNADEQTVRSLNGCRV 119 (655)
Q Consensus 74 ~~-----G------I~IDL~fa~l~~-~---~-ipe------------------~ldl~~d~lL~~lDe~svrSLNG~Rv 119 (655)
-. + ..|-|..+.... . + .|. .-...|..+|.++-.. .-
T Consensus 81 p~~~~~~~~~~~~~~~iRi~~~~~~~~F~~~rl~P~rnnvR~~~~~~~~~~~~~pTP~YNssIL~D~~~~--------~~ 152 (972)
T PF03813_consen 81 PKGKKDSDDFSKTKFRIRIIPSIPSDTFPLSRLAPSRNNVRPSWFDEEDSSSLPPTPHYNSSILEDMLME--------EH 152 (972)
T ss_pred ECCccccccccCCcEEEEEEecCCcccCCHHhcCCCCCccCcCcccccccCCCCCCCcchHHHHHHHhHH--------HH
Confidence 42 2 555555543110 0 0 011 1123455555543211 12
Q ss_pred HHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCC-CcccchHHHHHHHHHHHhh---------CCCCCHHHHHHHHHHhh
Q 006232 120 TDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNV-AGFLGGINWALLVARICQL---------YPNAVPSMLVSRFFRVY 189 (655)
Q Consensus 120 td~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~-~GfLGGiswAILVArvcQl---------yPnas~s~LL~~FF~~Y 189 (655)
.+.+-+..-..+.|+.++..+|.||++||+.+.. .|.+||+-|++|+|+.+|- .+..+.-+|+..+.++.
T Consensus 153 l~~l~~~~~~~p~f~dA~iLlkvWl~QRg~~~~~~~~Gf~~f~~s~lla~Ll~~g~~~~~~~l~~~mSsyQlFr~~l~fL 232 (972)
T PF03813_consen 153 LKYLHEASKSSPAFRDACILLKVWLRQRGFGSGISQGGFGGFEWSMLLAYLLQGGGRNGKKKLSKSMSSYQLFRAVLQFL 232 (972)
T ss_pred HHHHHHHHhcCHHHHHHHHHHHHHHhcCCCCcccCCCCcchHHHHHHHHHHHcCCCccCCcccCCCCCHHHHHHHHHHHH
Confidence 3445555566799999999999999999998875 5889999999999999875 35568889999999999
Q ss_pred ccCCC-CCceeecccccCCCcccccCCCCCCCCCCCceeeeCCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHhcc
Q 006232 190 TQWRW-PNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNE 268 (655)
Q Consensus 190 s~WdW-p~PV~L~~i~~g~lg~~vWdP~~~~~dr~hlMpIiTPa~P~~Nsa~NVs~STl~vI~~EF~RA~~Il~~i~~~~ 268 (655)
+..|| .+|+.++...+.......| .+.+.+..++|. -.+|.++++|.++++.|+.|-+++.+++++-. .
T Consensus 233 A~~d~~~~~l~~~~~~~~~~~~~~~-------~~~~~~vf~D~s-g~~Nl~~~ms~~s~~~L~~eA~~tl~lL~~~~--~ 302 (972)
T PF03813_consen 233 ATTDLSKKPLFFKSSSDSTESLEEF-------HSAFDPVFVDPS-GGLNLLAKMSPSSYEELQHEAKLTLELLDDSS--D 302 (972)
T ss_pred hccccccCceEEecCCCccchhhhh-------hccCCeEEEeCC-CCEEEEEcCCHHHHHHHHHHHHHHHHHhcccc--c
Confidence 99999 5688886544211101111 123445555654 56999999999999999999999999887521 1
Q ss_pred CCCCCccccC-c-cchhhhcccEEEEE---EE----ecChhhhcchhhhhHHHHHHHHH-HHh
Q 006232 269 ADVDWDTLFE-P-FTFFEAYKNYLRID---IS----AENADDLRNWKGWVESRLRQLTL-KIE 321 (655)
Q Consensus 269 ~~~~W~~Lfe-p-~~FF~~Yk~yl~I~---v~----a~~~e~~~~w~GwVESRlR~Lv~-~LE 321 (655)
. ..+.+|- + .++..+|.+++.|. .. .....+...|...++.++-.|+. .|-
T Consensus 303 d--~F~~lFl~~~~~~~~~fD~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lL~raLg 363 (972)
T PF03813_consen 303 D--GFDSLFLTKVDPPALRFDHVLRISPDSLLSSFSPDESLDFLSFSNYLLRKIYRLLKRALG 363 (972)
T ss_pred c--chhhhhcccCCcccccCCEEEEEcchhhcccccccccccccchhHHHHHHHHHHHHHHHH
Confidence 2 5676664 4 46778999999991 11 12223334444456667666553 343
No 13
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=98.46 E-value=1.9e-05 Score=86.72 Aligned_cols=308 Identities=17% Similarity=0.174 Sum_probs=174.5
Q ss_pred CCcEEEEeeccccCCcCC-CCCeeEEEEcCCCCCchh---hHHHHHHHHHhcCCCceeEeeecCCCcceEEEEEcCeeee
Q 006232 5 LPLVLIGLGYDKYSVHGP-GADIDTLCVGPRHATREE---DFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSID 80 (655)
Q Consensus 5 p~~~L~~FGSyrLGV~~p-~SDID~lcv~P~~vtr~e---dFF~~l~~~L~~~~~V~~l~~V~~ArVPIIKf~~~GI~ID 80 (655)
.++.+.-+|||+=|.|++ +.|||+.|..|....+++ .=.......|.+ .. -.+.-|-=|-+.-+++|++||
T Consensus 44 ~~aev~lVGS~AkgTwL~gd~DIDvFi~Fp~d~~~eel~~~GL~ig~~~l~~-~~----~~~~YAeHPYV~g~v~G~eVD 118 (443)
T COG1746 44 IDAEVVLVGSYAKGTWLRGDHDIDVFIAFPKDTSEEELEEKGLEIGREVLKR-GN----YEERYAEHPYVTGEVDGYEVD 118 (443)
T ss_pred CcceEEEEeecccCcccCCCcceeEEEECCCCCCHHHHHHHHHHHHHHHhcC-Cc----hhhhhccCCeeEEEEccEEEE
Confidence 578899999999999999 679999999998877641 112223334443 11 135578889999999999999
Q ss_pred EEeeeccccccCCCCCCChhhhhccchhhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCC--Ccccc
Q 006232 81 LLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNV--AGFLG 158 (655)
Q Consensus 81 L~fa~l~~~~ipe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~--~GfLG 158 (655)
+.=|--... ++ .+...+|-+- -=|.++..-+-. +=+.=+|.+|.+.|.=|+|++- .+.++
T Consensus 119 vVPCy~v~~--~~-------~~~sAVDRTp-------lHt~yv~e~L~~--~~~deVrLLK~FlK~iGvYGaE~rt~GFS 180 (443)
T COG1746 119 VVPCYKVED--GE-------KIISAVDRTP-------LHTRYVEEHLKG--RQKDEVRLLKQFLKGIGVYGAELRTQGFS 180 (443)
T ss_pred EEecccccC--cc-------cccccccCcc-------hhHHHHHHHhcc--cchhHHHHHHHHHhccCccceeeeeccch
Confidence 997732100 11 0111111100 012233322222 1113368899999999999985 57899
Q ss_pred hHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCCceeecccccCCCcccccCCCCCCCCCCCceeeeCCCCCCCCc
Q 006232 159 GINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNS 238 (655)
Q Consensus 159 GiswAILVArvcQlyPnas~s~LL~~FF~~Ys~WdWp~PV~L~~i~~g~lg~~vWdP~~~~~dr~hlMpIiTPa~P~~Ns 238 (655)
||-.=||++++= +-...|..+ + +|.-+++|. ++ .|.-.. -.| ..|-|++|..|..|+
T Consensus 181 GYL~ELLII~yG------sFe~vl~~a----~--~wrp~~~ID-~~-------~~~~e~-f~d--~PliVvDPVDP~RNV 237 (443)
T COG1746 181 GYLCELLIIHYG------SFENVLKAA----S--RWRPGKIID-LE-------GHKRER-FED--EPLIVVDPVDPKRNV 237 (443)
T ss_pred HHHHHHHHhhhc------cHHHHHHHH----h--ccCCCeEEe-cc-------chhhhc-cCC--CCeEecCCCCCccch
Confidence 999999998872 222333332 2 377776552 22 121110 011 279999999999999
Q ss_pred ccccChhhHHHHHHHHHHHHHHHHHHHhccCCCCCccccCccc--------hhhhcccEEEEEEEecChhhhcchhhhhH
Q 006232 239 SYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFT--------FFEAYKNYLRIDISAENADDLRNWKGWVE 310 (655)
Q Consensus 239 a~NVs~STl~vI~~EF~RA~~Il~~i~~~~~~~~W~~Lfep~~--------FF~~Yk~yl~I~v~a~~~e~~~~w~GwVE 310 (655)
|.+||..++..+. .|.+ ..+++. =...|.|.. ..++=.+-+.+.+-.++.-+ ...-|-++
T Consensus 238 AAalSl~~la~f~----~aar---~FL~~P----S~efF~p~~~~~~~~~~~~~rgt~v~~l~~~~pd~vd-DilypQl~ 305 (443)
T COG1746 238 AAALSLENLARFV----HAAR---EFLKNP----SPEFFFPRKPKPLLLSKLRRRGTHVLALVFPKPDLVD-DILYPQLE 305 (443)
T ss_pred hhhcCHHHHHHHH----HHHH---HHhcCC----ChhhcCCCCcCcccccchhhcCceEEEEEeCCCCCCc-chhhHHHH
Confidence 9999987766543 3332 222232 223333211 11121222333333344322 23457777
Q ss_pred HHHHHHHHHHhhccccceeeccCCCCCCCCCCCcEEEEEEeeeeccC--CCCCCCceechHHHHHHHHH
Q 006232 311 SRLRQLTLKIERHTYNMLQCHPHPGDFSDKSKPLYCSYFMGLQRKQG--VPVGEGEQFDIRLTVKEFKQ 377 (655)
Q Consensus 311 SRlR~Lv~~LE~~~~~~l~ahp~P~~f~~~~~~~~~~yfIGL~~~~~--~~~~~~~~~DL~~~v~eF~~ 377 (655)
---+.|...||...+.++..+.| .|... +++-|+=+....- .....|-+..-+.+++ |.+
T Consensus 306 r~~~~l~r~Le~~gF~vl~~~~~----~D~~~--~~~v~~E~~~~~l~~i~~r~GPp~~~e~a~r-F~~ 367 (443)
T COG1746 306 RTARSLFRALEEEGFRVLRSGVW----SDESE--RIYVLLELESKELPRIELRVGPPVWTEHAVR-FIE 367 (443)
T ss_pred HHHHHHHHHHHHcCCEEeeeeee----ecCCc--ceEEEEEEecccccceeeecCCCccchhHHH-HHH
Confidence 77778888888876666666555 22221 3455555543211 0011122333366777 766
No 14
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=98.14 E-value=1.6e-05 Score=93.95 Aligned_cols=271 Identities=17% Similarity=0.224 Sum_probs=167.3
Q ss_pred CCCcEEE-EeeccccC-CcCCCCCeeEEEEcCCCCCchhhHHH------------HHHHHHhcCCCceeEee---ecCCC
Q 006232 4 YLPLVLI-GLGYDKYS-VHGPGADIDTLCVGPRHATREEDFFG------------ELHQMLTEMPEVTELHP---VPDAH 66 (655)
Q Consensus 4 ~p~~~L~-~FGSyrLG-V~~p~SDID~lcv~P~~vtr~edFF~------------~l~~~L~~~~~V~~l~~---V~~Ar 66 (655)
+|+.++- ..||+.+| +..|+.-+|+++..|+..-..+|++. -+...|-+.+....+.. =-+-.
T Consensus 145 ~~p~~v~~vv~sal~~~~~~P~i~vDvll~mP~e~~~~kd~ln~Ryf~kra~yla~~~~hl~e~l~~~~~~f~~~n~d~~ 224 (1121)
T KOG2054|consen 145 LPPAQVTKVVGSALLGTCLRPDISVDVLLTMPREILQQKDGLNQRYFRKRALYLAYLAHHLLEDLLFGSLEFSYTNGDHL 224 (1121)
T ss_pred cCccccceeeeecccCcccCCcchhhhhhhhhHHhhcCcccccccccchHHHHHHHHHHHHHhccccceeeecccCCccc
Confidence 4566666 55666555 45688999999999975433233332 23334444342212211 12455
Q ss_pred cceEEEEEcCeeeeEEeeeccccccCCCC---------------------------CCChhhhhccchhhhhhhccchhh
Q 006232 67 VPVMKFKFSGVSIDLLYARLSLWVIPEDL---------------------------DISQDSILQNADEQTVRSLNGCRV 119 (655)
Q Consensus 67 VPIIKf~~~GI~IDL~fa~l~~~~ipe~l---------------------------dl~~d~lL~~lDe~svrSLNG~Rv 119 (655)
-||+.+.-.|-..|++-.+.+..-+|-.+ ...|..+|.+.-... .
T Consensus 225 ~pil~i~~~~~~~~~~~~~~~~~li~~~~~~f~~~kllp~~~~ir~~~e~~e~ppTP~yN~svL~~~~le~--------~ 296 (1121)
T KOG2054|consen 225 KPILLIRPRGKDERLVTVRPPDFLIPCRLLPFKNNKLLPWYNGIRPAGEGSEEPPTPRYNTSVLEDQVLEE--------Y 296 (1121)
T ss_pred cchhhccccCCccccccccCccccccccccccccccccchhcccCccccCCCCCCCCccchhHHHHHHHHH--------H
Confidence 68888877666666554443221122111 112222222111100 0
Q ss_pred HHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCcccchHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhhccCCCCC
Q 006232 120 TDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQ---LYPNAVPSMLVSRFFRVYTQWRWPN 196 (655)
Q Consensus 120 td~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfLGGiswAILVArvcQ---lyPnas~s~LL~~FF~~Ys~WdWp~ 196 (655)
.+++.+.....+.|+.++-..|.|+++|-. +-..|.+||+-|++++++... ++-+.+..+++..-+++.+.|||..
T Consensus 297 ~q~L~K~~s~~~~f~da~~Llk~WlrqRs~-~~~~~gfg~f~~s~lvv~L~s~~ki~~~~S~yqvfR~vl~flat~dlt~ 375 (1121)
T KOG2054|consen 297 LQLLSKTLSSAKGFKDALALLKVWLRQRSL-DIGQGGFGGFLLSALVVYLVSTRKIHTTLSAYQVFRSVLQFLATTDLTV 375 (1121)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHhhhh-hcccCcchHHHHHHHHHHHHhcCchhhcchHHHHHHHHHHHHhhhhhhc
Confidence 123333444568999999999999999921 114688999999999998863 4666788899999999999999986
Q ss_pred -ceeecccccCCCcccccCCCCCCCCCCCceeeeCCCCCCCCcccccChhhHHHHHHHHHHHHHHHHHHHhccCCCCCcc
Q 006232 197 -PVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDT 275 (655)
Q Consensus 197 -PV~L~~i~~g~lg~~vWdP~~~~~dr~hlMpIiTPa~P~~Nsa~NVs~STl~vI~~EF~RA~~Il~~i~~~~~~~~W~~ 275 (655)
-|.+++-. -+ .|....-+..+....++ +.-..|...|++.++++.+++|.+-+..++.+.... .++.
T Consensus 376 ~~~~l~~~~-~s------~~~~~~f~e~~~~~f~D-~s~~~NLc~~mt~s~y~~~q~ea~ltl~lL~~~~~~----~F~~ 443 (1121)
T KOG2054|consen 376 NGISLVPSS-PS------LPALADFHEGQLVTFID-SSGHLNLCANMTASTYEQVQEEARLTLMLLDSRADD----GFSL 443 (1121)
T ss_pred cceEeccCC-CC------chhhhhhhhcceeeEec-cCCcchhhhhccHHHHHHHHHHHHHHHHHHhhhhhc----Ccce
Confidence 45443210 00 01111111223333333 345689999999999999999999999999876533 5777
Q ss_pred cc-CccchhhhcccEEEEEEE
Q 006232 276 LF-EPFTFFEAYKNYLRIDIS 295 (655)
Q Consensus 276 Lf-ep~~FF~~Yk~yl~I~v~ 295 (655)
+| ++.+.|..|.|=+.+..-
T Consensus 444 IFmtkip~~~~yDh~l~l~~~ 464 (1121)
T KOG2054|consen 444 IFMTKIPVFRAYDHVLHLSPL 464 (1121)
T ss_pred eeeecCCchhhhheeeecccc
Confidence 76 778999999988877554
No 15
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=98.11 E-value=0.00017 Score=74.70 Aligned_cols=213 Identities=15% Similarity=0.164 Sum_probs=149.5
Q ss_pred EEEeeccccCCcCCCC-CeeEEEEcCCCCCchhhHHHHH----HHHHhcCCCceeEeeecCCCcceEEEEEc----Ceee
Q 006232 9 LIGLGYDKYSVHGPGA-DIDTLCVGPRHATREEDFFGEL----HQMLTEMPEVTELHPVPDAHVPVMKFKFS----GVSI 79 (655)
Q Consensus 9 L~~FGSyrLGV~~p~S-DID~lcv~P~~vtr~edFF~~l----~~~L~~~~~V~~l~~V~~ArVPIIKf~~~----GI~I 79 (655)
+.-+||+.-|+...|. +.|+|+++....|.+ ....+ .+-|+...+=.....|..+.+|.++..+. -...
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 6678999999999887 789999998888863 44444 44444432111223456677788877663 1223
Q ss_pred eEEeeeccccccCCCCCCChhhhhccch-hhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCcccc
Q 006232 80 DLLYARLSLWVIPEDLDISQDSILQNAD-EQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLG 158 (655)
Q Consensus 80 DL~fa~l~~~~ipe~ldl~~d~lL~~lD-e~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfLG 158 (655)
+...+ .+|+++.-.+.. .-+| +.|+.+|-..|-+.......-....|+.++|++|-|.+|--..+. |.
T Consensus 83 ~~~~~-----~~~~~~~~~~p~--~~ld~~~cl~aLAalRhakWFq~~a~~l~s~~iviRilKd~~~R~~~~~p----L~ 151 (246)
T smart00572 83 ELLIT-----TVPENLRKLDPE--DHLDRKKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQP----LS 151 (246)
T ss_pred ccccc-----ccCcccccCCcc--ccCCHHHHHHHHHHHHHhHHHHHhccCCcchhhHHHHHHHHHHhcccccc----cc
Confidence 33332 234443322211 1233 568888889999999999988889999999999999998766544 88
Q ss_pred hHHHHHHHHHHHhhCCC-CCHHHHHHHHHHhhccCC-CCCceeecccccCCCcccccCCCCCCCCCCCceeeeCCCCC-C
Q 006232 159 GINWALLVARICQLYPN-AVPSMLVSRFFRVYTQWR-WPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYP-C 235 (655)
Q Consensus 159 GiswAILVArvcQlyPn-as~s~LL~~FF~~Ys~Wd-Wp~PV~L~~i~~g~lg~~vWdP~~~~~dr~hlMpIiTPa~P-~ 235 (655)
++.+=+++++++--... .++++-+.+||++.++=- +|.. --|++|+.+ .
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 99999999998852221 368899999999988411 1110 246788987 8
Q ss_pred CCcccccChhhHHHHHHHHHHHHHHHH
Q 006232 236 MNSSYNVSTSTLRIMMDEFQRGHEICE 262 (655)
Q Consensus 236 ~Nsa~NVs~STl~vI~~EF~RA~~Il~ 262 (655)
.|++...|....+.|...-+.|.+++.
T Consensus 204 ~nv~~~lT~qqrd~It~sAQ~alRl~A 230 (246)
T smart00572 204 TDALTALTLQQREDVTASAQTALRLLA 230 (246)
T ss_pred ccHHHhcCHHHHHHHHHHHHHHHHHHH
Confidence 889999999999999998888888763
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=97.63 E-value=0.00026 Score=65.95 Aligned_cols=78 Identities=21% Similarity=0.203 Sum_probs=57.8
Q ss_pred CCcEEEEeeccccCCcCC-CCCeeEEEEcCCCCC----chhhHHHHHHHHHhcCCCceeEeeecCCCcceEEEEEc--Ce
Q 006232 5 LPLVLIGLGYDKYSVHGP-GADIDTLCVGPRHAT----REEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFS--GV 77 (655)
Q Consensus 5 p~~~L~~FGSyrLGV~~p-~SDID~lcv~P~~vt----r~edFF~~l~~~L~~~~~V~~l~~V~~ArVPIIKf~~~--GI 77 (655)
+...++.||||+.|...+ .||||++++.+.... ...++...+...|.+...- .......-|.+.++|. |+
T Consensus 26 ~~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~~~~~~~~~~~~l~~~L~~~~~~---~~~~~~~~~~v~v~~~~~~~ 102 (143)
T cd05400 26 RVAEVFLQGSYARGTALRGDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEYYGA---NEEVKAQHRSVTVKFKGQGF 102 (143)
T ss_pred cccEEEEEcceeCCCCCCCCCceeEEEEEcCcccccccCHHHHHHHHHHHHHHhcCc---ccccccCceEEEEEEcCCCe
Confidence 467899999999999977 899999999886543 1146777788888874331 1122355588888887 89
Q ss_pred eeeEEeee
Q 006232 78 SIDLLYAR 85 (655)
Q Consensus 78 ~IDL~fa~ 85 (655)
+|||+=|.
T Consensus 103 ~vDvvP~~ 110 (143)
T cd05400 103 HVDVVPAF 110 (143)
T ss_pred EEEEEEEe
Confidence 99997664
No 17
>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=97.09 E-value=0.00033 Score=60.04 Aligned_cols=34 Identities=18% Similarity=0.109 Sum_probs=30.8
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEEcCCCCC
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCVGPRHAT 37 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vt 37 (655)
++...++.||||+.|.+.|+||||++++.+....
T Consensus 12 ~~~~~v~lfGS~a~g~~~~~SDIDl~i~~~~~~~ 45 (93)
T PF01909_consen 12 FGVAEVYLFGSYARGDATPDSDIDLLIILDEPED 45 (93)
T ss_dssp HTTEEEEEEHHHHHTSSCTTSCEEEEEEESSTSC
T ss_pred CCCCEEEEECCcccCcCCCCCCEEEEEEeCCccc
Confidence 4567899999999999999999999999998765
No 18
>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=97.06 E-value=0.00046 Score=55.73 Aligned_cols=55 Identities=22% Similarity=0.423 Sum_probs=35.7
Q ss_pred CHHHHHHHHHHhhc-cCCCCCceeecccccCCC-c--ccccCCCCCCCCCCCceeeeCCCCCC
Q 006232 177 VPSMLVSRFFRVYT-QWRWPNPVLLCAIEEGSL-G--LQVWDPRRNPKDKYHLMPIITPAYPC 235 (655)
Q Consensus 177 s~s~LL~~FF~~Ys-~WdWp~PV~L~~i~~g~l-g--~~vWdP~~~~~dr~hlMpIiTPa~P~ 235 (655)
++++||..||+||+ .|||.+-|+ .+..|.. . ...|.. ....+...|+|++|..|.
T Consensus 1 slg~Ll~~Ff~~Y~~~Fd~~~~~I--si~~g~~~~k~~~~~~~--~~~~~~~~l~IeDP~~~~ 59 (60)
T PF03828_consen 1 SLGELLLGFFEYYGRKFDYENNVI--SIRNGGYFPKEEKNWSK--SRNQRKKRLCIEDPFDPS 59 (60)
T ss_dssp -HHHHHHHHHHHHHHTS-TTTEEE--ESSSSSEEEHHHHTGCH--CCCCECSSSEBBESSSTT
T ss_pred CHHHHHHHHHHHhCCcCCCCceEE--EecCCceEEhhhccccc--cccCCCCeEEEECCCCCC
Confidence 47899999999999 999999654 2334432 1 123431 112345789999999885
No 19
>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=97.02 E-value=0.00074 Score=53.39 Aligned_cols=28 Identities=21% Similarity=0.226 Sum_probs=25.6
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEE
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCV 31 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv 31 (655)
++..+++.||||+.|.+.+.||||++|+
T Consensus 15 ~~~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 15 VPGYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred cCCcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 4567899999999999999999999887
No 20
>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=96.27 E-value=0.013 Score=49.58 Aligned_cols=33 Identities=18% Similarity=0.067 Sum_probs=29.3
Q ss_pred CcEEEEeeccccCCcCCCCCeeEEEEcCCCCCc
Q 006232 6 PLVLIGLGYDKYSVHGPGADIDTLCVGPRHATR 38 (655)
Q Consensus 6 ~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr 38 (655)
-..++-||||.-|-+.++||||++++.+.....
T Consensus 18 i~~i~LfGS~arg~~~~~SDiDl~vi~~~~~~~ 50 (93)
T cd05403 18 VEKVYLFGSYARGDARPDSDIDLLVIFDDPLDP 50 (93)
T ss_pred ccEEEEEeeeecCCCCCCCCeeEEEEeCCCCCH
Confidence 467999999999999999999999999877653
No 21
>PF14091 DUF4269: Domain of unknown function (DUF4269)
Probab=96.17 E-value=0.055 Score=52.79 Aligned_cols=117 Identities=21% Similarity=0.321 Sum_probs=74.2
Q ss_pred EEeeccccCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhcCCCceeE-eeecCCCcceEEEEEcCeeeeEEeeeccc
Q 006232 10 IGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTEL-HPVPDAHVPVMKFKFSGVSIDLLYARLSL 88 (655)
Q Consensus 10 ~~FGSyrLGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~~~~V~~l-~~V~~ArVPIIKf~~~GI~IDL~fa~l~~ 88 (655)
.-.|.+-+|+..++||||++|..+.. +.|-..+.....+.++.+-- ..|..-..=+..|.+.|..|-|---..+
T Consensus 19 iL~GTiPi~Idi~~SDLDIic~~~d~----~~F~~~l~~~f~~~~~f~~~~~~i~~~~~~~~~F~~~~~~~EiF~Q~~P- 93 (152)
T PF14091_consen 19 ILVGTIPIGIDIPGSDLDIICEVPDP----EAFEQLLQSLFGQFEGFTIKEKTIRGEPSIVANFRYEGFPFEIFGQPIP- 93 (152)
T ss_pred EEecccccccCCCCCCccEEEEeCCH----HHHHHHHHHHhccCCCceeeeceeCCceeEEEEEEECCceEEEeecCCC-
Confidence 45799999999999999999998852 23444444444444443211 2344555556788889999987432322
Q ss_pred cccCCCCCCChhhhhccchhhhhhhccchhhHHHHHHhcCCc-hhHHHHHHHHH--------HHHHHcCCCCCC
Q 006232 89 WVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKI-QNFRTTLRCMR--------FWAKRRGVYSNV 153 (655)
Q Consensus 89 ~~ipe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~-~~FR~lLR~IK--------~WAKrRGIYsn~ 153 (655)
++.-||+|=-.--.+++-.. +.||.-+|-+| +||+--||-++.
T Consensus 94 ----------------------v~~QnayrHm~iE~rLL~~~g~~~r~~Ii~LK~~GlKTEPAFa~lLgL~GDP 145 (152)
T PF14091_consen 94 ----------------------VEEQNAYRHMLIEHRLLELHGPSFREEIIELKESGLKTEPAFAKLLGLEGDP 145 (152)
T ss_pred ----------------------hhhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHcCCcchHHHHHHhCCCCCh
Confidence 23457777543333444444 78999888887 466666665543
No 22
>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=95.98 E-value=0.03 Score=52.19 Aligned_cols=93 Identities=19% Similarity=0.308 Sum_probs=57.6
Q ss_pred HHHHHHHHHHcCCCCCC--CcccchHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCCceeecccccCCCcccccC
Q 006232 137 LRCMRFWAKRRGVYSNV--AGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWD 214 (655)
Q Consensus 137 LR~IK~WAKrRGIYsn~--~GfLGGiswAILVArvcQlyPnas~s~LL~~FF~~Ys~WdWp~PV~L~~i~~g~lg~~vWd 214 (655)
+|.+|.+.|.-|+|++- .+.++||-.=+||+++= +-..+|.. -+ +|..|+.|..-..+... +..
T Consensus 3 VrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~yG------sF~~~l~~----a~--~W~~~~~Id~~~~~~~~-~~f- 68 (114)
T PF09249_consen 3 VRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHYG------SFENVLEA----AA--KWKPPVVIDLEDHGEPS-KKF- 68 (114)
T ss_dssp HHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHHHS------SHHHHHHH----HT--T--TTEEEETT-TTE---EEE-
T ss_pred hHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHHHC------CHHHHHHH----HH--hcCCCeEEccCccchhh-hhc-
Confidence 58899999999999986 57899999999999873 33333333 24 66667766322111100 001
Q ss_pred CCCCCCCCCCceeeeCCCCCCCCcccccChhhHHHHH
Q 006232 215 PRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMM 251 (655)
Q Consensus 215 P~~~~~dr~hlMpIiTPa~P~~Nsa~NVs~STl~vI~ 251 (655)
...+.|++|..|..|+|.+||..++..+.
T Consensus 69 --------~~PlvviDPvDp~RNVAAalS~~~~~~fv 97 (114)
T PF09249_consen 69 --------DDPLVVIDPVDPNRNVAAALSLENLAEFV 97 (114)
T ss_dssp ---------SS-EEEETTEEEEETTTTS-HHHHHHHH
T ss_pred --------CCCeEEcCCCCCCchHhHhcCHHHHHHHH
Confidence 24699999999999999999987766544
No 23
>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=95.91 E-value=0.071 Score=65.20 Aligned_cols=157 Identities=22% Similarity=0.365 Sum_probs=102.3
Q ss_pred chhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCcccchHHHHHHHHHHH-hhCCC---CCHHHHHHHHHHhhcc
Q 006232 116 GCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARIC-QLYPN---AVPSMLVSRFFRVYTQ 191 (655)
Q Consensus 116 G~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfLGGiswAILVArvc-QlyPn---as~s~LL~~FF~~Ys~ 191 (655)
..+-+..|..+--....|..++|.+|.|.-.+-+ .|++.--.+=+|||++. +-+|- .++..=+.+|.++-++
T Consensus 668 ~p~h~~~i~~l~~~~p~fs~tvRL~KrW~~shlL----s~~i~~E~vELlva~vfl~~~p~~~P~S~~~GFlRfL~lLs~ 743 (972)
T PF03813_consen 668 LPKHTSAIHGLHTRFPSFSPTVRLAKRWLSSHLL----SGHISEEAVELLVASVFLSPAPWSPPSSPQTGFLRFLHLLST 743 (972)
T ss_pred hHHHHHHHHHHHhhCCchhHHHHHHHHHHHhccC----cccCCHHHHHHHHHHHhcCCCCCCCCCCHhHHHHHHHHHHHh
Confidence 4445566666666788999999999999998877 46778889999999976 34453 3444445666777889
Q ss_pred CCCCC-ceeecccccCC--------CcccccCCCCCCCCCCCceeeeCCCCCCCCcc--cccChhhHHHHHHHHHHHHHH
Q 006232 192 WRWPN-PVLLCAIEEGS--------LGLQVWDPRRNPKDKYHLMPIITPAYPCMNSS--YNVSTSTLRIMMDEFQRGHEI 260 (655)
Q Consensus 192 WdWp~-PV~L~~i~~g~--------lg~~vWdP~~~~~dr~hlMpIiTPa~P~~Nsa--~NVs~STl~vI~~EF~RA~~I 260 (655)
|||.+ |+++.--.+-. ..+..|.. ..+......|.|.||..|.-..- ..-+..-+++|+.--+.+.++
T Consensus 744 ~dW~~~PLiVd~~~~l~~~~~~~i~~~f~~~R~-~dp~~~~p~~~IaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~sl~~ 822 (972)
T PF03813_consen 744 WDWREEPLIVDFNNELTEEDRAEIETNFDAWRK-IDPAMNLPAMFIATPYDPEGSLWTRNGPSKVVAKRLTALAKASLKL 822 (972)
T ss_pred CCCCcCCEEEECCCCCCHHHHHHHHHHHHHhhc-cCccccCCcEEEEeCCCCCCCEeECCCCCHHHHHHHHHHHHHHHHH
Confidence 99995 88764321100 01223322 12233456899999999854321 234445567777766777777
Q ss_pred HHHHHhccCCCCCccccCc
Q 006232 261 CEAMEKNEADVDWDTLFEP 279 (655)
Q Consensus 261 l~~i~~~~~~~~W~~Lfep 279 (655)
++. .+-...+|..||.|
T Consensus 823 l~~--~~~~~~~~~~lF~~ 839 (972)
T PF03813_consen 823 LEE--QGLSDLDWKSLFRP 839 (972)
T ss_pred HHh--cCCCCCCHHHhcCC
Confidence 762 22124489999976
No 24
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=93.70 E-value=0.13 Score=45.80 Aligned_cols=29 Identities=24% Similarity=0.153 Sum_probs=26.3
Q ss_pred CCcEEEEeeccccCCcCCCCCeeEEEEcC
Q 006232 5 LPLVLIGLGYDKYSVHGPGADIDTLCVGP 33 (655)
Q Consensus 5 p~~~L~~FGSyrLGV~~p~SDID~lcv~P 33 (655)
....++-||||.-|=+.+.||||++++++
T Consensus 25 ~~~~v~LfGS~arG~~~~~SDiDv~vv~~ 53 (128)
T COG1708 25 GDLLIYLFGSYARGDFVKESDIDLLVVSD 53 (128)
T ss_pred CCeEEEEEccCcccccccCCCeeEEEEcC
Confidence 45779999999999999999999999983
No 25
>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=93.17 E-value=0.73 Score=49.40 Aligned_cols=113 Identities=22% Similarity=0.234 Sum_probs=73.1
Q ss_pred CCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhcCCCceeEeeecCCCcceEEEEEc------Cee
Q 006232 5 LPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFS------GVS 78 (655)
Q Consensus 5 p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~ArVPIIKf~~~------GI~ 78 (655)
|.+.+.+.||||=|-.+ .+|||+|+..+....+ .++..+...|.+.+.+..+. ..-..-....+. |+.
T Consensus 159 ~~~~v~i~GS~RRg~et-~gDiDilv~~~~~~~~--~~~~~v~~~l~~~~~~~~~~---~~g~~k~~~~~~~~~~~~~~r 232 (307)
T cd00141 159 PVLQVEIAGSYRRGKET-VGDIDILVTHPDATSR--GLLEKVVDALVELGFVTEVL---SKGDTKASGILKLPGGWKGRR 232 (307)
T ss_pred CceEEEEcccccCCCCc-cCCEEEEEecCCcccc--ccHHHHHHHHHhCCCeehhh---hCCCceEEEEEecCCCCCceE
Confidence 67889999999999865 4699999988765442 67788888898887765421 112222222222 899
Q ss_pred eeEEeeeccccccCCCCCCChhhhhccchhhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCccc
Q 006232 79 IDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFL 157 (655)
Q Consensus 79 IDL~fa~l~~~~ipe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfL 157 (655)
|||.++....+ .-.++-.-.+ ..| .|.++.||++||..=|..|..
T Consensus 233 VDl~~~p~~~~------------------------------~~all~fTGs-~~~---nr~lR~~A~~~G~~L~~~GL~ 277 (307)
T cd00141 233 VDLRVVPPEEF------------------------------GAALLYFTGS-KQF---NRALRRLAKEKGLKLNEYGLF 277 (307)
T ss_pred EEEEEeCHHHH------------------------------HHHHHHhhCC-HHH---HHHHHHHHHHcCCeeeccccc
Confidence 99999864311 0011111111 222 466799999999987777765
No 26
>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=93.12 E-value=4.2 Score=42.75 Aligned_cols=209 Identities=15% Similarity=0.184 Sum_probs=133.2
Q ss_pred eeccccCCcCCCC-CeeEEEEcCCCCCchhhHHHHHHHHHhc----CCCceeEeee------cCCCcceEEEEE--c--C
Q 006232 12 LGYDKYSVHGPGA-DIDTLCVGPRHATREEDFFGELHQMLTE----MPEVTELHPV------PDAHVPVMKFKF--S--G 76 (655)
Q Consensus 12 FGSyrLGV~~p~S-DID~lcv~P~~vtr~edFF~~l~~~L~~----~~~V~~l~~V------~~ArVPIIKf~~--~--G 76 (655)
.||+.-|+...|. +.|+|+++..-.|. ++...+.+.|.+ ...-.-...+ .....|.+...+ . .
T Consensus 2 VG~~aKGllL~Gd~~~eLVVlck~kPT~--~lL~~v~~~L~~~L~~~~~~ev~~~~e~~~~~~~~~~~~~~~~~~lts~~ 79 (248)
T PF07528_consen 2 VGSFAKGLLLKGDNDVELVVLCKEKPTK--ELLNRVAEKLPEQLKKVTPEEVTNSVEAAIIIDSCKEPKLEVGIDLTSPV 79 (248)
T ss_pred cceecCCceecCCceEeEEEEcCCCCcH--HHHHHHHHHHHHHHhhhCccccccchhhhhhhcccccccceeeEEecCCc
Confidence 5999999999887 78999999888886 566665555443 2211111222 222335555443 2 2
Q ss_pred eeeeEEeeeccccccCCCCCCChhhhhccch-hhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCc
Q 006232 77 VSIDLLYARLSLWVIPEDLDISQDSILQNAD-EQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAG 155 (655)
Q Consensus 77 I~IDL~fa~l~~~~ipe~ldl~~d~lL~~lD-e~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~G 155 (655)
+.+.+..+. .+++..-.+. -..+| +.|..+|-..|=+..+..........+.++|.+|--.+|--- ++
T Consensus 80 ~r~~~~~~~-----~~~~~~~~dp--~~~Ld~~~cl~aLaalRhakWFq~~a~~l~s~~~viRIlrDl~~R~p~----w~ 148 (248)
T PF07528_consen 80 MRVRVLITT-----IPENLSKLDP--EDHLDRKKCLSALAALRHAKWFQARANGLQSCVIVIRILRDLRQRVPT----WQ 148 (248)
T ss_pred eEEEEeccc-----cCccccccCh--hhcCCHHHHHHHHHHHHHhHHHHHHhccCCCcceehhhHHHHHHhCCC----CC
Confidence 333443332 2333321111 12244 367888888899988888888888899999999999887533 45
Q ss_pred ccchHHHHHHHHHHHhhCCC---CCHHHHHHHHHHhhcc-CCCCCceeecccccCCCcccccCCCCCCCCCCCceeeeCC
Q 006232 156 FLGGINWALLVARICQLYPN---AVPSMLVSRFFRVYTQ-WRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITP 231 (655)
Q Consensus 156 fLGGiswAILVArvcQlyPn---as~s~LL~~FF~~Ys~-WdWp~PV~L~~i~~g~lg~~vWdP~~~~~dr~hlMpIiTP 231 (655)
-|.+..+=+|+-+..---|+ .++++-+.+||+..|. +=-|. . | =|.||
T Consensus 149 ~L~~W~leLL~~~~i~~~~~~~~l~~g~a~RRvle~lasGillp~----------~-------~-----------gl~DP 200 (248)
T PF07528_consen 149 PLSSWALELLVEKAISNNSSRQPLSPGDAFRRVLECLASGILLPG----------S-------P-----------GLRDP 200 (248)
T ss_pred CCChhHHHHHHHHHeeeCCCCCCCChHHHHHHHHHHHhCceecCC----------C-------C-----------CCcCC
Confidence 68888888877766552333 4688999999999873 22221 0 1 13456
Q ss_pred CC-CCCCcccccChhhHHHHHHHHHHHHHHH
Q 006232 232 AY-PCMNSSYNVSTSTLRIMMDEFQRGHEIC 261 (655)
Q Consensus 232 a~-P~~Nsa~NVs~STl~vI~~EF~RA~~Il 261 (655)
+. ...++..+.|...++.|..--|.+.+++
T Consensus 201 cE~~~~~~~~~lt~qq~e~it~sAQ~~LRll 231 (248)
T PF07528_consen 201 CEKDPVDVLDTLTLQQREDITSSAQTALRLL 231 (248)
T ss_pred CCCCCceeeccCCHHHHHHHHHHHHHHHHHH
Confidence 65 5577777888888888887777766655
No 27
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=92.10 E-value=0.22 Score=52.60 Aligned_cols=31 Identities=19% Similarity=0.075 Sum_probs=27.9
Q ss_pred EEEEeeccccCCcCCCCCeeEEEEcCCCCCc
Q 006232 8 VLIGLGYDKYSVHGPGADIDTLCVGPRHATR 38 (655)
Q Consensus 8 ~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr 38 (655)
.++-|||+..|-..|.||||++++.....+.
T Consensus 30 ~vyLfGS~~~G~~~p~SDIDllvvv~~~l~~ 60 (262)
T PRK13746 30 AIHLYGSAVDGGLKPHSDIDLLVTVAVPLDE 60 (262)
T ss_pred EEEEECCcccCCCCCCCceeEEEEeCCCCCH
Confidence 4899999999999999999999999887664
No 28
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=90.96 E-value=0.38 Score=43.89 Aligned_cols=32 Identities=22% Similarity=0.119 Sum_probs=26.6
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEEcCCC
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCVGPRH 35 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~ 35 (655)
|.-..+-.||||.=|=..|+||||+++-.-.-
T Consensus 22 ~gv~~~~vFGS~aRgE~~~~SDIDILVef~~~ 53 (97)
T COG1669 22 YGVKRVAVFGSYARGEQKPDSDIDILVEFEPG 53 (97)
T ss_pred hCCceEEEeeeeecCCCCCCCCceeEEeecCC
Confidence 44567899999999999999999998855433
No 29
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=86.51 E-value=0.15 Score=54.12 Aligned_cols=26 Identities=19% Similarity=0.087 Sum_probs=22.8
Q ss_pred EEeeccccCCcCCCCCeeEEEEcCCC
Q 006232 10 IGLGYDKYSVHGPGADIDTLCVGPRH 35 (655)
Q Consensus 10 ~~FGSyrLGV~~p~SDID~lcv~P~~ 35 (655)
=.-||..+|++..+||||+|+.|+.+
T Consensus 125 GVTGSiL~gl~~~nSDIDfVVYG~~~ 150 (315)
T COG1665 125 GVTGSILLGLYDENSDIDFVVYGQMW 150 (315)
T ss_pred cccccccccccCCCCCceEEEEcHHH
Confidence 35699999999999999999999644
No 30
>PRK02098 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=85.90 E-value=0.96 Score=46.73 Aligned_cols=45 Identities=13% Similarity=-0.003 Sum_probs=32.5
Q ss_pred CcEEEEeeccc----cCC--cCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhc
Q 006232 6 PLVLIGLGYDK----YSV--HGPGADIDTLCVGPRHATREEDFFGELHQMLTE 52 (655)
Q Consensus 6 ~~~L~~FGSyr----LGV--~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~ 52 (655)
++.+.+|||+. +|. -.++||||+|+-.|.....+ ++ ..+.+.|..
T Consensus 120 g~~~gv~GS~a~qlaTG~~~l~~~SDLDLLi~~~~~~~~~-~~-~~ll~~l~~ 170 (221)
T PRK02098 120 GVDCRVFGSLAWQALTGLPYLSASSDLDLLWPLPAAAQIA-PL-LAGLAAIEA 170 (221)
T ss_pred CCcEEEeeehHHHHhhCCcccCCCCCeeEEEecCChhhHH-HH-HHHHHHHhh
Confidence 45789999999 999 89999999999888655542 33 334344443
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=84.45 E-value=1.1 Score=45.50 Aligned_cols=45 Identities=18% Similarity=0.096 Sum_probs=32.9
Q ss_pred CcEEEEeecc----ccCC--cCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhc
Q 006232 6 PLVLIGLGYD----KYSV--HGPGADIDTLCVGPRHATREEDFFGELHQMLTE 52 (655)
Q Consensus 6 ~~~L~~FGSy----rLGV--~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~ 52 (655)
++.+.+|||+ .+|. -.++||||+|+-.|....++ ++ ..+.+.|..
T Consensus 108 ~~~~gv~GS~~~qlaTg~~~~~~~SDLDLLi~~~~~~~~~-~~-~~ll~~l~~ 158 (202)
T TIGR03135 108 GVPWGVYGSAGWQLLTGLPYLHASSDLDLLLRAPSPLSLA-RL-LALLQALEA 158 (202)
T ss_pred CCcEEEecchHHHHhcCCcccCCCCCeeEEEcCCChhhHH-HH-HHHHHHHhc
Confidence 4578999999 8898 89999999999888655552 33 334444443
No 32
>cd05401 NT_GlnE_GlnD_like Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins. Escherichia coli GlnD and -E participate in the Glutamine synthetase (GS)/Glutamate synthase (GOGAT) pathway for the assimilation of ammonium nitrogen. In nitrogen sufficiency, GlnE adenylates GS, reducing GS activity; when nitrogen is limiting, GlnE deadenylates GS-AMP, restoring GS activity. When nitrogen is limiting, GlnD uridylylates the nitrogen regulatory protein PII to PII-UTP, and in nitrogen sufficiency, it removes the modifying groups. The activity of Escherichia coli GlnE is modulated by PII-proteins. PII-UMP promotes GlnE deadenylation activity, and PII promotes GlnE adenylation activity. Escherichia coli GlnE has two separate NT domains. The N-terminal NT domain catalyzes the deadenylylation of GS, and the C-terminal NT domain the adenylylation reaction. The majority of proteins in this family conta
Probab=83.53 E-value=2.1 Score=41.33 Aligned_cols=48 Identities=25% Similarity=0.385 Sum_probs=36.7
Q ss_pred CCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhc
Q 006232 5 LPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTE 52 (655)
Q Consensus 5 p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~ 52 (655)
.+.-++.+|||+=|=-.+.||||++++.+........+|..+.+.+.+
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 457899999999999999999999998875432123577777666554
No 33
>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=82.66 E-value=2.9 Score=42.42 Aligned_cols=47 Identities=11% Similarity=0.089 Sum_probs=32.3
Q ss_pred chhHHHHHHHHHHHHHHcCCCCCCC-cccchHHHHHHHHHHHhhCCCC
Q 006232 130 IQNFRTTLRCMRFWAKRRGVYSNVA-GFLGGINWALLVARICQLYPNA 176 (655)
Q Consensus 130 ~~~FR~lLR~IK~WAKrRGIYsn~~-GfLGGiswAILVArvcQlyPna 176 (655)
....+.++|.||+|-+.-.--.... +-+..|++-+|+++....-.+.
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 4788999999999998755443333 4567899999999998765443
No 34
>PF14792 DNA_pol_B_palm: DNA polymerase beta palm ; PDB: 1RZT_A 3PML_A 2PFN_A 3HX0_K 3HWT_A 2GWS_E 2BCQ_A 3UPQ_A 2BCS_A 3UQ2_A ....
Probab=79.62 E-value=2.9 Score=38.55 Aligned_cols=54 Identities=24% Similarity=0.208 Sum_probs=41.4
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCc---hhhHHHHHHHHHhcCCCcee
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATR---EEDFFGELHQMLTEMPEVTE 58 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr---~edFF~~l~~~L~~~~~V~~ 58 (655)
.|.+.+..-||||=|-.+.+ |||+|+..|..... ...++..+.+.|.+..-+++
T Consensus 22 ~p~~~v~i~GSyRRGK~~~g-DiDiLIt~~~~~~~~~~~~~~l~~lv~~L~~~g~i~~ 78 (112)
T PF14792_consen 22 DPGLEVEICGSYRRGKETSG-DIDILITHPDPSSVSKKLEGLLEKLVKRLEEKGFITD 78 (112)
T ss_dssp STT-EEEEEHHHHTT-SEES-SEEEEEEETTCSTTTCSTTCHHHHHHHHHHHTTSEEE
T ss_pred CCCcEEEEccccccCCCcCC-CeEEEEeCCCcCcchhhHHHHHHHHHHHHHhCCeEEE
Confidence 47789999999999987765 99999999976552 13789999999998655543
No 35
>PRK08609 hypothetical protein; Provisional
Probab=71.91 E-value=14 Score=43.03 Aligned_cols=109 Identities=16% Similarity=0.195 Sum_probs=63.9
Q ss_pred CCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhcCCCceeEeeecCCCcceEEEEE-cCeeeeEEe
Q 006232 5 LPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKF-SGVSIDLLY 83 (655)
Q Consensus 5 p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~ArVPIIKf~~-~GI~IDL~f 83 (655)
+..++..-||||=|--+ -.|||+|+..+.. ..+.+.|.+.+.|+++..-...+.- +.+.. .|+.|||.+
T Consensus 174 ~~~~v~~~GS~RR~~et-~gDiDili~~~~~--------~~~~~~l~~~~~v~~~~~~g~~~~~-~~~~~~~~~~vDl~~ 243 (570)
T PRK08609 174 EIIRFSRAGSLRRARET-VKDLDFIIATDEP--------EAVREQLLQLPNIVEVIAAGDTKVS-VELEYEYTISVDFRL 243 (570)
T ss_pred CccEEEeccchhccccc-cCCeeEEEecCCH--------HHHHHHHHcCccHHHHHhcCCceEE-EEEecCCCeEEEEEE
Confidence 45678899999999865 4699999977542 1233444555555443222222221 12332 399999998
Q ss_pred eeccccccCCCCCCChhhhhccchhhhhhhccchhhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCccc
Q 006232 84 ARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFL 157 (655)
Q Consensus 84 a~l~~~~ipe~ldl~~d~lL~~lDe~svrSLNG~Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfL 157 (655)
+....+ - -.++ +...-..| .|.++.||++||..=|-+|..
T Consensus 244 v~~~~~-------------~-----------------~aL~-yfTGS~~h---n~~lr~~A~~~g~~l~e~gl~ 283 (570)
T PRK08609 244 VEPEAF-------------A-----------------TTLH-HFTGSKDH---NVRMRQLAKERGEKISEYGVE 283 (570)
T ss_pred eCHHHH-------------H-----------------HHHH-HHhccHHH---HHHHHHHHHHcCCcccccccc
Confidence 864321 0 0111 11111222 456689999999998888875
No 36
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=65.11 E-value=36 Score=42.37 Aligned_cols=80 Identities=20% Similarity=0.310 Sum_probs=52.1
Q ss_pred hhHHHHHHhcCCchhHHHHHHHHHHHHHHcCCCCCCCcccchHHHHHHHHHHHh-hCC---CCCHHHHHHHHHHhhccCC
Q 006232 118 RVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQ-LYP---NAVPSMLVSRFFRVYTQWR 193 (655)
Q Consensus 118 Rvtd~IlrlVPn~~~FR~lLR~IK~WAKrRGIYsn~~GfLGGiswAILVArvcQ-lyP---nas~s~LL~~FF~~Ys~Wd 193 (655)
|.+-.|..+--.+..|-.++|.-|.|-..+=+-+ |.+ -=++=+|||...+ -+| ..++..=..+|-.+-|+||
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 4444444444457889999999999976553221 112 4456778887653 344 4455555678888889999
Q ss_pred CCC-ceeec
Q 006232 194 WPN-PVLLC 201 (655)
Q Consensus 194 Wp~-PV~L~ 201 (655)
|.. |.++.
T Consensus 882 W~~~PLIvd 890 (1121)
T KOG2054|consen 882 WKFDPLIVD 890 (1121)
T ss_pred ccCCceEEE
Confidence 986 76663
No 37
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=62.94 E-value=48 Score=36.17 Aligned_cols=31 Identities=19% Similarity=0.217 Sum_probs=25.1
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEEcCCC
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCVGPRH 35 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~ 35 (655)
.|.+.+..-||||=|-.+ ..|||+|+..+..
T Consensus 162 ~~~~~v~i~GSyRRgket-~gDIDili~~~~~ 192 (334)
T smart00483 162 LPDAIVTLTGSFRRGKET-GHDVDFLITSPHP 192 (334)
T ss_pred CCCcEEEEecccccCCCc-CCCeeEEEecCCc
Confidence 366789999999999865 4699999987763
No 38
>PF03445 DUF294: Putative nucleotidyltransferase DUF294; InterPro: IPR005105 This domain is found associated with an N-terminal cyclic nucleotide-binding domain (IPR000595 from INTERPRO) and two CBS domains (IPR000644 from INTERPRO). This domain, normally represents the C-terminal region, is uncharacterised; however, it seems to be similar to the nucleotidyltransferase domain (IPR002934 from INTERPRO), conserving the DXD motif, which strongly suggests that proteins containing this domain are also nucleotidyltransferases.; GO: 0008773 [protein-PII] uridylyltransferase activity
Probab=61.50 E-value=15 Score=34.85 Aligned_cols=49 Identities=18% Similarity=0.238 Sum_probs=38.2
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCch-hhHHHHHHHHHhc
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATRE-EDFFGELHQMLTE 52 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr~-edFF~~l~~~L~~ 52 (655)
..+.-++.+|||+=+=.++.||+|..+|.....+.+ ..+|..|.+.+..
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 456779999999999999999999988887733221 4788777776654
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=53.66 E-value=22 Score=36.43 Aligned_cols=43 Identities=19% Similarity=0.190 Sum_probs=29.6
Q ss_pred CCcEEEEeecccc------CCcCCCCCeeEEEEcCCCCCchhhHHHHHHH
Q 006232 5 LPLVLIGLGYDKY------SVHGPGADIDTLCVGPRHATREEDFFGELHQ 48 (655)
Q Consensus 5 p~~~L~~FGSyrL------GV~~p~SDID~lcv~P~~vtr~edFF~~l~~ 48 (655)
.++..-+|||+.. -+-.++||||+++-.+.....+ .+...+.+
T Consensus 115 ~~~~~gv~GS~g~qlaTGl~~l~~~SDLDLli~~~~~~~~~-~l~~~L~~ 163 (213)
T PF10620_consen 115 LGLRWGVYGSLGFQLATGLPYLHADSDLDLLIRPPSPSQAD-ALLALLQA 163 (213)
T ss_pred cCCCEEEehhHHHHHHhCccccCCCCCceEEEeCCChhHHH-HHHHHHHH
Confidence 3567889999853 3456999999999888766432 44444433
No 40
>PRK05007 PII uridylyl-transferase; Provisional
Probab=50.03 E-value=26 Score=43.05 Aligned_cols=34 Identities=24% Similarity=0.244 Sum_probs=29.5
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEEcCCCCC
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCVGPRHAT 37 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vt 37 (655)
.+++-|+..|+|+=|=-.|.||||++++.+....
T Consensus 78 ~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~ 111 (884)
T PRK05007 78 IPDLALVAVGGYGRGELHPLSDIDLLILSRKKLP 111 (884)
T ss_pred cCceEEEecCCCCCcccCCcccceEEEEeCCCCC
Confidence 4568999999999999999999999999884433
No 41
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=48.08 E-value=30 Score=41.63 Aligned_cols=45 Identities=22% Similarity=0.137 Sum_probs=33.3
Q ss_pred CCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHh
Q 006232 5 LPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLT 51 (655)
Q Consensus 5 p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~ 51 (655)
.++-|...|+|+=|=-.|.||||++++.+.... +++.+.|-..|=
T Consensus 26 ~~~aLvAvGGYGR~EL~P~SDIDLLiL~~~~~~--~~~i~~~~~~LW 70 (693)
T PRK00227 26 PGTALAATGSLARREMTPYSDLDLILLHPPGAT--PDGVEDLWYPIW 70 (693)
T ss_pred CCeEEEEeccccccCcCCCcCceEEEEeCCccc--HHHHHHHHHHHH
Confidence 466899999999999999999999999884333 244444444433
No 42
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=47.04 E-value=36 Score=33.97 Aligned_cols=81 Identities=21% Similarity=0.199 Sum_probs=47.3
Q ss_pred CcEEEEeeccc----cCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhcCCCceeEeeecCCCcceEEEEEcCeeeeE
Q 006232 6 PLVLIGLGYDK----YSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDL 81 (655)
Q Consensus 6 ~~~L~~FGSyr----LGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~ArVPIIKf~~~GI~IDL 81 (655)
+++.+..|++. +|.-....|||+++..+.... +.++|..+.....-.-+-+++ .....++++...++.|||
T Consensus 16 gv~~~ivGG~av~l~~g~~r~T~DIDlfi~~~~~~~-~~~~~~~~a~~~g~~~~~~~~----~~~~~~~~~~~~~v~IDl 90 (181)
T PF09970_consen 16 GVEYVIVGGAAVNLAYGRRRTTKDIDLFIENPSPNL-EADALREVAEENGWDLGWTDF----GTPRYVVKVGGEDVRIDL 90 (181)
T ss_pred CCeEEEECHHHHHHHhCCCCCCCCeEEEeCCCchHH-HHHHHHHHHHHcCCCcCcccc----CCCceEEEeCCCCeEEEc
Confidence 35678889885 477788999999886664332 235555554322111122222 223455666678999999
Q ss_pred EeeeccccccC
Q 006232 82 LYARLSLWVIP 92 (655)
Q Consensus 82 ~fa~l~~~~ip 92 (655)
+.++....+|
T Consensus 91 -~~ni~~~~v~ 100 (181)
T PF09970_consen 91 -LENIGDFYVP 100 (181)
T ss_pred -hhccCCcccC
Confidence 5555443343
No 43
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=46.89 E-value=32 Score=41.99 Aligned_cols=35 Identities=29% Similarity=0.301 Sum_probs=31.0
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCc
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATR 38 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr 38 (655)
-..+-|..+|.|+=|--.|.||||++++.|.-.+.
T Consensus 64 ~~~~aLvAVGGyGRgEL~P~SDiDlL~L~p~~~~~ 98 (867)
T COG2844 64 ASGLALVAVGGYGRGELHPLSDIDLLLLSPQKLTD 98 (867)
T ss_pred ccceEEEEeccccccccCCCccceEEEecCCCCCh
Confidence 34578999999999999999999999999987763
No 44
>PRK01293 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=46.79 E-value=27 Score=36.00 Aligned_cols=44 Identities=30% Similarity=0.314 Sum_probs=30.5
Q ss_pred CcEEEEeeccccC------CcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHh
Q 006232 6 PLVLIGLGYDKYS------VHGPGADIDTLCVGPRHATREEDFFGELHQMLT 51 (655)
Q Consensus 6 ~~~L~~FGSyrLG------V~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~ 51 (655)
+...-+|||...- +-.+.||||+++..|....+ +=+..+.+.|.
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 4567789997533 45799999999999877665 33444544454
No 45
>PHA02603 nrdC.11 hypothetical protein; Provisional
Probab=46.00 E-value=13 Score=40.73 Aligned_cols=24 Identities=21% Similarity=0.279 Sum_probs=20.3
Q ss_pred EEEEeeccccCCcCCCCCeeEEEE
Q 006232 8 VLIGLGYDKYSVHGPGADIDTLCV 31 (655)
Q Consensus 8 ~L~~FGSyrLGV~~p~SDID~lcv 31 (655)
.+-.+||+..|+.+|+||+|.--|
T Consensus 5 ~~~~~GShaYG~~tp~SD~D~rGV 28 (330)
T PHA02603 5 MKGLFGSHLYGTSTPESDVDYKGI 28 (330)
T ss_pred EEEecccceeCCCCCCccccccee
Confidence 356799999999999999998443
No 46
>PF12633 Adenyl_cycl_N: Adenylate cyclase NT domain; InterPro: IPR024685 Adenylate cyclase is the enzyme responsible for the synthesis of cAMP from ATP. On the basis of sequence similarity, it has been proposed that there are three different classes of adenylate cyclases [, ]. Class I cyclases are found in enterobacteria and related Gram-negative bacteria. This entry represents the N-terminal domain of class-I adenylate cyclases.
Probab=45.06 E-value=25 Score=36.22 Aligned_cols=30 Identities=17% Similarity=0.296 Sum_probs=24.4
Q ss_pred EEEEeeccccCCcCCCCCeeE-EEEcCCCCCc
Q 006232 8 VLIGLGYDKYSVHGPGADIDT-LCVGPRHATR 38 (655)
Q Consensus 8 ~L~~FGSyrLGV~~p~SDID~-lcv~P~~vtr 38 (655)
-|++-||...=-.++.||+|+ ||..+ ..+.
T Consensus 99 GlY~MGS~gSi~Qs~~SDlDiWvCh~~-~L~~ 129 (204)
T PF12633_consen 99 GLYSMGSTGSIGQSSSSDLDIWVCHDS-DLSP 129 (204)
T ss_pred EEEecCCCccccCCCCCCCeEEEEcCC-CCCH
Confidence 489999999999999999999 55554 4553
No 47
>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=40.86 E-value=28 Score=36.19 Aligned_cols=48 Identities=23% Similarity=0.263 Sum_probs=29.5
Q ss_pred CCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCc------hhhHHHHHHHHHhc
Q 006232 5 LPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATR------EEDFFGELHQMLTE 52 (655)
Q Consensus 5 p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr------~edFF~~l~~~L~~ 52 (655)
....|+-.|-++-+=-..+||||+++|.+..-.. ...||..+.+.|.+
T Consensus 126 ~~~~ViamGKlGg~ELny~SDiDLifvy~~~~~~~~~~~~~~~~~~rl~~~~~~ 179 (247)
T PF03710_consen 126 AGFAVIAMGKLGGRELNYSSDIDLIFVYDPDGETGRRSISNQEFFTRLAQRLIR 179 (247)
T ss_dssp -SEEEEE-HHHHTT---TT--EEEEEEE---TT-SSS-SBHHHHHHHHHHHHHH
T ss_pred CCeEEEEeccccccccCCccCCceEEEeccccccccChhhHHHHHHHHHHHHHH
Confidence 3677888999988888899999999997753321 13699988887765
No 48
>PF03281 Mab-21: Mab-21 protein
Probab=39.94 E-value=4.6e+02 Score=27.42 Aligned_cols=97 Identities=20% Similarity=0.275 Sum_probs=66.0
Q ss_pred chhHHHHHHHHHHHHHHcCCCCCCCcccchHHHHHHHHHHHhhCCCC---CHHHHHHHHHHhhccCCCCCceeecccccC
Q 006232 130 IQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNA---VPSMLVSRFFRVYTQWRWPNPVLLCAIEEG 206 (655)
Q Consensus 130 ~~~FR~lLR~IK~WAKrRGIYsn~~GfLGGiswAILVArvcQlyPna---s~s~LL~~FF~~Ys~WdWp~PV~L~~i~~g 206 (655)
....+.+||++|.-.++.. ...+-|++|++--++.+.|..+|.. ....|-.+|.++... ++....+|
T Consensus 190 ~~~~~~~l~llk~l~~~~~---~~~~~l~syhLkt~ll~~~~~~p~~~~W~~~~l~~~l~~~l~~-------L~~~L~~~ 259 (292)
T PF03281_consen 190 NGCRKKCLRLLKALRDRHL---TNLSGLSSYHLKTVLLWLCEKHPSSSDWSEENLGERLLDLLDF-------LIKCLQEG 259 (292)
T ss_pred cccHHHHHHHHHHHHHhcc---ccCCCccHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHH-------HHHHHhcC
Confidence 5567889999998877666 5567899999999999999999875 245555555555331 11223333
Q ss_pred CCcccccCCCCCCCCCCCceeeeCCCCCCCCcccccChhhHHHHHHHHHH
Q 006232 207 SLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMDEFQR 256 (655)
Q Consensus 207 ~lg~~vWdP~~~~~dr~hlMpIiTPa~P~~Nsa~NVs~STl~vI~~EF~R 256 (655)
.+ | | -+.|.+|.=.+.+..++..+..++.+
T Consensus 260 ~L------p--------h------ff~~~~NLf~~~~~~~~~~~~~~~~~ 289 (292)
T PF03281_consen 260 RL------P--------H------FFIPNLNLFQHLSPEELDELARKLER 289 (292)
T ss_pred CC------C--------c------cCCCCcccCCCCCHHHHHHHHHHHHH
Confidence 32 1 1 13578888888888888777776654
No 49
>COG3541 Predicted nucleotidyltransferase [General function prediction only]
Probab=37.44 E-value=16 Score=38.56 Aligned_cols=20 Identities=25% Similarity=0.351 Sum_probs=17.3
Q ss_pred EeeccccCCcCCCCCeeEEE
Q 006232 11 GLGYDKYSVHGPGADIDTLC 30 (655)
Q Consensus 11 ~FGSyrLGV~~p~SDID~lc 30 (655)
--||+.-|+..|+||+|+=-
T Consensus 15 esGS~~yGf~spdSDyDvR~ 34 (248)
T COG3541 15 ESGSHLYGFPSPDSDYDVRG 34 (248)
T ss_pred cccccccCCCCCCCccceee
Confidence 34999999999999999833
No 50
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=36.63 E-value=50 Score=40.56 Aligned_cols=30 Identities=27% Similarity=0.239 Sum_probs=27.1
Q ss_pred CcEEEEeeccccCCcCCCCCeeEEEEcCCC
Q 006232 6 PLVLIGLGYDKYSVHGPGADIDTLCVGPRH 35 (655)
Q Consensus 6 ~~~L~~FGSyrLGV~~p~SDID~lcv~P~~ 35 (655)
++-|...|+|+=|=-.|.||||++++.+..
T Consensus 56 ~iaLvAvGGYGR~eL~P~SDIDlliL~~~~ 85 (854)
T PRK01759 56 DLALIAVGGYGRREMFPLSDLDILILTEQP 85 (854)
T ss_pred CeEEEEeCCcccccCCCcccceEEEEeCCC
Confidence 468999999999999999999999998744
No 51
>PF15431 TMEM190: Transmembrane protein 190
Probab=36.00 E-value=23 Score=33.49 Aligned_cols=30 Identities=30% Similarity=0.672 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHcCCCCCC--CcccchHHH
Q 006232 133 FRTTLRCMRFWAKRRGVYSNV--AGFLGGINW 162 (655)
Q Consensus 133 FR~lLR~IK~WAKrRGIYsn~--~GfLGGisw 162 (655)
|-..+.|+=-|||||++|.|. .|||.||--
T Consensus 73 ~Li~~iclFWWAkRrd~~k~lh~P~fL~~~~c 104 (134)
T PF15431_consen 73 LLICSICLFWWAKRRDMCKHLHMPRFLSGFKC 104 (134)
T ss_pred HHHHHHHHHHHHHHhchHhhccCchhhccCcc
Confidence 556677888999999999875 477777543
No 52
>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=34.06 E-value=62 Score=39.51 Aligned_cols=31 Identities=23% Similarity=0.237 Sum_probs=27.7
Q ss_pred CCcEEEEeeccccCCcCCCCCeeEEEEcCCC
Q 006232 5 LPLVLIGLGYDKYSVHGPGADIDTLCVGPRH 35 (655)
Q Consensus 5 p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~ 35 (655)
.++-|+..|||+=|=-.|.||||++++.+..
T Consensus 42 ~~~aliA~GgyGR~El~p~SDiDll~l~~~~ 72 (850)
T TIGR01693 42 SGIALVAVGGYGRGELAPYSDIDLLFLHDGK 72 (850)
T ss_pred CCeEEEEeCCccccCcCCCCCCeEEEEeCCC
Confidence 5678999999999999999999999998754
No 53
>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=33.72 E-value=16 Score=38.83 Aligned_cols=21 Identities=43% Similarity=0.639 Sum_probs=17.3
Q ss_pred ecChhhhcchhhhhHHHHHHH
Q 006232 296 AENADDLRNWKGWVESRLRQL 316 (655)
Q Consensus 296 a~~~e~~~~w~GwVESRlR~L 316 (655)
-+|.-+...++||||||+-.+
T Consensus 95 DSn~~EGAVLKGWVESRFGL~ 115 (262)
T PF07357_consen 95 DSNSPEGAVLKGWVESRFGLL 115 (262)
T ss_pred CCCChhhhhhhhhhhhccCcC
Confidence 456678889999999999755
No 54
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=32.16 E-value=63 Score=39.94 Aligned_cols=32 Identities=22% Similarity=0.195 Sum_probs=28.2
Q ss_pred CcEEEEeeccccCCcCCCCCeeEEEEcCCCCC
Q 006232 6 PLVLIGLGYDKYSVHGPGADIDTLCVGPRHAT 37 (655)
Q Consensus 6 ~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vt 37 (655)
++.|+..|.|+=|--.|.||||++++.+....
T Consensus 78 ~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~ 109 (895)
T PRK00275 78 DIALVAVGGYGRGELHPYSDIDLLILLDSADH 109 (895)
T ss_pred CEEEEEcCCccccCcCCCCCceEEEEecCCCC
Confidence 57899999999999999999999999875443
No 55
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=30.58 E-value=86 Score=34.57 Aligned_cols=69 Identities=22% Similarity=0.208 Sum_probs=53.1
Q ss_pred EEEEeeccccCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhcCCCceeEeeecCCCcceEEEEEcCeeeeEEeee
Q 006232 8 VLIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYAR 85 (655)
Q Consensus 8 ~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~~~~V~~l~~V~~ArVPIIKf~~~GI~IDL~fa~ 85 (655)
++---||.|=|-.+ .+|||.+|.... .. .+.+.|.++|.|.++.+-.+.+|-++.-...|++||+-.+.
T Consensus 182 ~~~~aGs~RR~ret-v~DiD~~~s~~~-~~-------~v~~~~~~~~~~~~vi~~G~~k~s~~~~~~~~~svD~r~v~ 250 (326)
T COG1796 182 QASIAGSLRRGRET-VGDIDILISTSH-PE-------SVLEELLEMPNVQEVIAKGETKVSMLLILDEGTSVDFRVVP 250 (326)
T ss_pred eeeeccchhhcccc-ccceeeEeccCC-cH-------HHHHHHhcCCCcceeeecCCceeeEEEEecCCCeeEEEEcC
Confidence 34456888877665 579999875542 21 15566677899999999999999999988999999998775
No 56
>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=29.92 E-value=26 Score=36.13 Aligned_cols=25 Identities=24% Similarity=0.226 Sum_probs=21.1
Q ss_pred EEEeeccccCCcCCCCCeeEEEEcC
Q 006232 9 LIGLGYDKYSVHGPGADIDTLCVGP 33 (655)
Q Consensus 9 L~~FGSyrLGV~~p~SDID~lcv~P 33 (655)
...+||..-|+.+|+||.|+-+|.-
T Consensus 23 ~~~sGS~a~G~~s~dSD~D~r~vy~ 47 (247)
T PF10127_consen 23 ACESGSRAYGFASPDSDYDVRGVYI 47 (247)
T ss_pred EecccccccCCCCCCcCcccchhcc
Confidence 4568999999999999999866543
No 57
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=28.67 E-value=1e+02 Score=34.17 Aligned_cols=50 Identities=18% Similarity=0.158 Sum_probs=39.3
Q ss_pred CCCcEEEEeeccccCCcCCCCCeeEEEEcCCCCCchhhHHHHHHHHHhcCC
Q 006232 4 YLPLVLIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMP 54 (655)
Q Consensus 4 ~p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr~edFF~~l~~~L~~~~ 54 (655)
-|.+.+..-||||=|- ..+.|||+|+..|..-..+...+..+...|.+..
T Consensus 169 ~p~~~vt~~GsfRRGk-~~ggDvD~LithP~~~s~~~~~~~~l~~~le~~g 218 (353)
T KOG2534|consen 169 DPEAFVTVTGSFRRGK-KMGGDVDFLITHPGSTSTEAKLLQLLMILLEKKG 218 (353)
T ss_pred CCCcEEEEeccccCCc-ccCCCeeEEEeCCCCCchhhhHHHHHHHHHHhcC
Confidence 5788999999999995 5688999999988755433467778888888743
No 58
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=27.95 E-value=70 Score=40.08 Aligned_cols=47 Identities=19% Similarity=0.231 Sum_probs=36.8
Q ss_pred CcEEEEeeccccCCcCCCCCeeEEEEcCCCCC-c---hhhHHHHHHHHHhc
Q 006232 6 PLVLIGLGYDKYSVHGPGADIDTLCVGPRHAT-R---EEDFFGELHQMLTE 52 (655)
Q Consensus 6 ~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vt-r---~edFF~~l~~~L~~ 52 (655)
+.-|+.+|+|+=+=-+++||||+++|...... . ...||..+.+.+.+
T Consensus 723 ~~avia~Gk~Gr~EL~~~SDlDl~fl~~~~~~~~~~~~~~~~~rlaq~l~~ 773 (1007)
T PRK14109 723 RIAVIGMGRLGGRELGYGSDADVMFVHEPAPGADEAEAVRWATAVAEELRR 773 (1007)
T ss_pred CEEEEEeccccccccCCCCCCcEEEEeCCCCCCCchhHHHHHHHHHHHHHH
Confidence 46899999999999999999999999863211 1 12688888887775
No 59
>PRK05092 PII uridylyl-transferase; Provisional
Probab=27.83 E-value=89 Score=38.74 Aligned_cols=31 Identities=29% Similarity=0.385 Sum_probs=27.6
Q ss_pred CCcEEEEeeccccCCcCCCCCeeEEEEcCCC
Q 006232 5 LPLVLIGLGYDKYSVHGPGADIDTLCVGPRH 35 (655)
Q Consensus 5 p~~~L~~FGSyrLGV~~p~SDID~lcv~P~~ 35 (655)
.++.|+..|.|+=|--.|.||||++++.+..
T Consensus 104 ~~~alvA~GgyGr~EL~p~SDiDLl~l~~~~ 134 (931)
T PRK05092 104 ERLAVLAVGGYGRGELAPGSDIDLLFLLPYK 134 (931)
T ss_pred CceEEEEecCcCCcccCCCCCceEEEEeCCC
Confidence 3578999999999999999999999998753
No 60
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=27.82 E-value=82 Score=39.50 Aligned_cols=47 Identities=17% Similarity=0.099 Sum_probs=36.5
Q ss_pred CcEEEEeeccccCCcCCCCCeeEEEEcCCCCCc----hhhHHHHHHHHHhc
Q 006232 6 PLVLIGLGYDKYSVHGPGADIDTLCVGPRHATR----EEDFFGELHQMLTE 52 (655)
Q Consensus 6 ~~~L~~FGSyrLGV~~p~SDID~lcv~P~~vtr----~edFF~~l~~~L~~ 52 (655)
+..|+.+|+|+=+=-.++||||++++.+..... ...||..+.+.|.+
T Consensus 215 ~~aviamGklG~~EL~~~SDiDLi~ly~~~~~~~~~~~~~~~~rl~q~l~~ 265 (1007)
T PRK14109 215 RLAVIAMGKCGARELNYVSDVDVIFVAEPAEGVDEAAALAVATRLASELMR 265 (1007)
T ss_pred CeEEEEeccccccccCCccCCCEEEEeCCCCCcccccHHHHHHHHHHHHHH
Confidence 468999999999999999999999998643211 03678888777776
No 61
>PRK04374 PII uridylyl-transferase; Provisional
Probab=25.33 E-value=1.1e+02 Score=37.78 Aligned_cols=30 Identities=27% Similarity=0.264 Sum_probs=26.8
Q ss_pred CcEEEEeeccccCCcCCCCCeeEEEEcCCC
Q 006232 6 PLVLIGLGYDKYSVHGPGADIDTLCVGPRH 35 (655)
Q Consensus 6 ~~~L~~FGSyrLGV~~p~SDID~lcv~P~~ 35 (655)
.+-|...|+|+=|=-.|.||||++++.+..
T Consensus 72 ~~alvAvGgYGR~EL~p~SDIDLliL~~~~ 101 (869)
T PRK04374 72 GLSLHAVGGYGRGELFPRSDVDLLVLGETA 101 (869)
T ss_pred CEEEEEcCCccccccCCcccceEEEEecCC
Confidence 468999999999999999999999998743
No 62
>PRK03381 PII uridylyl-transferase; Provisional
Probab=23.73 E-value=1.1e+02 Score=37.26 Aligned_cols=30 Identities=17% Similarity=0.108 Sum_probs=27.1
Q ss_pred CCcEEEEeeccccCCcCCCCCeeEEEEcCC
Q 006232 5 LPLVLIGLGYDKYSVHGPGADIDTLCVGPR 34 (655)
Q Consensus 5 p~~~L~~FGSyrLGV~~p~SDID~lcv~P~ 34 (655)
.++-|...|+|+=|--.|.||||++++.+.
T Consensus 56 ~~~alvAvg~~gr~el~p~SD~Dll~l~~~ 85 (774)
T PRK03381 56 SGVALVAVGGLGRRELLPYSDLDLVLLHDG 85 (774)
T ss_pred CCeEEEEeCCcCCcCcCCCCCCeEEEEeCC
Confidence 357899999999999999999999999873
No 63
>PRK03059 PII uridylyl-transferase; Provisional
Probab=22.44 E-value=1.2e+02 Score=37.50 Aligned_cols=29 Identities=24% Similarity=0.227 Sum_probs=26.4
Q ss_pred CcEEEEeeccccCCcCCCCCeeEEEEcCC
Q 006232 6 PLVLIGLGYDKYSVHGPGADIDTLCVGPR 34 (655)
Q Consensus 6 ~~~L~~FGSyrLGV~~p~SDID~lcv~P~ 34 (655)
++-|+..|+|+=|=-.|.||||++++.+.
T Consensus 61 ~~alvAvGgyGR~EL~p~SDiDll~l~~~ 89 (856)
T PRK03059 61 GAALVAVGGYGRGELFPYSDVDLLVLLPD 89 (856)
T ss_pred CeEEEEcCCCCCcccCCCCCCEEEEEecC
Confidence 46899999999999999999999999864
No 64
>PRK14108 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=20.11 E-value=1.3e+02 Score=37.84 Aligned_cols=47 Identities=23% Similarity=0.305 Sum_probs=35.9
Q ss_pred CcEEEEeeccccCCcCCCCCeeEEEEcCCCC-C--c---hhhHHHHHHHHHhc
Q 006232 6 PLVLIGLGYDKYSVHGPGADIDTLCVGPRHA-T--R---EEDFFGELHQMLTE 52 (655)
Q Consensus 6 ~~~L~~FGSyrLGV~~p~SDID~lcv~P~~v-t--r---~edFF~~l~~~L~~ 52 (655)
...|+-.|-|+=+=-.+.||||++++.+... + + ...||..+.+.|..
T Consensus 186 ~~aViamGklGg~ELn~~SDiDLifly~~~~~~~~~~~~~~~~~~rl~q~li~ 238 (986)
T PRK14108 186 GLIVLGMGKLGAGELNYSSDIDLIVFFDETAPILGDPIEAQPFFVRLTRRLVR 238 (986)
T ss_pred CeEEEeeccccccccCCCCCCceEEEeCCCCCCccccchHHHHHHHHHHHHHH
Confidence 4689999999999999999999999987322 1 1 13688888876665
Done!