Query 003658
Match_columns 805
No_of_seqs 214 out of 575
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 03:35:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003658.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003658hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12047 DNMT1-RFD: Cytosine s 99.8 3.4E-20 7.4E-25 179.2 1.2 131 7-137 1-145 (146)
2 KOG4443 Putative transcription 98.0 2.5E-06 5.4E-11 98.9 3.3 83 277-380 19-102 (694)
3 COG5141 PHD zinc finger-contai 97.7 1.6E-05 3.5E-10 89.6 2.1 89 212-314 189-334 (669)
4 KOG4299 PHD Zn-finger protein 97.6 4.5E-05 9.7E-10 88.5 4.5 50 344-412 255-304 (613)
5 KOG4299 PHD Zn-finger protein 97.6 2E-05 4.3E-10 91.4 1.0 50 216-275 253-305 (613)
6 COG5034 TNG2 Chromatin remodel 97.5 8.9E-05 1.9E-09 78.3 4.1 48 213-274 218-269 (271)
7 KOG1973 Chromatin remodeling p 97.5 5.8E-05 1.2E-09 81.2 2.5 51 210-274 215-267 (274)
8 KOG4443 Putative transcription 97.5 3E-05 6.4E-10 90.3 0.2 141 213-376 15-178 (694)
9 KOG1244 Predicted transcriptio 97.5 4.2E-05 9.2E-10 81.2 1.3 85 213-317 221-315 (336)
10 KOG1512 PHD Zn-finger protein 97.4 4.9E-05 1.1E-09 81.2 1.1 84 214-319 256-350 (381)
11 smart00249 PHD PHD zinc finger 97.3 0.00019 4.2E-09 55.0 3.1 44 218-272 1-47 (47)
12 KOG0955 PHD finger protein BR1 97.3 0.00025 5.5E-09 87.4 5.3 142 210-383 213-368 (1051)
13 KOG1244 Predicted transcriptio 97.3 0.00021 4.7E-09 76.0 3.9 72 294-381 244-316 (336)
14 PF00628 PHD: PHD-finger; Int 97.2 8.2E-05 1.8E-09 59.8 0.2 46 218-274 1-50 (51)
15 KOG0954 PHD finger protein [Ge 97.1 0.00021 4.6E-09 84.0 1.6 157 215-414 270-440 (893)
16 KOG0956 PHD finger protein AF1 97.0 0.00036 7.7E-09 81.7 2.8 83 219-314 8-155 (900)
17 PHA03412 putative methyltransf 96.8 0.00079 1.7E-08 71.4 2.8 116 677-802 29-163 (241)
18 PF15446 zf-PHD-like: PHD/FYVE 96.7 0.003 6.4E-08 63.7 6.1 26 356-381 119-144 (175)
19 KOG0383 Predicted helicase [Ge 96.6 0.00072 1.6E-08 80.7 1.5 52 211-274 42-93 (696)
20 PRK00274 ksgA 16S ribosomal RN 96.6 0.0012 2.6E-08 70.5 3.0 121 676-803 18-143 (272)
21 TIGR02987 met_A_Alw26 type II 96.6 0.0067 1.5E-07 70.4 8.9 50 677-726 2-56 (524)
22 PF02384 N6_Mtase: N-6 DNA Met 96.4 0.0022 4.7E-08 69.0 3.1 46 676-723 23-68 (311)
23 smart00249 PHD PHD zinc finger 95.9 0.0094 2E-07 45.6 3.6 33 344-380 1-33 (47)
24 PF01170 UPF0020: Putative RNA 95.7 0.0069 1.5E-07 61.1 2.9 99 700-801 27-152 (179)
25 KOG1473 Nucleosome remodeling 95.6 0.0071 1.5E-07 74.4 2.9 51 211-273 339-389 (1414)
26 PRK14896 ksgA 16S ribosomal RN 95.6 0.0055 1.2E-07 65.0 1.7 114 677-801 6-125 (258)
27 TIGR00755 ksgA dimethyladenosi 95.4 0.025 5.3E-07 59.7 5.9 114 676-802 5-130 (253)
28 KOG4323 Polycomb-like PHD Zn-f 95.2 0.0087 1.9E-07 68.6 1.6 57 210-275 162-224 (464)
29 PF00628 PHD: PHD-finger; Int 95.2 0.016 3.5E-07 46.5 2.7 34 344-381 1-34 (51)
30 KOG0825 PHD Zn-finger protein 95.1 0.013 2.9E-07 69.8 2.7 47 216-274 215-265 (1134)
31 KOG1512 PHD Zn-finger protein 94.8 0.017 3.7E-07 62.4 2.3 69 294-378 277-346 (381)
32 PTZ00338 dimethyladenosine tra 94.3 0.093 2E-06 57.3 6.8 117 671-802 6-138 (294)
33 KOG1701 Focal adhesion adaptor 94.3 0.0069 1.5E-07 68.3 -1.9 86 212-313 271-361 (468)
34 KOG0825 PHD Zn-finger protein 93.5 0.037 8.1E-07 66.2 1.9 33 344-380 217-250 (1134)
35 KOG0383 Predicted helicase [Ge 92.7 0.056 1.2E-06 65.1 2.0 81 234-351 1-96 (696)
36 PF00398 RrnaAD: Ribosomal RNA 92.3 0.25 5.5E-06 52.6 6.1 115 675-802 5-135 (262)
37 PF13832 zf-HC5HC2H_2: PHD-zin 91.8 0.18 3.9E-06 46.7 3.7 85 218-315 2-87 (110)
38 PF13659 Methyltransf_26: Meth 91.7 0.087 1.9E-06 47.8 1.5 86 702-789 1-103 (117)
39 TIGR00479 rumA 23S rRNA (uraci 91.1 0.27 5.9E-06 55.8 5.0 112 684-799 273-395 (431)
40 PF13832 zf-HC5HC2H_2: PHD-zin 91.0 0.12 2.6E-06 47.8 1.8 105 278-410 2-110 (110)
41 KOG0957 PHD finger protein [Ge 91.0 0.067 1.5E-06 61.5 0.0 86 218-317 121-213 (707)
42 COG2263 Predicted RNA methylas 90.3 0.58 1.2E-05 48.7 6.0 107 657-795 6-140 (198)
43 smart00650 rADc Ribosomal RNA 88.1 1.4 3.1E-05 43.4 6.9 93 689-786 3-100 (169)
44 KOG4323 Polycomb-like PHD Zn-f 86.9 0.32 6.9E-06 56.3 1.7 55 345-414 171-225 (464)
45 PHA03411 putative methyltransf 86.2 0.33 7E-06 53.0 1.3 47 672-722 39-85 (279)
46 TIGR01177 conserved hypothetic 85.3 3 6.5E-05 45.9 8.2 29 689-719 172-200 (329)
47 KOG0957 PHD finger protein [Ge 85.0 0.42 9.1E-06 55.3 1.5 50 215-273 543-596 (707)
48 PRK13168 rumA 23S rRNA m(5)U19 84.1 1.7 3.6E-05 49.9 5.8 107 688-799 282-399 (443)
49 COG2265 TrmA SAM-dependent met 82.7 1.3 2.8E-05 51.1 4.2 117 672-799 260-395 (432)
50 KOG0956 PHD finger protein AF1 82.5 0.55 1.2E-05 56.2 1.0 58 212-274 113-179 (900)
51 TIGR03534 RF_mod_PrmC protein- 82.4 3 6.5E-05 43.0 6.3 96 672-776 57-167 (251)
52 TIGR02085 meth_trns_rumB 23S r 82.3 0.71 1.5E-05 51.9 1.8 110 683-798 213-332 (374)
53 PF13771 zf-HC5HC2H: PHD-like 81.8 0.74 1.6E-05 41.0 1.4 33 213-245 33-67 (90)
54 KOG1973 Chromatin remodeling p 80.8 1 2.3E-05 48.9 2.4 28 292-319 228-256 (274)
55 PF05175 MTS: Methyltransferas 79.9 0.67 1.5E-05 46.0 0.6 91 691-789 23-128 (170)
56 PRK03522 rumB 23S rRNA methylu 79.4 2.6 5.6E-05 46.2 4.9 93 701-799 173-273 (315)
57 TIGR03704 PrmC_rel_meth putati 78.9 0.67 1.4E-05 49.3 0.2 89 681-774 63-164 (251)
58 PRK10909 rsmD 16S rRNA m(2)G96 77.8 4.2 9.2E-05 42.2 5.7 96 700-798 52-157 (199)
59 PF07669 Eco57I: Eco57I restri 77.5 1.8 3.9E-05 40.3 2.6 36 765-801 5-53 (106)
60 COG2226 UbiE Methylase involve 76.6 2.2 4.7E-05 45.8 3.2 59 650-723 15-73 (238)
61 PRK11188 rrmJ 23S rRNA methylt 74.5 16 0.00034 38.0 8.7 65 685-753 36-102 (209)
62 PF13771 zf-HC5HC2H: PHD-like 73.3 1.9 4.2E-05 38.4 1.5 33 276-315 36-68 (90)
63 PF13901 DUF4206: Domain of un 73.2 2.6 5.7E-05 43.8 2.8 45 268-314 144-188 (202)
64 KOG0955 PHD finger protein BR1 70.9 3.2 7E-05 52.6 3.2 66 277-373 220-285 (1051)
65 KOG3420 Predicted RNA methylas 70.4 4.6 9.9E-05 41.0 3.5 107 683-790 28-142 (185)
66 KOG4628 Predicted E3 ubiquitin 70.1 2.3 5E-05 47.9 1.6 49 277-353 230-278 (348)
67 PRK09328 N5-glutamine S-adenos 69.8 7.7 0.00017 40.8 5.4 70 699-777 106-189 (275)
68 PF13831 PHD_2: PHD-finger; PD 68.6 1.3 2.9E-05 34.2 -0.5 35 226-273 2-36 (36)
69 PF15446 zf-PHD-like: PHD/FYVE 68.3 2.8 6.2E-05 42.9 1.6 37 344-381 1-37 (175)
70 PF14446 Prok-RING_1: Prokaryo 67.9 3.6 7.7E-05 34.9 1.9 34 277-316 6-39 (54)
71 KOG1245 Chromatin remodeling c 67.4 1.5 3.3E-05 57.1 -0.6 53 211-275 1103-1158(1404)
72 PRK05785 hypothetical protein; 66.2 7.3 0.00016 40.8 4.3 47 674-723 27-73 (226)
73 PF11793 FANCL_C: FANCL C-term 66.0 3.8 8.3E-05 35.8 1.8 39 277-317 3-41 (70)
74 PF02475 Met_10: Met-10+ like- 65.1 3.1 6.8E-05 43.3 1.3 28 694-721 94-121 (200)
75 COG0286 HsdM Type I restrictio 65.1 7.3 0.00016 45.7 4.4 49 677-727 164-212 (489)
76 TIGR00536 hemK_fam HemK family 65.0 3.2 6.8E-05 44.8 1.3 69 703-776 116-195 (284)
77 TIGR03533 L3_gln_methyl protei 64.2 4.5 9.7E-05 43.9 2.3 72 700-776 120-202 (284)
78 KOG1044 Actin-binding LIM Zn-f 62.9 5 0.00011 47.7 2.5 50 589-638 447-508 (670)
79 TIGR02143 trmA_only tRNA (urac 62.7 8.6 0.00019 43.1 4.3 91 702-798 198-309 (353)
80 COG0293 FtsJ 23S rRNA methylas 62.4 8.6 0.00019 40.5 3.9 54 685-739 30-85 (205)
81 PRK14967 putative methyltransf 61.4 12 0.00027 38.6 4.9 34 686-721 23-56 (223)
82 PRK11805 N5-glutamine S-adenos 61.1 4.5 9.8E-05 44.5 1.7 64 703-775 135-213 (307)
83 TIGR03587 Pse_Me-ase pseudamin 58.2 11 0.00023 39.1 3.7 51 672-722 14-64 (204)
84 TIGR00095 RNA methyltransferas 57.8 12 0.00026 38.3 3.9 37 685-722 33-70 (189)
85 PRK11783 rlmL 23S rRNA m(2)G24 57.6 13 0.00028 45.5 4.8 69 648-719 134-208 (702)
86 PLN02672 methionine S-methyltr 56.6 17 0.00037 46.8 5.7 146 623-777 22-217 (1082)
87 TIGR00080 pimt protein-L-isoas 55.4 15 0.00033 37.7 4.3 45 678-724 56-100 (215)
88 COG0030 KsgA Dimethyladenosine 55.0 14 0.0003 40.3 4.0 99 676-793 6-121 (259)
89 PRK14966 unknown domain/N5-glu 54.6 16 0.00034 42.5 4.7 36 687-722 237-272 (423)
90 KOG3362 Predicted BBOX Zn-fing 53.2 5.6 0.00012 39.8 0.7 32 338-377 114-146 (156)
91 PRK13944 protein-L-isoaspartat 51.0 19 0.00042 36.9 4.2 44 678-723 51-94 (205)
92 PF14446 Prok-RING_1: Prokaryo 50.5 8.6 0.00019 32.6 1.3 32 344-378 7-38 (54)
93 PRK13942 protein-L-isoaspartat 48.8 19 0.00041 37.3 3.7 45 677-723 54-98 (212)
94 PF01555 N6_N4_Mtase: DNA meth 48.0 12 0.00026 37.4 2.1 49 666-716 153-206 (231)
95 PF13489 Methyltransf_23: Meth 47.3 21 0.00046 33.6 3.6 36 687-722 8-43 (161)
96 PRK09489 rsmC 16S ribosomal RN 47.2 65 0.0014 36.2 7.9 21 702-722 197-217 (342)
97 PRK14968 putative methyltransf 46.6 48 0.001 32.4 6.1 38 683-722 7-44 (188)
98 PRK14890 putative Zn-ribbon RN 44.5 16 0.00035 31.5 2.0 32 264-305 23-55 (59)
99 PF13639 zf-RING_2: Ring finge 44.2 5.9 0.00013 30.9 -0.6 33 278-317 2-34 (44)
100 PTZ00098 phosphoethanolamine N 43.6 28 0.00061 37.3 4.2 51 669-721 10-72 (263)
101 COG5034 TNG2 Chromatin remodel 41.9 23 0.0005 38.6 3.1 27 293-319 231-258 (271)
102 KOG0804 Cytoplasmic Zn-finger 41.7 14 0.0003 43.0 1.6 29 216-245 175-207 (493)
103 cd04718 BAH_plant_2 BAH, or Br 41.2 17 0.00037 36.7 1.9 26 239-275 2-27 (148)
104 PF01209 Ubie_methyltran: ubiE 41.0 12 0.00026 39.7 0.9 44 674-722 25-68 (233)
105 PF01728 FtsJ: FtsJ-like methy 40.6 18 0.00039 35.9 2.1 38 686-723 7-45 (181)
106 KOG3612 PHD Zn-finger protein 40.0 20 0.00043 42.6 2.5 52 211-273 55-106 (588)
107 PRK00312 pcm protein-L-isoaspa 38.8 1E+02 0.0022 31.5 7.2 71 648-722 23-99 (212)
108 PF12678 zf-rbx1: RING-H2 zinc 38.2 7.4 0.00016 34.2 -1.0 17 302-318 48-64 (73)
109 COG2520 Predicted methyltransf 38.1 8.7 0.00019 43.4 -0.7 29 694-722 181-209 (341)
110 KOG2187 tRNA uracil-5-methyltr 37.5 61 0.0013 38.7 5.9 126 663-799 341-489 (534)
111 PF10237 N6-adenineMlase: Prob 36.8 28 0.0006 35.4 2.7 38 724-775 61-98 (162)
112 PTZ00146 fibrillarin; Provisio 34.7 39 0.00084 37.6 3.6 58 666-723 82-154 (293)
113 KOG4217 Nuclear receptors of t 34.5 13 0.00029 43.4 0.0 60 212-274 265-329 (605)
114 TIGR00438 rrmJ cell division p 34.3 46 0.00099 33.4 3.8 36 687-723 19-54 (188)
115 COG2888 Predicted Zn-ribbon RN 33.6 26 0.00056 30.5 1.6 32 264-305 25-57 (61)
116 PRK00121 trmB tRNA (guanine-N( 33.2 50 0.0011 33.8 4.0 28 695-722 34-61 (202)
117 PHA02929 N1R/p28-like protein; 33.0 31 0.00067 37.2 2.5 17 301-317 197-213 (238)
118 TIGR02469 CbiT precorrin-6Y C5 33.0 64 0.0014 29.0 4.3 35 686-722 6-40 (124)
119 PF03107 C1_2: C1 domain; Int 32.5 39 0.00085 24.9 2.2 29 343-376 1-30 (30)
120 KOG1169 Diacylglycerol kinase 32.2 27 0.00058 42.5 2.0 138 218-377 46-210 (634)
121 COG2890 HemK Methylase of poly 32.1 47 0.001 36.3 3.7 84 687-776 95-189 (280)
122 PRK07402 precorrin-6B methylas 31.9 68 0.0015 32.4 4.7 41 679-721 20-60 (196)
123 PF04405 ScdA_N: Domain of Unk 31.5 18 0.00038 30.7 0.3 9 706-714 24-32 (56)
124 PRK15001 SAM-dependent 23S rib 31.4 42 0.00091 38.4 3.3 114 673-793 199-333 (378)
125 TIGR00446 nop2p NOL1/NOP2/sun 31.3 31 0.00067 37.0 2.2 25 698-722 68-92 (264)
126 TIGR02752 MenG_heptapren 2-hep 31.2 42 0.00092 34.4 3.1 43 676-723 25-67 (231)
127 COG2230 Cfa Cyclopropane fatty 30.9 50 0.0011 36.6 3.7 34 687-722 60-93 (283)
128 PRK01544 bifunctional N5-gluta 30.2 25 0.00055 41.5 1.4 71 701-776 138-219 (506)
129 cd00315 Cyt_C5_DNA_methylase C 30.1 1.2E+02 0.0025 32.9 6.3 82 704-797 2-109 (275)
130 TIGR00406 prmA ribosomal prote 30.1 55 0.0012 35.5 3.9 39 679-721 141-179 (288)
131 PRK00050 16S rRNA m(4)C1402 me 29.7 42 0.00091 37.2 2.9 35 687-723 7-41 (296)
132 PF13831 PHD_2: PHD-finger; PD 29.3 19 0.00041 27.9 0.1 17 360-376 3-19 (36)
133 PRK13699 putative methylase; P 28.7 37 0.0008 35.9 2.1 22 696-717 158-179 (227)
134 PF12861 zf-Apc11: Anaphase-pr 28.3 25 0.00055 32.4 0.8 17 302-318 50-66 (85)
135 PRK08287 cobalt-precorrin-6Y C 28.2 93 0.002 31.1 4.8 42 679-722 11-52 (187)
136 KOG4628 Predicted E3 ubiquitin 27.7 33 0.00071 39.0 1.6 29 217-246 230-261 (348)
137 PF05413 Peptidase_C34: Putati 27.6 23 0.00051 32.4 0.4 15 635-649 41-55 (92)
138 PRK11524 putative methyltransf 27.2 49 0.0011 35.9 2.8 34 680-715 188-222 (284)
139 KOG4218 Nuclear hormone recept 27.1 27 0.00058 39.6 0.8 28 215-243 14-46 (475)
140 KOG3285 Spindle assembly check 27.0 55 0.0012 34.2 2.9 47 20-67 141-197 (203)
141 PF11793 FANCL_C: FANCL C-term 26.9 31 0.00067 30.2 1.0 33 344-377 4-38 (70)
142 KOG0804 Cytoplasmic Zn-finger 26.5 37 0.00079 39.7 1.8 35 278-318 177-211 (493)
143 COG1041 Predicted DNA modifica 26.4 1.3E+02 0.0028 34.4 6.0 91 699-800 195-311 (347)
144 TIGR01712 phage_N6A_met phage 26.3 51 0.0011 33.9 2.6 34 766-803 64-100 (166)
145 PF05869 Dam: DNA N-6-adenine- 26.2 66 0.0014 33.3 3.4 87 681-803 14-103 (181)
146 PF00130 C1_1: Phorbol esters/ 26.1 54 0.0012 26.4 2.2 34 343-378 12-45 (53)
147 PF14881 Tubulin_3: Tubulin do 26.0 44 0.00096 34.4 2.1 47 680-726 48-101 (180)
148 PF06524 NOA36: NOA36 protein; 25.3 35 0.00075 37.5 1.2 59 213-283 122-189 (314)
149 TIGR00762 DegV EDD domain prot 25.0 2.7E+02 0.0059 30.0 8.0 94 624-725 122-246 (275)
150 PF07227 DUF1423: Protein of u 24.8 45 0.00096 39.1 2.0 42 265-315 122-163 (446)
151 PRK04266 fibrillarin; Provisio 24.6 87 0.0019 33.2 4.1 27 697-723 68-94 (226)
152 KOG0827 Predicted E3 ubiquitin 24.3 28 0.0006 40.1 0.3 29 302-350 24-53 (465)
153 KOG2932 E3 ubiquitin ligase in 24.0 26 0.00057 39.2 0.1 64 216-309 90-158 (389)
154 PRK06202 hypothetical protein; 23.8 67 0.0014 33.3 3.0 39 700-738 59-97 (232)
155 TIGR00497 hsdM type I restrict 23.8 45 0.00098 39.1 1.9 47 671-717 187-233 (501)
156 PF02353 CMAS: Mycolic acid cy 23.7 77 0.0017 34.5 3.5 34 687-722 50-83 (273)
157 PF05958 tRNA_U5-meth_tr: tRNA 23.3 68 0.0015 36.1 3.1 50 673-722 165-217 (352)
158 smart00550 Zalpha Z-DNA-bindin 23.1 1.2E+02 0.0027 26.1 4.0 48 571-641 5-53 (68)
159 cd07168 NR_DBD_DHR4_like DNA-b 22.8 66 0.0014 29.6 2.4 29 214-243 4-37 (90)
160 COG4798 Predicted methyltransf 22.7 44 0.00095 35.7 1.3 49 696-744 43-91 (238)
161 KOG2752 Uncharacterized conser 22.7 1E+02 0.0022 34.8 4.1 33 347-379 132-167 (345)
162 PRK00377 cbiT cobalt-precorrin 22.6 1.2E+02 0.0025 30.9 4.4 39 682-722 23-61 (198)
163 TIGR02081 metW methionine bios 22.2 89 0.0019 31.5 3.5 31 688-722 4-34 (194)
164 PF09445 Methyltransf_15: RNA 21.8 13 0.00029 37.7 -2.5 72 703-775 1-81 (163)
165 KOG1098 Putative SAM-dependent 21.8 46 0.00099 40.6 1.4 31 685-716 29-59 (780)
166 smart00744 RINGv The RING-vari 21.7 48 0.001 27.2 1.1 37 278-317 1-37 (49)
167 COG3028 Uncharacterized protei 21.2 73 0.0016 33.1 2.5 33 623-662 94-126 (187)
168 KOG4215 Hepatocyte nuclear fac 21.2 32 0.0007 39.3 0.0 27 215-242 18-49 (432)
169 KOG4589 Cell division protein 21.1 62 0.0013 34.4 2.0 36 687-723 56-91 (232)
170 COG1107 Archaea-specific RecJ- 20.8 48 0.001 40.1 1.3 12 266-277 95-106 (715)
171 PF13679 Methyltransf_32: Meth 20.8 1.2E+02 0.0027 29.2 3.9 98 685-789 6-122 (141)
172 PHA02862 5L protein; Provision 20.8 44 0.00096 33.8 0.9 36 277-318 3-38 (156)
173 KOG1829 Uncharacterized conser 20.3 31 0.00068 41.6 -0.3 47 268-316 503-549 (580)
174 PRK14904 16S rRNA methyltransf 20.2 72 0.0016 36.9 2.6 25 699-723 248-272 (445)
175 PF10367 Vps39_2: Vacuolar sor 20.2 52 0.0011 29.7 1.2 30 278-315 80-109 (109)
176 PF12861 zf-Apc11: Anaphase-pr 20.1 41 0.00088 31.1 0.5 27 217-245 33-62 (85)
177 PF10235 Cript: Microtubule-as 20.1 55 0.0012 30.6 1.3 22 265-286 58-79 (90)
178 PRK14901 16S rRNA methyltransf 20.0 70 0.0015 36.8 2.4 24 699-722 250-273 (434)
No 1
>PF12047 DNMT1-RFD: Cytosine specific DNA methyltransferase replication foci domain; InterPro: IPR022702 This domain is part of a cytosine specific DNA methyltransferase enzyme. It functions non-catalytically to target the protein towards replication foci. This allows the DNMT1 protein to methylate the correct residues. This domain targets DMAP1 and HDAC2 to the replication foci during the S phase of mitosis. They are thought to have some importance in conversion of critical histone lysine moieties []. A structure exists for the human cytosine specific DNA methyltransferase replication foci domain. ; PDB: 3AV6_A 3AV5_A 3AV4_A 3EPZ_B.
Probab=99.78 E-value=3.4e-20 Score=179.20 Aligned_cols=131 Identities=24% Similarity=0.401 Sum_probs=100.8
Q ss_pred CCCccccccceeEeecCCCCeeEeEeeeeeecccccCCCCcceEEE----------ecccCCCccceeeeEEEEeeeccC
Q 003658 7 DDDTLTLYVSDYEFLDQNEESISFSVLPLQWDGCDIVGSSEMQVFL----------HGNIGDGPWNFNEQVIAWKFELSY 76 (805)
Q Consensus 7 ~~e~~~~~v~~y~f~d~~~~~v~fs~lp~~~~~~~~~~~~~~~v~l----------~g~~d~gl~~v~~~v~aW~~~l~~ 76 (805)
|++.++..++||+|.|+++++|+|+.||++|+...-+.|..+.+++ +|..++|++.++.+|++|.+++..
T Consensus 1 ~~~~p~r~L~~f~~~d~~~~~~~le~l~~~~~~~~~~sG~v~~~~~~~~~~~~~~~~g~~~~g~~~~l~~I~~W~i~~~~ 80 (146)
T PF12047_consen 1 EDDLPMRSLDDFSFYDSDGEPVSLELLPIEWNVDLFASGVVKPIGLWGDDEPSPKEKGVRDEGVRIRLGPIKEWWIDGGD 80 (146)
T ss_dssp -SSS-EEEEEEEEEEETTSBB--STTSTTTTT--EEEEEEEEETT-------SSTS-SEEEEC----ES-ECEEEEE-SS
T ss_pred CCCCcceEEEEEEEEeCCCCEEeeeeccccCCCcccceEEecccCcccccCccccccCccCCCcccceeceeEEEEEecC
Confidence 5788899999999999999999999999999998777777788887 799999999999999999999998
Q ss_pred CcceEEEEecCCceeEcCCCCch----HHHHHHHHHhhhheehhhccCcccchhHHHHHHHhhcc
Q 003658 77 AQPEIWVLSKQNNWIMLQSPKKS----FKNIVRTILITVHWLYCVKQNPEASRKYIREQMLKVFC 137 (805)
Q Consensus 77 ~~p~i~vls~~~~Wi~L~kPrk~----ye~~ir~vlitv~~LhfvkknP~~s~ksl~~~L~K~F~ 137 (805)
..|.+.+|+.+.+|++|+||+++ |+.++|++.||++++|+|++||..+..++|++|.++++
T Consensus 81 ~~~~~i~i~T~~awY~L~kPs~~Y~~~y~~~~~~~~l~~~v~~~l~~~~~~~~~s~~d~l~~v~~ 145 (146)
T PF12047_consen 81 DGPPIIWISTDYAWYRLMKPSKSYAPWYEPFLRKARLTVRVIHFLKKNPRASDLSYEDLLARVFR 145 (146)
T ss_dssp SSS-EEEEEESS-EEEE-SB-TTTHHHHCCHHHHHHHHHHHHHHHHHHT---T--HHHHHHHHHH
T ss_pred CCccEEEEEECCcEEEECCccHHHHHHHHHHHHHHHHHHHHHHHHhhCcccccCCHHHHHHHHhc
Confidence 88899999999999999999999 56788999999999999999999999999999999864
No 2
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=98.04 E-value=2.5e-06 Score=98.87 Aligned_cols=83 Identities=29% Similarity=0.737 Sum_probs=63.8
Q ss_pred cccccccccCCCCCCCCCceeeccCCCcCCCCccchhcccCCCCchhHHHHHHHHhhcCCceecCCc-ccccCcCCcccc
Q 003658 277 HQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCPVH-KCFVCQQSEDMN 355 (805)
Q Consensus 277 h~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~~p~~~~~~~eL~krV~~g~~F~CPlH-~C~~C~~~edk~ 355 (805)
+.|++|+-.|.. ..+.++.| ..||.+||+.|+..+.. .++ .+..|+||-| .|+.|+..++-
T Consensus 19 ~mc~l~~s~G~~---~ag~m~ac--~~c~~~yH~~cvt~~~~-----------~~~-l~~gWrC~~crvCe~c~~~gD~- 80 (694)
T KOG4443|consen 19 LMCPLCGSSGKG---RAGRLLAC--SDCGQKYHPYCVTSWAQ-----------HAV-LSGGWRCPSCRVCEACGTTGDP- 80 (694)
T ss_pred hhhhhhcccccc---ccCcchhh--hhhcccCCcchhhHHHh-----------HHH-hcCCcccCCceeeeeccccCCc-
Confidence 379999877752 34568889 89999999999987642 122 2456999976 58888876653
Q ss_pred ccccceeeccccccccccccCCCCc
Q 003658 356 VEDLQLAICRRCPKAYHRKCLPTEI 380 (805)
Q Consensus 356 ~~~~qL~~C~RCPkAYH~kCLP~g~ 380 (805)
.++..|.+|..+||.+|+.+..
T Consensus 81 ---~kf~~Ck~cDvsyh~yc~~P~~ 102 (694)
T KOG4443|consen 81 ---KKFLLCKRCDVSYHCYCQKPPN 102 (694)
T ss_pred ---ccccccccccccccccccCCcc
Confidence 4899999999999999997653
No 3
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=97.69 E-value=1.6e-05 Score=89.60 Aligned_cols=89 Identities=27% Similarity=0.631 Sum_probs=64.0
Q ss_pred cCCCcccccccCCCC-----ceeecCcccccccccccccCccccccccCCcccccCCCCceecccccccCcc---ccccc
Q 003658 212 DENYFAVCAICDDGG-----DVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQEHQ---CFACG 283 (805)
Q Consensus 212 dd~~d~vC~IC~~gG-----eLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~gqh~---CfiCg 283 (805)
++..++.|.+|.... .++.||| |.-+.|..| -|+.- -+++.|+|..|.++.|+ |.-|-
T Consensus 189 ~d~~d~~C~~c~~t~~eN~naiVfCdg-C~i~VHq~C----------YGI~f---~peG~WlCrkCi~~~~~i~~C~fCp 254 (669)
T COG5141 189 SDEFDDICTKCTSTHNENSNAIVFCDG-CEICVHQSC----------YGIQF---LPEGFWLCRKCIYGEYQIRCCSFCP 254 (669)
T ss_pred chhhhhhhHhccccccCCcceEEEecC-cchhhhhhc----------cccee---cCcchhhhhhhcccccceeEEEecc
Confidence 335689999997653 4999997 999999996 56532 25789999999988654 55553
Q ss_pred ccCC-----CCC--------------------------------------------CCCCceeeccCCCcCCCCccchhc
Q 003658 284 MLGS-----SDK--------------------------------------------SSSQEVFPCVSATCGQFYHPECVS 314 (805)
Q Consensus 284 klGs-----sd~--------------------------------------------~s~~eV~kCsv~~CGrfYHp~CL~ 314 (805)
...- +|. .-+|.-++|+..+|-+.||..|..
T Consensus 255 s~dGaFkqT~dgrW~H~iCA~~~pelsF~~l~~~dpI~~i~sVs~srwkl~C~iCk~~~GtcIqCs~~nC~~aYHVtCAr 334 (669)
T COG5141 255 SSDGAFKQTSDGRWGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFNCTRAYHVTCAR 334 (669)
T ss_pred CCCCceeeccCCchHhHhHHHhcchhccccccccchhhhhcccchhhHhheeeEEcccCcceeeecccchhhhhhhhhhh
Confidence 2110 000 013567899999999999999975
No 4
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.62 E-value=4.5e-05 Score=88.54 Aligned_cols=50 Identities=28% Similarity=0.707 Sum_probs=38.8
Q ss_pred ccccCcCCccccccccceeeccccccccccccCCCCcccccccchhhhhhhhccCCCCceeEEcCCCcc
Q 003658 344 KCFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPTEITFSDADENNFQRAWVDLLPNNRILIYCLEHKI 412 (805)
Q Consensus 344 ~C~~C~~~edk~~~~~qL~~C~RCPkAYH~kCLP~g~~f~~~~~e~~~raW~~ll~~~riLI~C~kH~i 412 (805)
+|..|++.+.- ..++.|+.||.+||..||.+++.-++ +|.+ -|+|+.|.+
T Consensus 255 fCsaCn~~~~F----~~~i~CD~Cp~sFH~~CLePPl~~en-------------iP~g--~W~C~ec~~ 304 (613)
T KOG4299|consen 255 FCSACNGSGLF----NDIICCDGCPRSFHQTCLEPPLEPEN-------------IPPG--SWFCPECKI 304 (613)
T ss_pred HHHHhCCcccc----ccceeecCCchHHHHhhcCCCCCccc-------------CCCC--ccccCCCee
Confidence 89999998752 46799999999999999999875332 3322 378888885
No 5
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.59 E-value=2e-05 Score=91.40 Aligned_cols=50 Identities=30% Similarity=0.689 Sum_probs=39.9
Q ss_pred cccccccCCCCce---eecCcccccccccccccCccccccccCCcccccCCCCceeccccccc
Q 003658 216 FAVCAICDDGGDV---TFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQ 275 (805)
Q Consensus 216 d~vC~IC~~gGeL---L~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~g 275 (805)
+++|+.|.+.|.. ||||| |+++||++|+++. ++...+ |.+.|+|++|..+
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~-Cp~sFH~~CLePP--------l~~eni-P~g~W~C~ec~~k 305 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDG-CPRSFHQTCLEPP--------LEPENI-PPGSWFCPECKIK 305 (613)
T ss_pred HHHHHHhCCccccccceeecC-CchHHHHhhcCCC--------CCcccC-CCCccccCCCeee
Confidence 6699999999976 99997 9999999988752 333333 4689999999843
No 6
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.49 E-value=8.9e-05 Score=78.33 Aligned_cols=48 Identities=27% Similarity=0.627 Sum_probs=37.5
Q ss_pred CCCcccccccCCC--CceeecCcc-ccc-ccccccccCccccccccCCcccccCCCCceecccccc
Q 003658 213 ENYFAVCAICDDG--GDVTFCDGR-CLR-SFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVY 274 (805)
Q Consensus 213 d~~d~vC~IC~~g--GeLL~CdG~-C~R-sFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~ 274 (805)
.....+|+ |.++ |++|-|||. |.| |||+.| +||... |.+.|||++|..
T Consensus 218 e~e~lYCf-CqqvSyGqMVaCDn~nCkrEWFH~~C----------VGLk~p---PKG~WYC~eCk~ 269 (271)
T COG5034 218 EGEELYCF-CQQVSYGQMVACDNANCKREWFHLEC----------VGLKEP---PKGKWYCPECKK 269 (271)
T ss_pred cCceeEEE-ecccccccceecCCCCCchhheeccc----------cccCCC---CCCcEeCHHhHh
Confidence 34467775 8875 999999985 765 999996 688654 589999999973
No 7
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.46 E-value=5.8e-05 Score=81.18 Aligned_cols=51 Identities=27% Similarity=0.565 Sum_probs=41.0
Q ss_pred cccCCCcccccccCCCCceeecCcc-cc-cccccccccCccccccccCCcccccCCCCceecccccc
Q 003658 210 DKDENYFAVCAICDDGGDVTFCDGR-CL-RSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVY 274 (805)
Q Consensus 210 ~edd~~d~vC~IC~~gGeLL~CdG~-C~-RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~ 274 (805)
+.+...-.+|. |..+|++|-||+. |. .|||+.| +||+.+ |.+.|||++|..
T Consensus 215 d~~e~~yC~Cn-qvsyg~Mi~CDn~~C~~eWFH~~C----------VGL~~~---PkgkWyC~~C~~ 267 (274)
T KOG1973|consen 215 DPDEPTYCICN-QVSYGKMIGCDNPGCPIEWFHFTC----------VGLKTK---PKGKWYCPRCKA 267 (274)
T ss_pred CCCCCEEEEec-ccccccccccCCCCCCcceEEEec----------cccccC---CCCcccchhhhh
Confidence 44555566777 8889999999974 99 9999996 788754 468899999974
No 8
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=97.46 E-value=3e-05 Score=90.26 Aligned_cols=141 Identities=21% Similarity=0.440 Sum_probs=87.1
Q ss_pred CCCcccccccCCCC-----ceeecCcccccccccccccCccccccccCCcccccCCCCceecccccccCcccccccccCC
Q 003658 213 ENYFAVCAICDDGG-----DVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQEHQCFACGMLGS 287 (805)
Q Consensus 213 d~~d~vC~IC~~gG-----eLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~gqh~CfiCgklGs 287 (805)
......|.+|+..| -|+.|. .|...||..|+. +=++.+.+ ..-|.|+.|+ .|-.|+..|.
T Consensus 15 ~~~~~mc~l~~s~G~~~ag~m~ac~-~c~~~yH~~cvt--------~~~~~~~l--~~gWrC~~cr----vCe~c~~~gD 79 (694)
T KOG4443|consen 15 IIVCLMCPLCGSSGKGRAGRLLACS-DCGQKYHPYCVT--------SWAQHAVL--SGGWRCPSCR----VCEACGTTGD 79 (694)
T ss_pred hhhhhhhhhhccccccccCcchhhh-hhcccCCcchhh--------HHHhHHHh--cCCcccCCce----eeeeccccCC
Confidence 34466788888765 499999 799999999753 33333332 4559999999 5999997764
Q ss_pred CCCCCCCceeeccCCCcCCCCccchhcccCCCCchhHH---HHHH------------HHhh--cCCceecCC-cccccCc
Q 003658 288 SDKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLA---EELR------------ERIA--AGESFTCPV-HKCFVCQ 349 (805)
Q Consensus 288 sd~~s~~eV~kCsv~~CGrfYHp~CL~~~~~p~~~~~~---~eL~------------krV~--~g~~F~CPl-H~C~~C~ 349 (805)
....+.| ..|.-.||-.|+.+.........+ ..+. -++. -..+|.|-. -+|.+|.
T Consensus 80 -----~~kf~~C--k~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~c~qc~~~lpg~s~~~~~~~~~~~~c~s~~~cPvc~ 152 (694)
T KOG4443|consen 80 -----PKKFLLC--KRCDVSYHCYCQKPPNDKVPSGPWLCKKCTRCRQCDSTLPGLSLDLQEGYLQCAPCASLSYCPVCL 152 (694)
T ss_pred -----ccccccc--ccccccccccccCCccccccCcccccHHHHhhhhccccccccchhhhccCcccccccccccCchHH
Confidence 3578889 899999999998765421100000 0000 0000 012233332 3444444
Q ss_pred CCccccccccceeeccccccccccccC
Q 003658 350 QSEDMNVEDLQLAICRRCPKAYHRKCL 376 (805)
Q Consensus 350 ~~edk~~~~~qL~~C~RCPkAYH~kCL 376 (805)
.-.. ......++.|..|-+|-|-.|.
T Consensus 153 ~~Y~-~~e~~~~~~c~~c~rwsh~~c~ 178 (694)
T KOG4443|consen 153 IVYQ-DSESLPMVCCSICQRWSHGGCD 178 (694)
T ss_pred Hhhh-hccchhhHHHHHhcccccCCCC
Confidence 4332 1223446889999999998885
No 9
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.46 E-value=4.2e-05 Score=81.24 Aligned_cols=85 Identities=24% Similarity=0.532 Sum_probs=62.6
Q ss_pred CCCcccccccCCC----------CceeecCcccccccccccccCccccccccCCcccccCCCCceecccccccCcccccc
Q 003658 213 ENYFAVCAICDDG----------GDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQEHQCFAC 282 (805)
Q Consensus 213 d~~d~vC~IC~~g----------GeLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~gqh~CfiC 282 (805)
.+...+|-+|-.+ .+|+.|. .|.|+=|+.|+.-..+ +..+ + ..-.|.|-+|.+ |.+|
T Consensus 221 a~Pn~YCDFclgdsr~nkkt~~peelvscs-dcgrsghpsclqft~n------m~~a-v-k~yrwqcieck~----csic 287 (336)
T KOG1244|consen 221 AQPNPYCDFCLGDSRENKKTGMPEELVSCS-DCGRSGHPSCLQFTAN------MIAA-V-KTYRWQCIECKY----CSIC 287 (336)
T ss_pred ccCCcccceeccccccccccCCchhhcchh-hcCCCCCcchhhhhHH------HHHH-H-Hhheeeeeecce----eccc
Confidence 4557889999643 3699999 6999999997542211 1111 1 135899999995 9999
Q ss_pred cccCCCCCCCCCceeeccCCCcCCCCccchhcccC
Q 003658 283 GMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLL 317 (805)
Q Consensus 283 gklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~ 317 (805)
|-.. +..+++.| ..|.|-||-.|+.+.+
T Consensus 288 gtse-----nddqllfc--ddcdrgyhmyclsppm 315 (336)
T KOG1244|consen 288 GTSE-----NDDQLLFC--DDCDRGYHMYCLSPPM 315 (336)
T ss_pred cCcC-----CCceeEee--cccCCceeeEecCCCc
Confidence 8543 24689999 9999999999998654
No 10
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.41 E-value=4.9e-05 Score=81.17 Aligned_cols=84 Identities=19% Similarity=0.219 Sum_probs=63.4
Q ss_pred CCcccccccCCCC---------ceeecCcccccccccccccCccccccccCCcccccC--CCCceecccccccCcccccc
Q 003658 214 NYFAVCAICDDGG---------DVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQID--AVPNFLCQNCVYQEHQCFAC 282 (805)
Q Consensus 214 ~~d~vC~IC~~gG---------eLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~--~~~~w~C~eC~~gqh~CfiC 282 (805)
.....|.+|-++- -+|+|. +|--++|+.|++ ++.+-+. ..-.|.|.+|+ .|.+|
T Consensus 256 ~~~~~~~~~~~~~~~~~~~r~~S~I~C~-~C~~~~HP~Ci~----------M~~elv~~~KTY~W~C~~C~----lC~IC 320 (381)
T KOG1512|consen 256 QRRNERKHFWDIQTNIIQSRRNSWIVCK-PCATRPHPYCVA----------MIPELVGQYKTYFWKCSSCE----LCRIC 320 (381)
T ss_pred cchhhhhhhhcchhhhhhhhhccceeec-ccccCCCCcchh----------cCHHHHhHHhhcchhhcccH----hhhcc
Confidence 4467799998762 399999 799999999743 3322110 13579999999 69999
Q ss_pred cccCCCCCCCCCceeeccCCCcCCCCccchhcccCCC
Q 003658 283 GMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLHP 319 (805)
Q Consensus 283 gklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~~p 319 (805)
+++.. ..+++.| ..|.|-||..||+..-.|
T Consensus 321 ~~P~~-----E~E~~FC--D~CDRG~HT~CVGL~~lP 350 (381)
T KOG1512|consen 321 LGPVI-----ESEHLFC--DVCDRGPHTLCVGLQDLP 350 (381)
T ss_pred CCccc-----chheecc--ccccCCCCcccccccccc
Confidence 98763 4588899 899999999999854433
No 11
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=97.28 E-value=0.00025 Score=87.42 Aligned_cols=142 Identities=25% Similarity=0.475 Sum_probs=88.4
Q ss_pred cccCCCcccccccCCCC-----ceeecCcccccccccccccCccccccccCCcccccCCCCceecccccccC---ccccc
Q 003658 210 DKDENYFAVCAICDDGG-----DVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQE---HQCFA 281 (805)
Q Consensus 210 ~edd~~d~vC~IC~~gG-----eLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~gq---h~Cfi 281 (805)
+.++..|.+|.||.++. .+|.||| |.-+.|+.| .|.. ..+++.|+|..|...+ ..|..
T Consensus 213 ~~~~~~D~~C~iC~~~~~~n~n~ivfCD~-Cnl~VHq~C----------ygi~---~ipeg~WlCr~Cl~s~~~~v~c~~ 278 (1051)
T KOG0955|consen 213 DALLEEDAVCCICLDGECQNSNVIVFCDG-CNLAVHQEC----------YGIP---FIPEGQWLCRRCLQSPQRPVRCLL 278 (1051)
T ss_pred ccccCCCccceeecccccCCCceEEEcCC-Ccchhhhhc----------cCCC---CCCCCcEeehhhccCcCcccceEe
Confidence 35667799999998863 4999996 999999996 5642 2258999999998754 46778
Q ss_pred ccccCCCCCCCCCceeeccCCCcCCCCccchhcccCCCCchhHHHHHHHH---hhcCCceecCCcccccCcCCccccccc
Q 003658 282 CGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRER---IAAGESFTCPVHKCFVCQQSEDMNVED 358 (805)
Q Consensus 282 CgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~~p~~~~~~~eL~kr---V~~g~~F~CPlH~C~~C~~~edk~~~~ 358 (805)
|-..| .-|+ ...=|+.-|.-|..-.++...... -+.+- |..-..-+ =.-+|..|+..+ -
T Consensus 279 cp~~~--------gAFk--qt~dgrw~Hv~caiwipev~F~nt--~~~E~I~~i~~i~~aR-wkL~cy~cK~~~-----~ 340 (1051)
T KOG0955|consen 279 CPSKG--------GAFK--QTDDGRWAHVVCAIWIPEVSFANT--VFLEPIDSIENIPPAR-WKLTCYICKQKG-----L 340 (1051)
T ss_pred ccCCC--------Ccce--eccCCceeeeehhhcccccccccc--hhhccccchhcCcHhh-hhceeeeeccCC-----C
Confidence 75332 2222 256688888888754332211100 00000 00001000 023688898866 1
Q ss_pred cceeec--cccccccccccC-CCCcccc
Q 003658 359 LQLAIC--RRCPKAYHRKCL-PTEITFS 383 (805)
Q Consensus 359 ~qL~~C--~RCPkAYH~kCL-P~g~~f~ 383 (805)
+..++| .+|-+|||..|- .+|+.+.
T Consensus 341 gaciqcs~~~c~~a~hvtca~~agl~m~ 368 (1051)
T KOG0955|consen 341 GACIQCSKANCYTAFHVTCARRAGLYMK 368 (1051)
T ss_pred CcceecchhhhhhhhhhhhHhhcCceEe
Confidence 357788 579999999997 4555443
No 13
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.26 E-value=0.00021 Score=76.04 Aligned_cols=72 Identities=28% Similarity=0.712 Sum_probs=52.3
Q ss_pred CceeeccCCCcCCCCccchhcccCCCCchhHHHHHHHHhhcCCceecC-CcccccCcCCccccccccceeeccccccccc
Q 003658 294 QEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCP-VHKCFVCQQSEDMNVEDLQLAICRRCPKAYH 372 (805)
Q Consensus 294 ~eV~kCsv~~CGrfYHp~CL~~~~~p~~~~~~~eL~krV~~g~~F~CP-lH~C~~C~~~edk~~~~~qL~~C~RCPkAYH 372 (805)
.+++-| ..|||.=||.|+.--. .+..-| ..-.|.|= -.+|..|+.++|++ ||+-|+-|.+.||
T Consensus 244 eelvsc--sdcgrsghpsclqft~---------nm~~av-k~yrwqcieck~csicgtsendd----qllfcddcdrgyh 307 (336)
T KOG1244|consen 244 EELVSC--SDCGRSGHPSCLQFTA---------NMIAAV-KTYRWQCIECKYCSICGTSENDD----QLLFCDDCDRGYH 307 (336)
T ss_pred hhhcch--hhcCCCCCcchhhhhH---------HHHHHH-HhheeeeeecceeccccCcCCCc----eeEeecccCCcee
Confidence 478899 8999999999986321 111111 11235443 25788899888754 9999999999999
Q ss_pred cccCCCCcc
Q 003658 373 RKCLPTEIT 381 (805)
Q Consensus 373 ~kCLP~g~~ 381 (805)
.+||.++.+
T Consensus 308 myclsppm~ 316 (336)
T KOG1244|consen 308 MYCLSPPMV 316 (336)
T ss_pred eEecCCCcC
Confidence 999988775
No 14
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=97.22 E-value=8.2e-05 Score=59.77 Aligned_cols=46 Identities=28% Similarity=0.735 Sum_probs=33.1
Q ss_pred cccccCC---CCceeecCcccccccccccccCccccccccCCcccccC-CCCceecccccc
Q 003658 218 VCAICDD---GGDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQID-AVPNFLCQNCVY 274 (805)
Q Consensus 218 vC~IC~~---gGeLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~-~~~~w~C~eC~~ 274 (805)
+|.+|++ .+++|.|+ .|.++||+.|+ +++..... ....|+|++|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~-~C~~~~H~~C~----------~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCD-SCNRWYHQECV----------GPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBS-TTSCEEETTTS----------TSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcC-CCChhhCcccC----------CCChhhccCCCCcEECcCCcC
Confidence 5888987 56799999 59999999974 33322111 134899999974
No 15
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=97.06 E-value=0.00021 Score=84.03 Aligned_cols=157 Identities=20% Similarity=0.452 Sum_probs=93.4
Q ss_pred CcccccccCCC-----CceeecCcccccccccccccCccccccccCCcccccCCCCceecccccccC-cccccccccCCC
Q 003658 215 YFAVCAICDDG-----GDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQE-HQCFACGMLGSS 288 (805)
Q Consensus 215 ~d~vC~IC~~g-----GeLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~gq-h~CfiCgklGss 288 (805)
.+.+|-+|..+ .+|++|| .|.-..|+.| .|+.+. +.+.|+|.-|..+. ..|..|=+.|-+
T Consensus 270 edviCDvCrspD~e~~neMVfCd-~Cn~cVHqaC----------yGIle~---p~gpWlCr~Calg~~ppCvLCPkkGGa 335 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCD-KCNICVHQAC----------YGILEV---PEGPWLCRTCALGIEPPCVLCPKKGGA 335 (893)
T ss_pred ccceeceecCCCccccceeEEec-cchhHHHHhh----------hceeec---CCCCeeehhccccCCCCeeeccccCCc
Confidence 57889999876 4699999 7999999996 677644 46999999999874 679999776643
Q ss_pred CCCCCCceeeccCCCcCCCCccchhcccCCCCchhHHHHHHHHhhcC-----CceecCCcccccCcCCccccccccceee
Q 003658 289 DKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAG-----ESFTCPVHKCFVCQQSEDMNVEDLQLAI 363 (805)
Q Consensus 289 d~~s~~eV~kCsv~~CGrfYHp~CL~~~~~p~~~~~~~eL~krV~~g-----~~F~CPlH~C~~C~~~edk~~~~~qL~~ 363 (805)
-+++ ..=.++-|..|.--.|....+ -.++.+=|... ..| .-.|..|+... +.-++
T Consensus 336 mK~~---------~sgT~wAHvsCALwIPEVsie--~~ekmePItkfs~IpesRw---slvC~LCk~k~------GACIq 395 (893)
T KOG0954|consen 336 MKPT---------KSGTKWAHVSCALWIPEVSIE--CPEKMEPITKFSHIPESRW---SLVCNLCKVKS------GACIQ 395 (893)
T ss_pred cccc---------CCCCeeeEeeeeeccceeecc--CHhhcCcccccCCCcHHHH---HHHHHHhcccC------cceEE
Confidence 2221 122277899996443322211 11111101100 011 13588887733 23455
Q ss_pred c--cccccccccccC-CCCcccccccchhhhhhhhccCCCCceeEEcCCCcccc
Q 003658 364 C--RRCPKAYHRKCL-PTEITFSDADENNFQRAWVDLLPNNRILIYCLEHKIIS 414 (805)
Q Consensus 364 C--~RCPkAYH~kCL-P~g~~f~~~~~e~~~raW~~ll~~~riLI~C~kH~i~~ 414 (805)
| ..|-.+||..|. .+|..+.....++ ..-...-||.+|....
T Consensus 396 Cs~k~C~t~fHv~CA~~aG~~~~~~~~~~---------D~v~~~s~c~khs~~~ 440 (893)
T KOG0954|consen 396 CSNKTCRTAFHVTCAFEAGLEMKTILKEN---------DEVKFKSYCSKHSDHR 440 (893)
T ss_pred ecccchhhhccchhhhhcCCeeeeeeccC---------Cchhheeecccccccc
Confidence 5 367799999986 3454443322221 1113345788877543
No 16
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.02 E-value=0.00036 Score=81.65 Aligned_cols=83 Identities=28% Similarity=0.808 Sum_probs=65.3
Q ss_pred ccccCCC-C----ceeecCcc-cccccccccccCccccccccCCcccccCCCCceeccccccc-----------------
Q 003658 219 CAICDDG-G----DVTFCDGR-CLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQ----------------- 275 (805)
Q Consensus 219 C~IC~~g-G----eLL~CdG~-C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~g----------------- 275 (805)
|-+|.+. | -||.|||. |--+.|+.| .|+ .+| +.+.|+|.-|+..
T Consensus 8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaC----------YGI--vqV-PtGpWfCrKCesqeraarvrCeLCP~kdGA 74 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGHNCSVAVHQAC----------YGI--VQV-PTGPWFCRKCESQERAARVRCELCPHKDGA 74 (900)
T ss_pred eeeecCcCCCccCceeeecCCCceeeeehhc----------cee--Eec-CCCchhhhhhhhhhhhccceeecccCcccc
Confidence 8899763 2 39999995 999999996 576 344 5899999999743
Q ss_pred ------------------------------------------CcccccccccCCCCCCCCCceeeccCCCcCCCCccchh
Q 003658 276 ------------------------------------------EHQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECV 313 (805)
Q Consensus 276 ------------------------------------------qh~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL 313 (805)
...|+||.+.|-..+...+--+.|.-..|.+.||..|.
T Consensus 75 LKkTDn~GWAHVVCALYIPEVrFgNV~TMEPIiLq~VP~dRfnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCA 154 (900)
T KOG0956|consen 75 LKKTDNGGWAHVVCALYIPEVRFGNVHTMEPIILQDVPHDRFNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCA 154 (900)
T ss_pred eecccCCCceEEEEEeeccceeecccccccceeeccCchhhhcceeeeecccCCccccccccceecccccchhhhhhhHh
Confidence 13799999887665544566688999999999999997
Q ss_pred c
Q 003658 314 S 314 (805)
Q Consensus 314 ~ 314 (805)
.
T Consensus 155 Q 155 (900)
T KOG0956|consen 155 Q 155 (900)
T ss_pred h
Confidence 5
No 17
>PHA03412 putative methyltransferase; Provisional
Probab=96.77 E-value=0.00079 Score=71.44 Aligned_cols=116 Identities=21% Similarity=0.328 Sum_probs=68.2
Q ss_pred ccCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHHHcC------CcccccCCCCCCCCC--CCcccc
Q 003658 677 SFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQMG------KSCSFRNYDLIQPKN--DFSFEK 748 (805)
Q Consensus 677 s~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~~~------~~~~~~n~d~~~~~~--~~~f~~ 748 (805)
..|.+||+..-.+.++ .|.. .+..|+|+|||+..|+-.+-++..+.. -..+-....+.. .| ...|..
T Consensus 29 ~~GqFfTP~~iAr~~~---i~~~-~~grVLDlG~GSG~Lalala~~~~~~~~~~V~aVEID~~Al~~Ar-~n~~~~~~~~ 103 (241)
T PHA03412 29 ELGAFFTPIGLARDFT---IDAC-TSGSVVDLCAGIGGLSFAMVHMMMYAKPREIVCVELNHTYYKLGK-RIVPEATWIN 103 (241)
T ss_pred cCCccCCCHHHHHHHH---Hhcc-CCCEEEEccChHHHHHHHHHHhcccCCCcEEEEEECCHHHHHHHH-hhccCCEEEE
Confidence 6799999998555544 2222 478999999999999998876532111 011111111110 00 123333
Q ss_pred ccccccCCCCCCCCCceeeecCCCcchhh-----------hhHHHHhhhhhccCCcEEEEecCCC
Q 003658 749 RDWMTVRPEELPDGSQLIMGLNPPFGVKA-----------SLANKFISQALKFKPKLIVLIVPQE 802 (805)
Q Consensus 749 ~~w~~~~~~~l~~g~~li~gl~ppfg~~~-----------~~a~kf~~~~~~f~p~~~~li~p~~ 802 (805)
.|.+... +..-=-+|++ ||||+..+ .+.++||.+|+..-+.-.. |+|.-
T Consensus 104 ~D~~~~~---~~~~FDlIIs-NPPY~~~~~~d~~ar~~g~~~~~~li~~A~~Ll~~G~~-ILP~~ 163 (241)
T PHA03412 104 ADALTTE---FDTLFDMAIS-NPPFGKIKTSDFKGKYTGAEFEYKVIERASQIARQGTF-IIPQM 163 (241)
T ss_pred cchhccc---ccCCccEEEE-CCCCCCccccccCCcccccHHHHHHHHHHHHHcCCCEE-EeCcc
Confidence 4433322 1112348888 99999322 4578899999987766664 88863
No 18
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=96.71 E-value=0.003 Score=63.68 Aligned_cols=26 Identities=31% Similarity=0.494 Sum_probs=22.1
Q ss_pred ccccceeeccccccccccccCCCCcc
Q 003658 356 VEDLQLAICRRCPKAYHRKCLPTEIT 381 (805)
Q Consensus 356 ~~~~qL~~C~RCPkAYH~kCLP~g~~ 381 (805)
..+.-|++|..|-+|||...||+...
T Consensus 119 N~~nVLFRC~~C~RawH~~HLP~~~~ 144 (175)
T PF15446_consen 119 NPDNVLFRCTSCHRAWHFEHLPPPSG 144 (175)
T ss_pred ChhheEEecCCccceeehhhCCCCcC
Confidence 35668999999999999999998653
No 19
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=96.64 E-value=0.00072 Score=80.66 Aligned_cols=52 Identities=35% Similarity=0.775 Sum_probs=40.0
Q ss_pred ccCCCcccccccCCCCceeecCcccccccccccccCccccccccCCcccccCCCCceecccccc
Q 003658 211 KDENYFAVCAICDDGGDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVY 274 (805)
Q Consensus 211 edd~~d~vC~IC~~gGeLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~ 274 (805)
.++.....|.||.++|++|+|+ .|+.+||..|+ +....++ +.+.|+|+.|..
T Consensus 42 ~~~~~~e~c~ic~~~g~~l~c~-tC~~s~h~~cl----------~~pl~~~-p~~~~~c~Rc~~ 93 (696)
T KOG0383|consen 42 WDDAEQEACRICADGGELLWCD-TCPASFHASCL----------GPPLTPQ-PNGEFICPRCFC 93 (696)
T ss_pred cchhhhhhhhhhcCCCcEEEec-cccHHHHHHcc----------CCCCCcC-Cccceeeeeecc
Confidence 3455678999999999999999 79999999964 3333333 345599999954
No 20
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=96.63 E-value=0.0012 Score=70.48 Aligned_cols=121 Identities=17% Similarity=0.285 Sum_probs=75.6
Q ss_pred cccCcccc-hhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHHH-cCCcccccCCCCCC---CCCCCcccccc
Q 003658 676 TSFGRHFT-KVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQ-MGKSCSFRNYDLIQ---PKNDFSFEKRD 750 (805)
Q Consensus 676 ~s~~rhft-~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~-~~~~~~~~n~d~~~---~~~~~~f~~~~ 750 (805)
.+||.||. ...-+..|++.+. +.+|+.|+|+.||...++..+-++..+ ++-+.+-.-.+... ....+.+...|
T Consensus 18 k~~gq~fl~~~~i~~~i~~~l~--~~~~~~VLEiG~G~G~lt~~L~~~~~~v~avE~d~~~~~~~~~~~~~~~v~~i~~D 95 (272)
T PRK00274 18 KSLGQNFLIDENILDKIVDAAG--PQPGDNVLEIGPGLGALTEPLLERAAKVTAVEIDRDLAPILAETFAEDNLTIIEGD 95 (272)
T ss_pred cccCcCcCCCHHHHHHHHHhcC--CCCcCeEEEeCCCccHHHHHHHHhCCcEEEEECCHHHHHHHHHhhccCceEEEECh
Confidence 58999995 4556677888774 578999999999999999888765210 00010100000000 01457788888
Q ss_pred ccccCCCCCCCCCceeeecCCCcchhhhhHHHHhhhhhccCCcEEEEecCCCC
Q 003658 751 WMTVRPEELPDGSQLIMGLNPPFGVKASLANKFISQALKFKPKLIVLIVPQET 803 (805)
Q Consensus 751 w~~~~~~~l~~g~~li~gl~ppfg~~~~~a~kf~~~~~~f~p~~~~li~p~~~ 803 (805)
++++...++. ..+|+| ||||+.-+.+-.+++... +...-++|++..|+
T Consensus 96 ~~~~~~~~~~--~~~vv~-NlPY~iss~ii~~~l~~~--~~~~~~~l~~QkE~ 143 (272)
T PRK00274 96 ALKVDLSELQ--PLKVVA-NLPYNITTPLLFHLLEER--DPIRDMVVMVQKEV 143 (272)
T ss_pred hhcCCHHHcC--cceEEE-eCCccchHHHHHHHHhcC--CCCCeeEEEeHHHH
Confidence 8887665543 357888 999996555555554332 22345778777664
No 21
>TIGR02987 met_A_Alw26 type II restriction m6 adenine DNA methyltransferase, Alw26I/Eco31I/Esp3I family. Members of this family are the m6-adenine DNA methyltransferase protein, or domain of a fusion protein that also carries m5 cytosine methyltransferase activity, of type II restriction systems of the Alw26I/Eco31I/Esp3I family. A methyltransferase of this family is alway accompanied by a type II restriction endonuclease from the Alw26I/Eco31I/Esp3I family (TIGR02986) and by an adenine-specific modification methyltransferase. Members of this family are unusual in that regions of similarity to homologs outside this family are circularly permuted.
Probab=96.58 E-value=0.0067 Score=70.43 Aligned_cols=50 Identities=26% Similarity=0.473 Sum_probs=40.9
Q ss_pred ccCcccchhhhHHHHHHhhcceec-----cCCeEEeeccCcchhhHHHHHHHHHc
Q 003658 677 SFGRHFTKVEKLKEIVDRLHWYVR-----SGDTIVDFCCGANDFSCMMKVKLEQM 726 (805)
Q Consensus 677 s~~rhft~~ekl~~i~~~l~~~~~-----~~d~~~d~~~g~~~~~~~~~~~~~~~ 726 (805)
+.|.+||++.-.+.|++.+.-+.. .+.+|+|+|||+..|...+-+++.+.
T Consensus 2 ~~GqfyTP~~ia~~mv~~~~~~~~~~~~~~~~~ilDP~cGsG~fl~~~~~~~~~~ 56 (524)
T TIGR02987 2 AYGTFFTPPDIAKAMVANLVNEIGKNDKSTKTKIIDPCCGDGRLIAALLKKNEEI 56 (524)
T ss_pred CCcccCCcHHHHHHHHHHHhhhcchhhcccceEEEeCCCCccHHHHHHHHHHHhc
Confidence 579999999999999988754433 34589999999999999888887653
No 22
>PF02384 N6_Mtase: N-6 DNA Methylase; InterPro: IPR003356 This domain is fpound in N-6 adenine-specific DNA methylase (2.1.1.72 from EC) from Type I and Type IC restriction systems. These enzymes are responsible for the methylation of specific DNA sequences in order to prevent the host from digesting its own genome via its restriction enzymes. These methylases have the same sequence specificity as their corresponding restriction enzymes. The type I restriction and modification system is composed of three polypeptides R, M and S. The M and S subunits together form a methyltransferase that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. In the presence of the R subunit, the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence. When the target site is unmodified, the DNA is cut. When the target site is hemimethylated, the complex acts as a maintenance methyltransferase, modifying the DNA so that both strands become methylated.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2F8L_A 2Y7C_C 2Y7H_C 2AR0_B 3KHK_A 3LKD_A 2OKC_B.
Probab=96.39 E-value=0.0022 Score=68.99 Aligned_cols=46 Identities=24% Similarity=0.463 Sum_probs=33.2
Q ss_pred cccCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHH
Q 003658 676 TSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 676 ~s~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
-+.|.+||+.+-.+-+++-+ -..+|++|+|+|||+..|.--.-+.+
T Consensus 23 k~~G~~~TP~~i~~l~~~~~--~~~~~~~VlDPacGsG~fL~~~~~~i 68 (311)
T PF02384_consen 23 KKLGQFYTPREIVDLMVKLL--NPKKGDSVLDPACGSGGFLVAAMEYI 68 (311)
T ss_dssp TSCGGC---HHHHHHHHHHH--TT-TTEEEEETT-TTSHHHHHHHHHH
T ss_pred cccceeehHHHHHHHHHhhh--hccccceeechhhhHHHHHHHHHHhh
Confidence 47899999998777777777 55678899999999999977666654
No 23
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF01170 UPF0020: Putative RNA methylase family UPF0020; InterPro: IPR000241 This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains [].; PDB: 3LDU_A 3LDG_A 3K0B_A 3V8V_B 3V97_A 3TLJ_A 3TM5_B 3TM4_A 3TMA_A.
Probab=95.72 E-value=0.0069 Score=61.10 Aligned_cols=99 Identities=22% Similarity=0.383 Sum_probs=53.2
Q ss_pred ccCCeEEeeccCcchhhHHHHHHHHHcC------------Ccccc-------cCCCCCCCCCCCccccccccccCCCCCC
Q 003658 700 RSGDTIVDFCCGANDFSCMMKVKLEQMG------------KSCSF-------RNYDLIQPKNDFSFEKRDWMTVRPEELP 760 (805)
Q Consensus 700 ~~~d~~~d~~~g~~~~~~~~~~~~~~~~------------~~~~~-------~n~d~~~~~~~~~f~~~~w~~~~~~~l~ 760 (805)
++|+.|+|.+||+.++..+.--.....- .+.+- .|..-..-.+...|...|...+. ++
T Consensus 27 ~~~~~vlDP~CGsGtiliEaa~~~~~~~~~~~~~~~~~~g~Di~~~~v~~a~~N~~~ag~~~~i~~~~~D~~~l~---~~ 103 (179)
T PF01170_consen 27 RPGDVVLDPFCGSGTILIEAALMGANIPPLNDINELKIIGSDIDPKAVRGARENLKAAGVEDYIDFIQWDARELP---LP 103 (179)
T ss_dssp -TTS-EEETT-TTSHHHHHHHHHHTTTSTTTH-CH--EEEEESSHHHHHHHHHHHHHTT-CGGEEEEE--GGGGG---GT
T ss_pred CCCCEEeecCCCCCHHHHHHHHHhhCcccccccccccEEecCCCHHHHHHHHHHHHhcccCCceEEEecchhhcc---cc
Confidence 7899999999999999855433222211 11111 11111122334456666666555 44
Q ss_pred CCCceeeecCCCcchhhhh-------HHHHhhhhhc-cCCcEEEEecCC
Q 003658 761 DGSQLIMGLNPPFGVKASL-------ANKFISQALK-FKPKLIVLIVPQ 801 (805)
Q Consensus 761 ~g~~li~gl~ppfg~~~~~-------a~kf~~~~~~-f~p~~~~li~p~ 801 (805)
.|+--++--|||||.+... -.+|.+.+.. ++|...+|++..
T Consensus 104 ~~~~d~IvtnPPyG~r~~~~~~~~~ly~~~~~~~~~~l~~~~v~l~~~~ 152 (179)
T PF01170_consen 104 DGSVDAIVTNPPYGRRLGSKKDLEKLYRQFLRELKRVLKPRAVFLTTSN 152 (179)
T ss_dssp TSBSCEEEEE--STTSHCHHHHHHHHHHHHHHHHHCHSTTCEEEEEESC
T ss_pred cCCCCEEEECcchhhhccCHHHHHHHHHHHHHHHHHHCCCCEEEEEECC
Confidence 5665455669999987553 3466777777 888777666654
No 25
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=95.62 E-value=0.0071 Score=74.39 Aligned_cols=51 Identities=24% Similarity=0.495 Sum_probs=38.3
Q ss_pred ccCCCcccccccCCCCceeecCcccccccccccccCccccccccCCcccccCCCCceeccccc
Q 003658 211 KDENYFAVCAICDDGGDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCV 273 (805)
Q Consensus 211 edd~~d~vC~IC~~gGeLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~ 273 (805)
.....+++|.+|.+.|+++||+ .|+|.+|..|..... | ..+...|.|.-|.
T Consensus 339 ~~~~~ddhcrf~~d~~~~lc~E-t~prvvhlEcv~hP~--~---------~~~s~~~e~evc~ 389 (1414)
T KOG1473|consen 339 GEIEYDDHCRFCHDLGDLLCCE-TCPRVVHLECVFHPR--F---------AVPSAFWECEVCN 389 (1414)
T ss_pred cceeecccccccCcccceeecc-cCCceEEeeecCCcc--c---------cCCCccchhhhhh
Confidence 3567799999999999999999 799999999864321 1 1135678887544
No 26
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=95.59 E-value=0.0055 Score=64.95 Aligned_cols=114 Identities=16% Similarity=0.256 Sum_probs=67.8
Q ss_pred ccCccc-chhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHHH-cCCcccccCCCC----CCCCCCCcccccc
Q 003658 677 SFGRHF-TKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQ-MGKSCSFRNYDL----IQPKNDFSFEKRD 750 (805)
Q Consensus 677 s~~rhf-t~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~-~~~~~~~~n~d~----~~~~~~~~f~~~~ 750 (805)
+||.|| +.+.-+..|++.+. +.+|+.|+|+.||...++..|-++..+ ++.+.+-.-++. +....++.|...|
T Consensus 6 ~~GQnfl~d~~~~~~iv~~~~--~~~~~~VLEIG~G~G~lt~~L~~~~~~v~~vEid~~~~~~l~~~~~~~~~v~ii~~D 83 (258)
T PRK14896 6 KLGQHFLIDDRVVDRIVEYAE--DTDGDPVLEIGPGKGALTDELAKRAKKVYAIELDPRLAEFLRDDEIAAGNVEIIEGD 83 (258)
T ss_pred cCCccccCCHHHHHHHHHhcC--CCCcCeEEEEeCccCHHHHHHHHhCCEEEEEECCHHHHHHHHHHhccCCCEEEEEec
Confidence 799999 67778899999875 678999999999999999988775110 011111000000 0001235555566
Q ss_pred ccccCCCCCCCCCceeeecCCCcchhhhhHHHHhhhhhccCCcEEEEecCC
Q 003658 751 WMTVRPEELPDGSQLIMGLNPPFGVKASLANKFISQALKFKPKLIVLIVPQ 801 (805)
Q Consensus 751 w~~~~~~~l~~g~~li~gl~ppfg~~~~~a~kf~~~~~~f~p~~~~li~p~ 801 (805)
.+.+....+ ..|+| ||||+....+ +.+.+.+...-.+|.+..
T Consensus 84 ~~~~~~~~~----d~Vv~-NlPy~i~s~~----~~~l~~~~~~~~~l~~q~ 125 (258)
T PRK14896 84 ALKVDLPEF----NKVVS-NLPYQISSPI----TFKLLKHGFEPAVLMYQK 125 (258)
T ss_pred cccCCchhc----eEEEE-cCCcccCcHH----HHHHHhhccceeEEEeeH
Confidence 655543222 47888 9999964444 444444443334444433
No 27
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=95.44 E-value=0.025 Score=59.67 Aligned_cols=114 Identities=20% Similarity=0.370 Sum_probs=74.4
Q ss_pred cccCccc-chhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHHHcCCcccccCCCC-----------CCCCCC
Q 003658 676 TSFGRHF-TKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQMGKSCSFRNYDL-----------IQPKND 743 (805)
Q Consensus 676 ~s~~rhf-t~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~~~~~~~~~n~d~-----------~~~~~~ 743 (805)
.+||-|| +...-+.+|++.+. +.+|+.|+|+.||...++..|-++.. .. --+|+ ++....
T Consensus 5 k~~gq~fl~d~~i~~~i~~~~~--~~~~~~VLEiG~G~G~lt~~L~~~~~----~v--~~iE~d~~~~~~l~~~~~~~~~ 76 (253)
T TIGR00755 5 KSLGQNFLIDESVIQKIVEAAN--VLEGDVVLEIGPGLGALTEPLLKRAK----KV--TAIEIDPRLAEILRKLLSLYER 76 (253)
T ss_pred CCCCCccCCCHHHHHHHHHhcC--CCCcCEEEEeCCCCCHHHHHHHHhCC----cE--EEEECCHHHHHHHHHHhCcCCc
Confidence 4789988 67778888888875 46899999999999999999977631 11 00111 111234
Q ss_pred CccccccccccCCCCCCCCCceeeecCCCcchhhhhHHHHhhhhhccCCcEEEEecCCC
Q 003658 744 FSFEKRDWMTVRPEELPDGSQLIMGLNPPFGVKASLANKFISQALKFKPKLIVLIVPQE 802 (805)
Q Consensus 744 ~~f~~~~w~~~~~~~l~~g~~li~gl~ppfg~~~~~a~kf~~~~~~f~p~~~~li~p~~ 802 (805)
+.+...|.+.+...++.. .-+|+| |+||..-..+..++++ ...+...+|++..|
T Consensus 77 v~v~~~D~~~~~~~~~d~-~~~vvs-NlPy~i~~~il~~ll~---~~~~~~~~~~~q~e 130 (253)
T TIGR00755 77 LEVIEGDALKVDLPDFPK-QLKVVS-NLPYNISSPLIFKLLE---KPKFRLAVLMVQKE 130 (253)
T ss_pred EEEEECchhcCChhHcCC-cceEEE-cCChhhHHHHHHHHhc---cCCCceEEEEehHH
Confidence 556666666655443321 247888 9999955444444443 56667788887766
No 28
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=95.16 E-value=0.0087 Score=68.59 Aligned_cols=57 Identities=21% Similarity=0.473 Sum_probs=39.9
Q ss_pred cccCCCcccccccCCCC-----ceeecCcccccccccccccCccccccccCCccccc-CCCCceeccccccc
Q 003658 210 DKDENYFAVCAICDDGG-----DVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQI-DAVPNFLCQNCVYQ 275 (805)
Q Consensus 210 ~edd~~d~vC~IC~~gG-----eLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev-~~~~~w~C~eC~~g 275 (805)
|.....+..|.||..|| .||.|++ |..+||..|..... +.+.. ++...|+|..|.++
T Consensus 162 D~~~~~n~qc~vC~~g~~~~~NrmlqC~~-C~~~fHq~Chqp~i--------~~~l~~D~~~~w~C~~C~~~ 224 (464)
T KOG4323|consen 162 DSGHKVNLQCSVCYCGGPGAGNRMLQCDK-CRQWYHQACHQPLI--------KDELAGDPFYEWFCDVCNRG 224 (464)
T ss_pred CccccccceeeeeecCCcCccceeeeecc-cccHHHHHhccCCC--------CHhhccCccceEeehhhccc
Confidence 44444455599998664 5999995 99999999865321 21211 24679999999875
No 29
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=95.15 E-value=0.016 Score=46.47 Aligned_cols=34 Identities=35% Similarity=0.774 Sum_probs=27.8
Q ss_pred ccccCcCCccccccccceeeccccccccccccCCCCcc
Q 003658 344 KCFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPTEIT 381 (805)
Q Consensus 344 ~C~~C~~~edk~~~~~qL~~C~RCPkAYH~kCLP~g~~ 381 (805)
+|.+|++.++ +..++.|..|..+||..|+.+...
T Consensus 1 ~C~vC~~~~~----~~~~i~C~~C~~~~H~~C~~~~~~ 34 (51)
T PF00628_consen 1 YCPVCGQSDD----DGDMIQCDSCNRWYHQECVGPPEK 34 (51)
T ss_dssp EBTTTTSSCT----TSSEEEBSTTSCEEETTTSTSSHS
T ss_pred eCcCCCCcCC----CCCeEEcCCCChhhCcccCCCChh
Confidence 4788988443 458999999999999999987654
No 30
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.06 E-value=0.013 Score=69.85 Aligned_cols=47 Identities=23% Similarity=0.605 Sum_probs=35.0
Q ss_pred cccccccCCCCc---eeecCcccccc-cccccccCccccccccCCcccccCCCCceecccccc
Q 003658 216 FAVCAICDDGGD---VTFCDGRCLRS-FHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVY 274 (805)
Q Consensus 216 d~vC~IC~~gGe---LL~CdG~C~Rs-FH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~ 274 (805)
..-|.||+.... ||.|++ |... ||..|+++ .+. ++ +.+.|||.+|..
T Consensus 215 ~~~C~IC~~~DpEdVLLLCDs-CN~~~YH~YCLDP--------dl~--ei-P~~eWYC~NC~d 265 (1134)
T KOG0825|consen 215 EVKCDICTVHDPEDVLLLCDS-CNKVYYHVYCLDP--------DLS--ES-PVNEWYCTNCSL 265 (1134)
T ss_pred cccceeeccCChHHhheeecc-cccceeeccccCc--------ccc--cc-cccceecCcchh
Confidence 455999998753 999995 9988 99997543 232 22 468999999973
No 31
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=94.75 E-value=0.017 Score=62.37 Aligned_cols=69 Identities=22% Similarity=0.490 Sum_probs=46.6
Q ss_pred CceeeccCCCcCCCCccchhcccCCCCchhHHHHHHHHhhcCCceecCC-cccccCcCCccccccccceeeccccccccc
Q 003658 294 QEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCPV-HKCFVCQQSEDMNVEDLQLAICRRCPKAYH 372 (805)
Q Consensus 294 ~eV~kCsv~~CGrfYHp~CL~~~~~p~~~~~~~eL~krV~~g~~F~CPl-H~C~~C~~~edk~~~~~qL~~C~RCPkAYH 372 (805)
..++.| +.|-..|||.|+.-.+ +|..-+ .--.|.|-- ..|..|.+... +..++-|++|.+.||
T Consensus 277 ~S~I~C--~~C~~~~HP~Ci~M~~---------elv~~~-KTY~W~C~~C~lC~IC~~P~~----E~E~~FCD~CDRG~H 340 (381)
T KOG1512|consen 277 NSWIVC--KPCATRPHPYCVAMIP---------ELVGQY-KTYFWKCSSCELCRICLGPVI----ESEHLFCDVCDRGPH 340 (381)
T ss_pred ccceee--cccccCCCCcchhcCH---------HHHhHH-hhcchhhcccHhhhccCCccc----chheeccccccCCCC
Confidence 357788 8999999999997443 121111 112355532 45777777553 347889999999999
Q ss_pred cccCCC
Q 003658 373 RKCLPT 378 (805)
Q Consensus 373 ~kCLP~ 378 (805)
+.|+-.
T Consensus 341 T~CVGL 346 (381)
T KOG1512|consen 341 TLCVGL 346 (381)
T ss_pred cccccc
Confidence 999743
No 32
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=94.32 E-value=0.093 Score=57.31 Aligned_cols=117 Identities=18% Similarity=0.343 Sum_probs=74.6
Q ss_pred cccccc-ccCccc-chhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHHHcCCcccccCCCCC----------
Q 003658 671 HGMRYT-SFGRHF-TKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQMGKSCSFRNYDLI---------- 738 (805)
Q Consensus 671 ~g~~y~-s~~rhf-t~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~~~~~~~~~n~d~~---------- 738 (805)
||+|.. ++|.|| +.+.-+..|++.+. +.+||+|+|+-||...+...+-++ +. ..--+|+-
T Consensus 6 ~~~~~kk~~GQnFL~d~~i~~~Iv~~~~--~~~~~~VLEIG~G~G~LT~~Ll~~----~~--~V~avEiD~~li~~l~~~ 77 (294)
T PTZ00338 6 SGMVFNKKFGQHILKNPLVLDKIVEKAA--IKPTDTVLEIGPGTGNLTEKLLQL----AK--KVIAIEIDPRMVAELKKR 77 (294)
T ss_pred CCcCcCCCCCccccCCHHHHHHHHHhcC--CCCcCEEEEecCchHHHHHHHHHh----CC--cEEEEECCHHHHHHHHHH
Confidence 455543 999999 68888999999874 579999999999999998777553 11 01111110
Q ss_pred ----CCCCCCccccccccccCCCCCCCCCceeeecCCCcchhhhhHHHHhhhhhccCCcEEEEecCCC
Q 003658 739 ----QPKNDFSFEKRDWMTVRPEELPDGSQLIMGLNPPFGVKASLANKFISQALKFKPKLIVLIVPQE 802 (805)
Q Consensus 739 ----~~~~~~~f~~~~w~~~~~~~l~~g~~li~gl~ppfg~~~~~a~kf~~~~~~f~p~~~~li~p~~ 802 (805)
.....+.+...|++.+...++ ..|++ ||||++-+.+--+.+.....| +-.+|++-.|
T Consensus 78 ~~~~~~~~~v~ii~~Dal~~~~~~~----d~Vva-NlPY~Istpil~~ll~~~~~~--~~~vlm~QkE 138 (294)
T PTZ00338 78 FQNSPLASKLEVIEGDALKTEFPYF----DVCVA-NVPYQISSPLVFKLLAHRPLF--RCAVLMFQKE 138 (294)
T ss_pred HHhcCCCCcEEEEECCHhhhccccc----CEEEe-cCCcccCcHHHHHHHhcCCCC--ceeeeeehHH
Confidence 012346666777776554332 36666 999997777766666543333 3455554433
No 33
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=94.27 E-value=0.0069 Score=68.29 Aligned_cols=86 Identities=21% Similarity=0.506 Sum_probs=55.5
Q ss_pred cCCCcccccccCCC--CceeecCcccccccccccccCccccc-cccCCccccc-CCCCceecccccc-cCcccccccccC
Q 003658 212 DENYFAVCAICDDG--GDVTFCDGRCLRSFHATITAGKNALC-QSLGYTQAQI-DAVPNFLCQNCVY-QEHQCFACGMLG 286 (805)
Q Consensus 212 dd~~d~vC~IC~~g--GeLL~CdG~C~RsFH~~Cl~g~~s~C-~sLglt~~ev-~~~~~w~C~eC~~-gqh~CfiCgklG 286 (805)
++.+. +|..|.++ |+-.-|. -=.+.||..|.+=.. | ..|.- ... .-.+.-+|..|-. -...|.+|++..
T Consensus 271 ~~~~~-iC~~C~K~V~g~~~ac~-Am~~~fHv~CFtC~~--C~r~L~G--q~FY~v~~k~~CE~cyq~tlekC~~Cg~~I 344 (468)
T KOG1701|consen 271 EDYFG-ICAFCHKTVSGQGLAVE-AMDQLFHVQCFTCRT--CRRQLAG--QSFYQVDGKPYCEGCYQDTLEKCNKCGEPI 344 (468)
T ss_pred hhhhh-hhhhcCCcccCcchHHH-HhhhhhcccceehHh--hhhhhcc--ccccccCCcccchHHHHHHHHHHhhhhhHH
Confidence 33334 99999986 7777786 467999999864110 2 01110 000 1246788999864 357899999864
Q ss_pred CCCCCCCCceeeccCCCcCCCCccchh
Q 003658 287 SSDKSSSQEVFPCVSATCGQFYHPECV 313 (805)
Q Consensus 287 ssd~~s~~eV~kCsv~~CGrfYHp~CL 313 (805)
. ..++ ..||+.||+.|.
T Consensus 345 ~------d~iL----rA~GkayHp~CF 361 (468)
T KOG1701|consen 345 M------DRIL----RALGKAYHPGCF 361 (468)
T ss_pred H------HHHH----HhcccccCCCce
Confidence 2 2444 479999999984
No 34
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=93.47 E-value=0.037 Score=66.24 Aligned_cols=33 Identities=33% Similarity=0.837 Sum_probs=27.7
Q ss_pred ccccCcCCccccccccceeeccccccc-cccccCCCCc
Q 003658 344 KCFVCQQSEDMNVEDLQLAICRRCPKA-YHRKCLPTEI 380 (805)
Q Consensus 344 ~C~~C~~~edk~~~~~qL~~C~RCPkA-YH~kCLP~g~ 380 (805)
.|..|..... +.-|+.|+-|..+ ||.+||+++.
T Consensus 217 ~C~IC~~~Dp----EdVLLLCDsCN~~~YH~YCLDPdl 250 (1134)
T KOG0825|consen 217 KCDICTVHDP----EDVLLLCDSCNKVYYHVYCLDPDL 250 (1134)
T ss_pred cceeeccCCh----HHhheeecccccceeeccccCccc
Confidence 5888887654 4479999999999 9999999965
No 35
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=92.71 E-value=0.056 Score=65.06 Aligned_cols=81 Identities=28% Similarity=0.728 Sum_probs=57.2
Q ss_pred ccccccccccccCccccccccCCcccccCCCCceeccccccc---------------CcccccccccCCCCCCCCCceee
Q 003658 234 RCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQ---------------EHQCFACGMLGSSDKSSSQEVFP 298 (805)
Q Consensus 234 ~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~g---------------qh~CfiCgklGssd~~s~~eV~k 298 (805)
.|.|.+|..|..+. +.. ++...|.|+.|... +..|.+|+. +++++.
T Consensus 1 ~~~r~~~~~~~~p~--------~~~---~~~~~~k~~~~e~~~~~~~~~~~~~~~~~~e~c~ic~~--------~g~~l~ 61 (696)
T KOG0383|consen 1 TCPRAYHRVCLDPK--------LKE---EPEMDPKCPGCESSSAQVEAKDDDWDDAEQEACRICAD--------GGELLW 61 (696)
T ss_pred CCCcccCcCCCCcc--------ccc---CCcCCccCcchhhcccccccccCCcchhhhhhhhhhcC--------CCcEEE
Confidence 38999999976531 221 23678999988732 357999985 457888
Q ss_pred ccCCCcCCCCccchhcccCCCCchhHHHHHHHHhhcCCceecCCcccccCcCC
Q 003658 299 CVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCPVHKCFVCQQS 351 (805)
Q Consensus 299 Csv~~CGrfYHp~CL~~~~~p~~~~~~~eL~krV~~g~~F~CPlH~C~~C~~~ 351 (805)
| ..|...||..|+...+.+ +..+. |.|| .| .|-..
T Consensus 62 c--~tC~~s~h~~cl~~pl~~------------~p~~~-~~c~--Rc-~~p~~ 96 (696)
T KOG0383|consen 62 C--DTCPASFHASCLGPPLTP------------QPNGE-FICP--RC-FCPKN 96 (696)
T ss_pred e--ccccHHHHHHccCCCCCc------------CCccc-eeee--ee-ccCCC
Confidence 9 999999999999755432 22345 9998 56 55554
No 36
>PF00398 RrnaAD: Ribosomal RNA adenine dimethylase; InterPro: IPR001737 This family of proteins include rRNA adenine dimethylases (e.g. KsgA) and the Erythromycin resistance methylases (Erm). The bacterial enzyme KsgA catalyses the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In Saccharomyces cerevisiae (Baker's yeast), and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding domain. The crystal structure of KsgA from Escherichia coli has been solved to a resolution of 2.1A. It bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to the yeast mitochondrial transcription factor, sc-mtTFB []. The Erm family of RNA methyltransferases, which methylate a single adenosine base in 23S rRNA confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. Other orthologs, of this family include the yeast and Homo sapiens (Human) mitochondrial transcription factors (MTF1 and h-mtTFB respectively), which are nuclear encoded []. Human-mtTFB is able to stimulate transcription in vitro independently of its S-adenosylmethionine binding and rRNA methyltransferase activity [].; GO: 0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity, 0008649 rRNA methyltransferase activity, 0000154 rRNA modification; PDB: 3FTF_A 3R9X_B 3FTE_A 3FTC_A 3FTD_A 3GRY_A 3FYC_A 3GRU_A 3FYD_A 3GRV_A ....
Probab=92.32 E-value=0.25 Score=52.56 Aligned_cols=115 Identities=23% Similarity=0.403 Sum_probs=74.4
Q ss_pred ccccCcccc-hhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHHHc---CCc-----------ccccCCCCCC
Q 003658 675 YTSFGRHFT-KVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQM---GKS-----------CSFRNYDLIQ 739 (805)
Q Consensus 675 y~s~~rhft-~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~~---~~~-----------~~~~n~d~~~ 739 (805)
..++|-||- .+.-+..|++.+... +|++|||+-.|...+++.+-++...+ ..+ -...|+.+|
T Consensus 5 kk~~gQnFL~~~~~~~~Iv~~~~~~--~~~~VlEiGpG~G~lT~~L~~~~~~v~~vE~d~~~~~~L~~~~~~~~~~~vi- 81 (262)
T PF00398_consen 5 KKSLGQNFLVDPNIADKIVDALDLS--EGDTVLEIGPGPGALTRELLKRGKRVIAVEIDPDLAKHLKERFASNPNVEVI- 81 (262)
T ss_dssp -CGCTSSEEEHHHHHHHHHHHHTCG--TTSEEEEESSTTSCCHHHHHHHSSEEEEEESSHHHHHHHHHHCTTCSSEEEE-
T ss_pred CCCCCcCeeCCHHHHHHHHHhcCCC--CCCEEEEeCCCCccchhhHhcccCcceeecCcHhHHHHHHHHhhhcccceee-
Confidence 358999997 556788899988655 99999999999999999987664111 000 023344444
Q ss_pred CCCCCccccccccccCCCC-CCCCCceeeecCCCcchhhhhHHHHhhhhhccCCcEEEEecCCC
Q 003658 740 PKNDFSFEKRDWMTVRPEE-LPDGSQLIMGLNPPFGVKASLANKFISQALKFKPKLIVLIVPQE 802 (805)
Q Consensus 740 ~~~~~~f~~~~w~~~~~~~-l~~g~~li~gl~ppfg~~~~~a~kf~~~~~~f~p~~~~li~p~~ 802 (805)
..|.++++..+ +....-+|+| |.||..-+.+-.++++ ...+...-.+|+++.|
T Consensus 82 --------~~D~l~~~~~~~~~~~~~~vv~-NlPy~is~~il~~ll~-~~~~g~~~~~l~vq~e 135 (262)
T PF00398_consen 82 --------NGDFLKWDLYDLLKNQPLLVVG-NLPYNISSPILRKLLE-LYRFGRVRMVLMVQKE 135 (262)
T ss_dssp --------ES-TTTSCGGGHCSSSEEEEEE-EETGTGHHHHHHHHHH-HGGGCEEEEEEEEEHH
T ss_pred --------ecchhccccHHhhcCCceEEEE-EecccchHHHHHHHhh-cccccccceEEEEehh
Confidence 45555555554 4556667888 9999866666666665 2223225566666654
No 37
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=91.78 E-value=0.18 Score=46.70 Aligned_cols=85 Identities=19% Similarity=0.395 Sum_probs=48.8
Q ss_pred cccccCCC-CceeecCcccccccccccccCccccccccCCcccccCCCCceecccccccCcccccccccCCCCCCCCCce
Q 003658 218 VCAICDDG-GDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQEHQCFACGMLGSSDKSSSQEV 296 (805)
Q Consensus 218 vC~IC~~g-GeLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~gqh~CfiCgklGssd~~s~~eV 296 (805)
.|.+|... |-|..-. -.++.|..|..-....-..-+.+..++. .... =++ .....|.+|++. .+-.
T Consensus 2 ~C~lC~~~~Galk~t~--~~~WvHv~Cal~~~~~~~~~~~~~~~v~-~~~i-~~~--~~~~~C~iC~~~-------~G~~ 68 (110)
T PF13832_consen 2 SCVLCPKRGGALKRTS--DGQWVHVLCALWIPEVIFNNGESMEPVD-ISNI-PPS--RFKLKCSICGKS-------GGAC 68 (110)
T ss_pred ccEeCCCCCCcccCcc--CCcEEEeEccceeCccEEeechhcCccc-ceee-cch--hcCCcCcCCCCC-------Ccee
Confidence 59999876 4455444 4899999985321100000000000010 0000 010 135679999864 3578
Q ss_pred eeccCCCcCCCCccchhcc
Q 003658 297 FPCVSATCGQFYHPECVSK 315 (805)
Q Consensus 297 ~kCsv~~CGrfYHp~CL~~ 315 (805)
++|....|.+.||+.|...
T Consensus 69 i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 69 IKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred EEcCCCCCCcCCCHHHHHH
Confidence 9999999999999999753
No 38
>PF13659 Methyltransf_26: Methyltransferase domain; PDB: 3GJY_A 3LPM_B 2NP6_D 1AQI_B 2ADM_B 2IH2_A 2JG3_A 2IBS_D 2NP7_A 2IBT_A ....
Probab=91.69 E-value=0.087 Score=47.84 Aligned_cols=86 Identities=28% Similarity=0.426 Sum_probs=52.7
Q ss_pred CCeEEeeccCcchhhHHHHHHH--HHcCCccc-------ccCCCCCCCCCCCccccccccccCCCCCCCCCc-eeeecCC
Q 003658 702 GDTIVDFCCGANDFSCMMKVKL--EQMGKSCS-------FRNYDLIQPKNDFSFEKRDWMTVRPEELPDGSQ-LIMGLNP 771 (805)
Q Consensus 702 ~d~~~d~~~g~~~~~~~~~~~~--~~~~~~~~-------~~n~d~~~~~~~~~f~~~~w~~~~~~~l~~g~~-li~gl~p 771 (805)
|+.|+|++||+..|...+-++. .-+|-+.+ -.|+....-.....|...|+.++. ..++.+.. +|++ ||
T Consensus 1 g~~vlD~~~G~G~~~~~~~~~~~~~~~gvdi~~~~~~~a~~~~~~~~~~~~~~~~~~D~~~~~-~~~~~~~~D~Iv~-np 78 (117)
T PF13659_consen 1 GDRVLDPGCGSGTFLLAALRRGAARVTGVDIDPEAVELARRNLPRNGLDDRVEVIVGDARDLP-EPLPDGKFDLIVT-NP 78 (117)
T ss_dssp TEEEEEETSTTCHHHHHHHHHCTCEEEEEESSHHHHHHHHHHCHHCTTTTTEEEEESHHHHHH-HTCTTT-EEEEEE---
T ss_pred CCEEEEcCcchHHHHHHHHHHCCCeEEEEEECHHHHHHHHHHHHHccCCceEEEEECchhhch-hhccCceeEEEEE-CC
Confidence 7899999999999999998874 00011100 122222222345788888988886 44555665 5555 99
Q ss_pred Ccchh-------hhhHHHHhhhhhc
Q 003658 772 PFGVK-------ASLANKFISQALK 789 (805)
Q Consensus 772 pfg~~-------~~~a~kf~~~~~~ 789 (805)
||+.. ..++..|+.++..
T Consensus 79 P~~~~~~~~~~~~~~~~~~~~~~~~ 103 (117)
T PF13659_consen 79 PYGPRSGDKAALRRLYSRFLEAAAR 103 (117)
T ss_dssp STTSBTT----GGCHHHHHHHHHHH
T ss_pred CCccccccchhhHHHHHHHHHHHHH
Confidence 99953 2356788877754
No 39
>TIGR00479 rumA 23S rRNA (uracil-5-)-methyltransferase RumA. This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA.
Probab=91.06 E-value=0.27 Score=55.80 Aligned_cols=112 Identities=21% Similarity=0.325 Sum_probs=62.7
Q ss_pred hhhhHHHHHHhhccee--ccCCeEEeeccCcchhhHHHHHHHHH-cCCccc-------ccCCCCCCCCCCCccccccccc
Q 003658 684 KVEKLKEIVDRLHWYV--RSGDTIVDFCCGANDFSCMMKVKLEQ-MGKSCS-------FRNYDLIQPKNDFSFEKRDWMT 753 (805)
Q Consensus 684 ~~ekl~~i~~~l~~~~--~~~d~~~d~~~g~~~~~~~~~~~~~~-~~~~~~-------~~n~d~~~~~~~~~f~~~~w~~ 753 (805)
+++-.+.+++++..++ .+|++|+|++||...|+-.|-+.... +|.+.+ -+|..... -++..|...|+..
T Consensus 273 N~~~~~~l~~~~~~~l~~~~~~~vLDl~cG~G~~sl~la~~~~~V~~vE~~~~av~~a~~n~~~~~-~~nv~~~~~d~~~ 351 (431)
T TIGR00479 273 NSGQNEKLVDRALEALELQGEELVVDAYCGVGTFTLPLAKQAKSVVGIEVVPESVEKAQQNAELNG-IANVEFLAGTLET 351 (431)
T ss_pred CHHHHHHHHHHHHHHhccCCCCEEEEcCCCcCHHHHHHHHhCCEEEEEEcCHHHHHHHHHHHHHhC-CCceEEEeCCHHH
Confidence 4566666677666655 46789999999999999888654210 111100 01111110 1235566667654
Q ss_pred cCCCC-CCCCCceeeecCCCcchhhhhHHHHhhhhhccCCcEEEEec
Q 003658 754 VRPEE-LPDGSQLIMGLNPPFGVKASLANKFISQALKFKPKLIVLIV 799 (805)
Q Consensus 754 ~~~~~-l~~g~~li~gl~ppfg~~~~~a~kf~~~~~~f~p~~~~li~ 799 (805)
.-++. +..++-=++-+|||. +-++..+++.....+|+-||.|.
T Consensus 352 ~l~~~~~~~~~~D~vi~dPPr---~G~~~~~l~~l~~l~~~~ivyvs 395 (431)
T TIGR00479 352 VLPKQPWAGQIPDVLLLDPPR---KGCAAEVLRTIIELKPERIVYVS 395 (431)
T ss_pred HHHHHHhcCCCCCEEEECcCC---CCCCHHHHHHHHhcCCCEEEEEc
Confidence 32211 112222233468984 23667777777778888777664
No 40
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=91.03 E-value=0.12 Score=47.84 Aligned_cols=105 Identities=21% Similarity=0.393 Sum_probs=58.4
Q ss_pred ccccccccCCCCCCCCCceeeccCCCcCCCCccchhcccCCCCchhHHHHHH-HHhhcCCceecCCcccccCcCCccccc
Q 003658 278 QCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELR-ERIAAGESFTCPVHKCFVCQQSEDMNV 356 (805)
Q Consensus 278 ~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~~p~~~~~~~eL~-krV~~g~~F~CPlH~C~~C~~~edk~~ 356 (805)
.|.+|...| ..++- ..-+.+.|.-|....+.....+.. .++ ..+..-..-+ -...|..|+...
T Consensus 2 ~C~lC~~~~--------Galk~--t~~~~WvHv~Cal~~~~~~~~~~~-~~~~v~~~~i~~~~-~~~~C~iC~~~~---- 65 (110)
T PF13832_consen 2 SCVLCPKRG--------GALKR--TSDGQWVHVLCALWIPEVIFNNGE-SMEPVDISNIPPSR-FKLKCSICGKSG---- 65 (110)
T ss_pred ccEeCCCCC--------CcccC--ccCCcEEEeEccceeCccEEeech-hcCcccceeecchh-cCCcCcCCCCCC----
Confidence 588998654 23333 235899999998754432221110 000 0000000000 135789999853
Q ss_pred cccceeeccc--cccccccccCCC-CcccccccchhhhhhhhccCCCCceeEEcCCC
Q 003658 357 EDLQLAICRR--CPKAYHRKCLPT-EITFSDADENNFQRAWVDLLPNNRILIYCLEH 410 (805)
Q Consensus 357 ~~~qL~~C~R--CPkAYH~kCLP~-g~~f~~~~~e~~~raW~~ll~~~riLI~C~kH 410 (805)
+..++|.. |..+||..|.-. |..+.... .+ .+....+||.+|
T Consensus 66 --G~~i~C~~~~C~~~fH~~CA~~~g~~~~~~~-~~---------~~~~~~~~C~~H 110 (110)
T PF13832_consen 66 --GACIKCSHPGCSTAFHPTCARKAGLYFEIEN-EE---------DNVQFIAYCPKH 110 (110)
T ss_pred --ceeEEcCCCCCCcCCCHHHHHHCCCeEEeee-cC---------CCceEEEECCCC
Confidence 46899999 999999999743 33332111 00 023678999988
No 41
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=90.95 E-value=0.067 Score=61.53 Aligned_cols=86 Identities=20% Similarity=0.511 Sum_probs=55.7
Q ss_pred cccccCC-----CCceeecCcccccccccccccCccccccccCCcccccCCCCceecccccccC--cccccccccCCCCC
Q 003658 218 VCAICDD-----GGDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQE--HQCFACGMLGSSDK 290 (805)
Q Consensus 218 vC~IC~~-----gGeLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~gq--h~CfiCgklGssd~ 290 (805)
+|.+|-+ .|++|.|| .|.-..|-.|---.+|. ++.-+... -..+.|+|.-|.+|. .-|-.|-..
T Consensus 121 iCcVClg~rs~da~ei~qCd-~CGi~VHEgCYGv~dn~--si~s~~s~-~stepWfCeaC~~Gvs~P~CElCPn~----- 191 (707)
T KOG0957|consen 121 ICCVCLGQRSVDAGEILQCD-KCGINVHEGCYGVLDNV--SIPSGSSD-CSTEPWFCEACLYGVSLPHCELCPNR----- 191 (707)
T ss_pred EEEEeecCccccccceeecc-ccCceeccccccccccc--ccCCCCcc-CCCCchhhhhHhcCCCCCccccCCCc-----
Confidence 8999954 58899999 69999999973211111 11111110 024689999999985 468888432
Q ss_pred CCCCceeeccCCCcCCCCccchhcccC
Q 003658 291 SSSQEVFPCVSATCGQFYHPECVSKLL 317 (805)
Q Consensus 291 ~s~~eV~kCsv~~CGrfYHp~CL~~~~ 317 (805)
..+|+= ..=||+-|.-|.-+-+
T Consensus 192 ---~GifKe--tDigrWvH~iCALYvp 213 (707)
T KOG0957|consen 192 ---FGIFKE--TDIGRWVHAICALYVP 213 (707)
T ss_pred ---CCcccc--cchhhHHHHHHHhhcC
Confidence 344443 4567888998876544
No 42
>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=90.30 E-value=0.58 Score=48.72 Aligned_cols=107 Identities=22% Similarity=0.366 Sum_probs=62.1
Q ss_pred HHhhccccccccccccccccccCcccchhhhHHHHHHhhccee-----ccCCeEEeeccCcchhhHH-------------
Q 003658 657 QWKRKLDVYLAPFLHGMRYTSFGRHFTKVEKLKEIVDRLHWYV-----RSGDTIVDFCCGANDFSCM------------- 718 (805)
Q Consensus 657 ~~~~~l~~~l~p~~~g~~y~s~~rhft~~ekl~~i~~~l~~~~-----~~~d~~~d~~~g~~~~~~~------------- 718 (805)
+--.||+.+..|=+.=.-|+..+ + ++..+.|.+ ..|-+|+|++||..-|+.-
T Consensus 6 ~~l~kl~~f~~p~~~LEQY~Tp~------~----~Aa~il~~a~~~g~l~g~~V~DlG~GTG~La~ga~~lGa~~V~~vd 75 (198)
T COG2263 6 ILLEKLKGFPNPKLGLEQYRTPA------P----LAAYILWVAYLRGDLEGKTVLDLGAGTGILAIGAALLGASRVLAVD 75 (198)
T ss_pred hhhhhhcCCCCCCccceecCCCh------H----HHHHHHHHHHHcCCcCCCEEEEcCCCcCHHHHHHHhcCCcEEEEEe
Confidence 33456666667766666666443 3 444444444 4666799999999888642
Q ss_pred --------HHHHHHHcCCcccccCCCCCCCCCCCccccccccccCCCCCCCCC-ceeeecCCCcchhhhhH-HHHhhhhh
Q 003658 719 --------MKVKLEQMGKSCSFRNYDLIQPKNDFSFEKRDWMTVRPEELPDGS-QLIMGLNPPFGVKASLA-NKFISQAL 788 (805)
Q Consensus 719 --------~~~~~~~~~~~~~~~n~d~~~~~~~~~f~~~~w~~~~~~~l~~g~-~li~gl~ppfg~~~~~a-~kf~~~~~ 788 (805)
.+++..+.++.-.|-.=|+.... ..- -.|| |||||.+.-=| ..|+++||
T Consensus 76 iD~~a~ei~r~N~~~l~g~v~f~~~dv~~~~-------------------~~~dtvim--NPPFG~~~rhaDr~Fl~~Al 134 (198)
T COG2263 76 IDPEALEIARANAEELLGDVEFVVADVSDFR-------------------GKFDTVIM--NPPFGSQRRHADRPFLLKAL 134 (198)
T ss_pred cCHHHHHHHHHHHHhhCCceEEEEcchhhcC-------------------CccceEEE--CCCCccccccCCHHHHHHHH
Confidence 33343333333333333333211 111 2333 99999886555 46999999
Q ss_pred ccCCcEE
Q 003658 789 KFKPKLI 795 (805)
Q Consensus 789 ~f~p~~~ 795 (805)
+-. +++
T Consensus 135 e~s-~vV 140 (198)
T COG2263 135 EIS-DVV 140 (198)
T ss_pred Hhh-heE
Confidence 876 443
No 43
>smart00650 rADc Ribosomal RNA adenine dimethylases.
Probab=88.06 E-value=1.4 Score=43.44 Aligned_cols=93 Identities=15% Similarity=0.251 Sum_probs=51.9
Q ss_pred HHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHH-HcCCcccccCCCC----CCCCCCCccccccccccCCCCCCCCC
Q 003658 689 KEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLE-QMGKSCSFRNYDL----IQPKNDFSFEKRDWMTVRPEELPDGS 763 (805)
Q Consensus 689 ~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~-~~~~~~~~~n~d~----~~~~~~~~f~~~~w~~~~~~~l~~g~ 763 (805)
..|++.+.+ .+|+.|+|+.||...+...+-++.. -++-+-+-.-.+. +...+.+.+...|.+.....+. .-
T Consensus 3 ~~i~~~~~~--~~~~~vLEiG~G~G~lt~~l~~~~~~v~~vE~~~~~~~~~~~~~~~~~~v~ii~~D~~~~~~~~~--~~ 78 (169)
T smart00650 3 DKIVRAANL--RPGDTVLEIGPGKGALTEELLERAARVTAIEIDPRLAPRLREKFAAADNLTVIHGDALKFDLPKL--QP 78 (169)
T ss_pred HHHHHhcCC--CCcCEEEEECCCccHHHHHHHhcCCeEEEEECCHHHHHHHHHHhccCCCEEEEECchhcCCcccc--CC
Confidence 456666653 6889999999999999998866510 0111111000000 0111245566667766643321 12
Q ss_pred ceeeecCCCcchhhhhHHHHhhh
Q 003658 764 QLIMGLNPPFGVKASLANKFISQ 786 (805)
Q Consensus 764 ~li~gl~ppfg~~~~~a~kf~~~ 786 (805)
..|+| ||||.....+-.+++..
T Consensus 79 d~vi~-n~Py~~~~~~i~~~l~~ 100 (169)
T smart00650 79 YKVVG-NLPYNISTPILFKLLEE 100 (169)
T ss_pred CEEEE-CCCcccHHHHHHHHHhc
Confidence 47777 99998655554555443
No 44
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=86.95 E-value=0.32 Score=56.26 Aligned_cols=55 Identities=18% Similarity=0.311 Sum_probs=39.6
Q ss_pred cccCcCCccccccccceeeccccccccccccCCCCcccccccchhhhhhhhccCCCCceeEEcCCCcccc
Q 003658 345 CFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPTEITFSDADENNFQRAWVDLLPNNRILIYCLEHKIIS 414 (805)
Q Consensus 345 C~~C~~~edk~~~~~qL~~C~RCPkAYH~kCLP~g~~f~~~~~e~~~raW~~ll~~~riLI~C~kH~i~~ 414 (805)
|.+|..+... ... +|+.|.+|-.+||..|..+.+.-+. ..+....|+|..|--..
T Consensus 171 c~vC~~g~~~-~~N-rmlqC~~C~~~fHq~Chqp~i~~~l-------------~~D~~~~w~C~~C~~~~ 225 (464)
T KOG4323|consen 171 CSVCYCGGPG-AGN-RMLQCDKCRQWYHQACHQPLIKDEL-------------AGDPFYEWFCDVCNRGP 225 (464)
T ss_pred eeeeecCCcC-ccc-eeeeecccccHHHHHhccCCCCHhh-------------ccCccceEeehhhccch
Confidence 8888876643 122 8999999999999999988775221 22335678999888443
No 45
>PHA03411 putative methyltransferase; Provisional
Probab=86.19 E-value=0.33 Score=53.05 Aligned_cols=47 Identities=19% Similarity=0.273 Sum_probs=33.7
Q ss_pred cccccccCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 672 GMRYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 672 g~~y~s~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
|+--+-.|-+||+..-+..++ .....+.+|+|++||+..|+..+-++
T Consensus 39 g~~~~~~G~FfTP~~i~~~f~----~~~~~~grVLDLGcGsGilsl~la~r 85 (279)
T PHA03411 39 GDGLGGSGAFFTPEGLAWDFT----IDAHCTGKVLDLCAGIGRLSFCMLHR 85 (279)
T ss_pred cccccCceeEcCCHHHHHHHH----hccccCCeEEEcCCCCCHHHHHHHHh
Confidence 442333599999988765543 23346789999999999998877554
No 46
>TIGR01177 conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea.
Probab=85.32 E-value=3 Score=45.91 Aligned_cols=29 Identities=28% Similarity=0.550 Sum_probs=21.4
Q ss_pred HHHHHhhcceeccCCeEEeeccCcchhhHHH
Q 003658 689 KEIVDRLHWYVRSGDTIVDFCCGANDFSCMM 719 (805)
Q Consensus 689 ~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~ 719 (805)
..++.... +++|+.|+|++||+..|...+
T Consensus 172 ~~~~~l~~--~~~g~~vLDp~cGtG~~liea 200 (329)
T TIGR01177 172 RAMVNLAR--VTEGDRVLDPFCGTGGFLIEA 200 (329)
T ss_pred HHHHHHhC--CCCcCEEEECCCCCCHHHHHH
Confidence 34444444 489999999999999986543
No 47
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=85.02 E-value=0.42 Score=55.32 Aligned_cols=50 Identities=24% Similarity=0.486 Sum_probs=37.6
Q ss_pred CcccccccCCCCc---eeecCcccccccccccccCccccccccCCcccccCC-CCceeccccc
Q 003658 215 YFAVCAICDDGGD---VTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDA-VPNFLCQNCV 273 (805)
Q Consensus 215 ~d~vC~IC~~gGe---LL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~-~~~w~C~eC~ 273 (805)
....|.||....+ |+.|| .|.-.||+-|+. ..||..+-.. ...|.|.+|-
T Consensus 543 ~~ysCgiCkks~dQHll~~CD-tC~lhYHlGCL~--------PPLTR~Pkk~kn~gWqCsECd 596 (707)
T KOG0957|consen 543 MNYSCGICKKSTDQHLLTQCD-TCHLHYHLGCLS--------PPLTRLPKKNKNFGWQCSECD 596 (707)
T ss_pred cceeeeeeccchhhHHHhhcc-hhhceeeccccC--------CccccCcccccCcceeecccc
Confidence 3556999998765 89999 799999999754 4566655433 4679888874
No 48
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=84.14 E-value=1.7 Score=49.93 Aligned_cols=107 Identities=20% Similarity=0.273 Sum_probs=58.2
Q ss_pred HHHHHHhhcce--eccCCeEEeeccCcchhhHHHHHHHHH-cCCccc-------ccCCCCCCCCCCCccccccccccCCC
Q 003658 688 LKEIVDRLHWY--VRSGDTIVDFCCGANDFSCMMKVKLEQ-MGKSCS-------FRNYDLIQPKNDFSFEKRDWMTVRPE 757 (805)
Q Consensus 688 l~~i~~~l~~~--~~~~d~~~d~~~g~~~~~~~~~~~~~~-~~~~~~-------~~n~d~~~~~~~~~f~~~~w~~~~~~ 757 (805)
.+.+++.+.-+ +.+|+.|+|++||+..|+..|-++... +|-+.+ -+|.....- ++..|...||...-++
T Consensus 282 ~e~l~~~vl~~l~~~~~~~VLDlgcGtG~~sl~la~~~~~V~gvD~s~~al~~A~~n~~~~~~-~~v~~~~~d~~~~l~~ 360 (443)
T PRK13168 282 NQKMVARALEWLDPQPGDRVLDLFCGLGNFTLPLARQAAEVVGVEGVEAMVERARENARRNGL-DNVTFYHANLEEDFTD 360 (443)
T ss_pred HHHHHHHHHHHhcCCCCCEEEEEeccCCHHHHHHHHhCCEEEEEeCCHHHHHHHHHHHHHcCC-CceEEEEeChHHhhhh
Confidence 33444443333 358899999999999999888665210 011111 012111111 2367888888654321
Q ss_pred -CCCCCCceeeecCCCcchhhhhHHHHhhhhhccCCcEEEEec
Q 003658 758 -ELPDGSQLIMGLNPPFGVKASLANKFISQALKFKPKLIVLIV 799 (805)
Q Consensus 758 -~l~~g~~li~gl~ppfg~~~~~a~kf~~~~~~f~p~~~~li~ 799 (805)
.++.++.=++-+|||..- +.+.+......+|+-||.|.
T Consensus 361 ~~~~~~~fD~Vi~dPPr~g----~~~~~~~l~~~~~~~ivyvS 399 (443)
T PRK13168 361 QPWALGGFDKVLLDPPRAG----AAEVMQALAKLGPKRIVYVS 399 (443)
T ss_pred hhhhcCCCCEEEECcCCcC----hHHHHHHHHhcCCCeEEEEE
Confidence 122333223346999863 23455666667888877664
No 49
>COG2265 TrmA SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=82.74 E-value=1.3 Score=51.13 Aligned_cols=117 Identities=20% Similarity=0.431 Sum_probs=72.4
Q ss_pred cccccccCcccchhh--hHHHHHHhhcceec--cCCeEEeeccCcchhhHHHHHHH-------------HHcCCcccccC
Q 003658 672 GMRYTSFGRHFTKVE--KLKEIVDRLHWYVR--SGDTIVDFCCGANDFSCMMKVKL-------------EQMGKSCSFRN 734 (805)
Q Consensus 672 g~~y~s~~rhft~~e--kl~~i~~~l~~~~~--~~d~~~d~~~g~~~~~~~~~~~~-------------~~~~~~~~~~n 734 (805)
|..|.=+.|.|+.+- -.+.+++...-+++ .+|+++|++||..+|+--+-++- ++......-++
T Consensus 260 ~~~~~~~~~sF~Q~N~~~~ekl~~~a~~~~~~~~~~~vlDlYCGvG~f~l~lA~~~~~V~gvEi~~~aV~~A~~NA~~n~ 339 (432)
T COG2265 260 GVSFQISPRSFFQVNPAVAEKLYETALEWLELAGGERVLDLYCGVGTFGLPLAKRVKKVHGVEISPEAVEAAQENAAANG 339 (432)
T ss_pred ceEEEeCCCCceecCHHHHHHHHHHHHHHHhhcCCCEEEEeccCCChhhhhhcccCCEEEEEecCHHHHHHHHHHHHHcC
Confidence 566777788998764 44444454444444 56889999999999998776332 22222222222
Q ss_pred C--CCCCCCCCCccccccccccCCCCCCCCCceeeecCCCcchhhhhHHHHhhhhhccCCcEEEEec
Q 003658 735 Y--DLIQPKNDFSFEKRDWMTVRPEELPDGSQLIMGLNPPFGVKASLANKFISQALKFKPKLIVLIV 799 (805)
Q Consensus 735 ~--d~~~~~~~~~f~~~~w~~~~~~~l~~g~~li~gl~ppfg~~~~~a~kf~~~~~~f~p~~~~li~ 799 (805)
- --+..-..+.|-..-|....|+ .|+ |||| ++-+...|++..++++|+-||-|.
T Consensus 340 i~N~~f~~~~ae~~~~~~~~~~~~d-------~Vv-vDPP---R~G~~~~~lk~l~~~~p~~IvYVS 395 (432)
T COG2265 340 IDNVEFIAGDAEEFTPAWWEGYKPD-------VVV-VDPP---RAGADREVLKQLAKLKPKRIVYVS 395 (432)
T ss_pred CCcEEEEeCCHHHHhhhccccCCCC-------EEE-ECCC---CCCCCHHHHHHHHhcCCCcEEEEe
Confidence 2 2334444455544445333333 444 4776 344888999999999999888775
No 50
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=82.46 E-value=0.55 Score=56.21 Aligned_cols=58 Identities=26% Similarity=0.634 Sum_probs=36.7
Q ss_pred cCCCcccccccCCCC--------ceeec-CcccccccccccccCccccccccCCcccccCCCCceecccccc
Q 003658 212 DENYFAVCAICDDGG--------DVTFC-DGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVY 274 (805)
Q Consensus 212 dd~~d~vC~IC~~gG--------eLL~C-dG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~ 274 (805)
.|.+...|+||+..| .-..| .-.|.++||.+|.....-+|..-|.-. ..--||-.|.|
T Consensus 113 ~dRfnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~-----dNVKYCGYCk~ 179 (900)
T KOG0956|consen 113 HDRFNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNIS-----DNVKYCGYCKY 179 (900)
T ss_pred hhhhcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceecccccc-----ccceechhHHH
Confidence 456788899998764 34455 446999999999765444453222211 22357877775
No 51
>TIGR03534 RF_mod_PrmC protein-(glutamine-N5) methyltransferase, release factor-specific. Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in prep.) shows the motif [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers specificity for the release factors rather than for ribosomal protein L3.
Probab=82.37 E-value=3 Score=42.98 Aligned_cols=96 Identities=18% Similarity=0.343 Sum_probs=51.7
Q ss_pred cccccccCcccchhhhHHHHHHhhcce-eccCCeEEeeccCcchhhHHHHHHHHHcCCcccccCCCCCC-----------
Q 003658 672 GMRYTSFGRHFTKVEKLKEIVDRLHWY-VRSGDTIVDFCCGANDFSCMMKVKLEQMGKSCSFRNYDLIQ----------- 739 (805)
Q Consensus 672 g~~y~s~~rhft~~ekl~~i~~~l~~~-~~~~d~~~d~~~g~~~~~~~~~~~~~~~~~~~~~~n~d~~~----------- 739 (805)
|.+|.-.+..|++..-..++++.+.-. -..+..|+|++||+..|...+.+... .+.+--.|+.+
T Consensus 57 ~~~~~~~~~~~~p~~~~~~l~~~~l~~~~~~~~~ilDig~G~G~~~~~l~~~~~----~~~v~~iD~~~~~~~~a~~~~~ 132 (251)
T TIGR03534 57 GLDFKVSPGVLIPRPDTEELVEAALERLKKGPLRVLDLGTGSGAIALALAKERP----DARVTAVDISPEALAVARKNAA 132 (251)
T ss_pred ceEEEECCCcccCCCChHHHHHHHHHhcccCCCeEEEEeCcHhHHHHHHHHHCC----CCEEEEEECCHHHHHHHHHHHH
Confidence 344443444555444344444443222 24456899999999999888876531 11222222211
Q ss_pred --CCCCCccccccccccCCCCCCCCC-ceeeecCCCcchh
Q 003658 740 --PKNDFSFEKRDWMTVRPEELPDGS-QLIMGLNPPFGVK 776 (805)
Q Consensus 740 --~~~~~~f~~~~w~~~~~~~l~~g~-~li~gl~ppfg~~ 776 (805)
.-++..|...|+.+. ++.++ .+|+. ||||...
T Consensus 133 ~~~~~~~~~~~~d~~~~----~~~~~fD~Vi~-npPy~~~ 167 (251)
T TIGR03534 133 RLGLDNVTFLQSDWFEP----LPGGKFDLIVS-NPPYIPE 167 (251)
T ss_pred HcCCCeEEEEECchhcc----CcCCceeEEEE-CCCCCch
Confidence 011366777777652 23343 46665 9999853
No 52
>TIGR02085 meth_trns_rumB 23S rRNA (uracil-5-)-methyltransferase RumB. This family consists of RNA methyltransferases designated RumB, formerly YbjF. Members act on 23S rRNA U747 and the equivalent position in other proteobacterial species. This family is homologous to the other 23S rRNA methyltransferase RumA and to the tRNA methyltransferase TrmA.
Probab=82.30 E-value=0.71 Score=51.90 Aligned_cols=110 Identities=15% Similarity=0.224 Sum_probs=59.6
Q ss_pred chhhhHHHHHHhhccee--ccCCeEEeeccCcchhhHHHHHHHHH-cCCcccc-------cCCCCCCCCCCCcccccccc
Q 003658 683 TKVEKLKEIVDRLHWYV--RSGDTIVDFCCGANDFSCMMKVKLEQ-MGKSCSF-------RNYDLIQPKNDFSFEKRDWM 752 (805)
Q Consensus 683 t~~ekl~~i~~~l~~~~--~~~d~~~d~~~g~~~~~~~~~~~~~~-~~~~~~~-------~n~d~~~~~~~~~f~~~~w~ 752 (805)
|..+-.+.+++.+.-++ .+|.+|+|++||+..|+-.+-.+... +|.+.+- .|.....- ++..|...|..
T Consensus 213 ~n~~~~~~l~~~~~~~l~~~~~~~vLDL~cG~G~~~l~la~~~~~v~~vE~~~~av~~a~~N~~~~~~-~~~~~~~~d~~ 291 (374)
T TIGR02085 213 TNPKVAAQLYATARQWVREIPVTQMWDLFCGVGGFGLHCAGPDTQLTGIEIESEAIACAQQSAQMLGL-DNLSFAALDSA 291 (374)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCCEEEEccCCccHHHHHHhhcCCeEEEEECCHHHHHHHHHHHHHcCC-CcEEEEECCHH
Confidence 33343344444433333 35789999999999999877643211 1111111 11111110 13455555543
Q ss_pred ccCCCCCCCCCceeeecCCCcchhhhhHHHHhhhhhccCCcEEEEe
Q 003658 753 TVRPEELPDGSQLIMGLNPPFGVKASLANKFISQALKFKPKLIVLI 798 (805)
Q Consensus 753 ~~~~~~l~~g~~li~gl~ppfg~~~~~a~kf~~~~~~f~p~~~~li 798 (805)
..-+. + .+..=++-+|||. +-+..++++..++++|+-||.|
T Consensus 292 ~~~~~-~-~~~~D~vi~DPPr---~G~~~~~l~~l~~~~p~~ivyv 332 (374)
T TIGR02085 292 KFATA-Q-MSAPELVLVNPPR---RGIGKELCDYLSQMAPKFILYS 332 (374)
T ss_pred HHHHh-c-CCCCCEEEECCCC---CCCcHHHHHHHHhcCCCeEEEE
Confidence 32221 1 1222345569996 3577899999999999776665
No 53
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=81.78 E-value=0.74 Score=41.02 Aligned_cols=33 Identities=30% Similarity=0.595 Sum_probs=27.6
Q ss_pred CCCcccccccCCC-Cceeec-Cccccccccccccc
Q 003658 213 ENYFAVCAICDDG-GDVTFC-DGRCLRSFHATITA 245 (805)
Q Consensus 213 d~~d~vC~IC~~g-GeLL~C-dG~C~RsFH~~Cl~ 245 (805)
......|.+|... |-.|.| .+.|.++||+.|..
T Consensus 33 ~~~~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~ 67 (90)
T PF13771_consen 33 RRRKLKCSICKKKGGACIGCSHPGCSRSFHVPCAR 67 (90)
T ss_pred HHhCCCCcCCCCCCCeEEEEeCCCCCcEEChHHHc
Confidence 4557899999999 998888 44699999999854
No 54
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=80.81 E-value=1 Score=48.86 Aligned_cols=28 Identities=25% Similarity=0.603 Sum_probs=23.5
Q ss_pred CCCceeeccCCCcC-CCCccchhcccCCC
Q 003658 292 SSQEVFPCVSATCG-QFYHPECVSKLLHP 319 (805)
Q Consensus 292 s~~eV~kCsv~~CG-rfYHp~CL~~~~~p 319 (805)
+.++++.|-..+|. ..||..||+--..|
T Consensus 228 syg~Mi~CDn~~C~~eWFH~~CVGL~~~P 256 (274)
T KOG1973|consen 228 SYGKMIGCDNPGCPIEWFHFTCVGLKTKP 256 (274)
T ss_pred ccccccccCCCCCCcceEEEeccccccCC
Confidence 35799999989999 99999999866444
No 55
>PF05175 MTS: Methyltransferase small domain; InterPro: IPR007848 This domain is found in ribosomal RNA small subunit methyltransferase C and in other methyltransferases.; GO: 0008168 methyltransferase activity; PDB: 1WY7_A 1DUS_A 2OZV_A 2PJD_A 1VQ1_A 1NV9_A 1SG9_C 1NV8_A 3Q87_B 3DMF_A ....
Probab=79.95 E-value=0.67 Score=46.04 Aligned_cols=91 Identities=29% Similarity=0.450 Sum_probs=52.0
Q ss_pred HHHhhcceeccCCeEEeeccCcchhhHHHHHHHHHcC----------CcccccCCCCCCCCCCCccccccccccCCCCCC
Q 003658 691 IVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQMG----------KSCSFRNYDLIQPKNDFSFEKRDWMTVRPEELP 760 (805)
Q Consensus 691 i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~~~----------~~~~~~n~d~~~~~~~~~f~~~~w~~~~~~~l~ 760 (805)
+++.+... .+..|+|++||+.-.+-.+.++..... ..+.-+|.....-.+ ..+...||.. .++
T Consensus 23 L~~~l~~~--~~~~vLDlG~G~G~i~~~la~~~~~~~v~~vDi~~~a~~~a~~n~~~n~~~~-v~~~~~d~~~----~~~ 95 (170)
T PF05175_consen 23 LLDNLPKH--KGGRVLDLGCGSGVISLALAKRGPDAKVTAVDINPDALELAKRNAERNGLEN-VEVVQSDLFE----ALP 95 (170)
T ss_dssp HHHHHHHH--TTCEEEEETSTTSHHHHHHHHTSTCEEEEEEESBHHHHHHHHHHHHHTTCTT-EEEEESSTTT----TCC
T ss_pred HHHHHhhc--cCCeEEEecCChHHHHHHHHHhCCCCEEEEEcCCHHHHHHHHHHHHhcCccc-cccccccccc----ccc
Confidence 33444444 788999999999999988877633200 012223333333333 6666777764 333
Q ss_pred CCC-ceeeecCCCcchhhh----hHHHHhhhhhc
Q 003658 761 DGS-QLIMGLNPPFGVKAS----LANKFISQALK 789 (805)
Q Consensus 761 ~g~-~li~gl~ppfg~~~~----~a~kf~~~~~~ 789 (805)
.+. -+|+. ||||..... +..+|+..|..
T Consensus 96 ~~~fD~Iv~-NPP~~~~~~~~~~~~~~~i~~a~~ 128 (170)
T PF05175_consen 96 DGKFDLIVS-NPPFHAGGDDGLDLLRDFIEQARR 128 (170)
T ss_dssp TTCEEEEEE----SBTTSHCHHHHHHHHHHHHHH
T ss_pred ccceeEEEE-ccchhcccccchhhHHHHHHHHHH
Confidence 333 35555 999965544 77888887754
No 56
>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed
Probab=79.42 E-value=2.6 Score=46.18 Aligned_cols=93 Identities=15% Similarity=0.229 Sum_probs=48.5
Q ss_pred cCCeEEeeccCcchhhHHHHHHHHH-cCCcccc-------cCCCCCCCCCCCccccccccccCCCCCCCCCceeeecCCC
Q 003658 701 SGDTIVDFCCGANDFSCMMKVKLEQ-MGKSCSF-------RNYDLIQPKNDFSFEKRDWMTVRPEELPDGSQLIMGLNPP 772 (805)
Q Consensus 701 ~~d~~~d~~~g~~~~~~~~~~~~~~-~~~~~~~-------~n~d~~~~~~~~~f~~~~w~~~~~~~l~~g~~li~gl~pp 772 (805)
+|+.|+|++||...|+..+-++... +|.+.+- +|.....- ++..|...|..+..+. ..+..=++-+|||
T Consensus 173 ~~~~VLDl~cG~G~~sl~la~~~~~V~gvD~s~~av~~A~~n~~~~~l-~~v~~~~~D~~~~~~~--~~~~~D~Vv~dPP 249 (315)
T PRK03522 173 PPRSMWDLFCGVGGFGLHCATPGMQLTGIEISAEAIACAKQSAAELGL-TNVQFQALDSTQFATA--QGEVPDLVLVNPP 249 (315)
T ss_pred CCCEEEEccCCCCHHHHHHHhcCCEEEEEeCCHHHHHHHHHHHHHcCC-CceEEEEcCHHHHHHh--cCCCCeEEEECCC
Confidence 6899999999999999877653110 0111110 01100000 1345666665443221 1122234446998
Q ss_pred cchhhhhHHHHhhhhhccCCcEEEEec
Q 003658 773 FGVKASLANKFISQALKFKPKLIVLIV 799 (805)
Q Consensus 773 fg~~~~~a~kf~~~~~~f~p~~~~li~ 799 (805)
- +-+..+.+.-.....|+-||.|.
T Consensus 250 r---~G~~~~~~~~l~~~~~~~ivyvs 273 (315)
T PRK03522 250 R---RGIGKELCDYLSQMAPRFILYSS 273 (315)
T ss_pred C---CCccHHHHHHHHHcCCCeEEEEE
Confidence 3 33555556666667887776653
No 57
>TIGR03704 PrmC_rel_meth putative protein-(glutamine-N5) methyltransferase, unknown substrate-specific. This protein family is closely related to two different families of protein-(glutamine-N5) methyltransferase. The first is PrmB, which modifies ribosomal protein L3 in some bacteria. The second is PrmC (HemK), which modifies peptide chain release factors 1 and 2 in most bacteria and also in eukaryotes. The glutamine side chain-binding motif NPPY shared by PrmB and PrmC is N[VAT]PY in this family. The protein substrate is unknown.
Probab=78.86 E-value=0.67 Score=49.34 Aligned_cols=89 Identities=19% Similarity=0.324 Sum_probs=45.6
Q ss_pred ccchhhhHHHHHHhhcceec---cCCeEEeeccCcchhhHHHHHHHHH---cCCccc-------ccCCCCCCCCCCCccc
Q 003658 681 HFTKVEKLKEIVDRLHWYVR---SGDTIVDFCCGANDFSCMMKVKLEQ---MGKSCS-------FRNYDLIQPKNDFSFE 747 (805)
Q Consensus 681 hft~~ekl~~i~~~l~~~~~---~~d~~~d~~~g~~~~~~~~~~~~~~---~~~~~~-------~~n~d~~~~~~~~~f~ 747 (805)
-|.+..-++.+++...-++. .+..|+|+|||+..++-.+-++... ++-+.+ -+|... |...|.
T Consensus 63 vf~pr~~Te~Lv~~~l~~~~~~~~~~~vLDlg~GsG~i~l~la~~~~~~~v~~vDis~~al~~A~~N~~~----~~~~~~ 138 (251)
T TIGR03704 63 VFVPRRRTEFLVDEAAALARPRSGTLVVVDLCCGSGAVGAALAAALDGIELHAADIDPAAVRCARRNLAD----AGGTVH 138 (251)
T ss_pred CcCCCccHHHHHHHHHHhhcccCCCCEEEEecCchHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHH----cCCEEE
Confidence 44444444444444322333 2357999999999999877654211 111111 112111 123577
Q ss_pred cccccccCCCCCCCCCceeeecCCCcc
Q 003658 748 KRDWMTVRPEELPDGSQLIMGLNPPFG 774 (805)
Q Consensus 748 ~~~w~~~~~~~l~~g~~li~gl~ppfg 774 (805)
..||...-+..+...=.+|+. ||||-
T Consensus 139 ~~D~~~~l~~~~~~~fDlVv~-NPPy~ 164 (251)
T TIGR03704 139 EGDLYDALPTALRGRVDILAA-NAPYV 164 (251)
T ss_pred EeechhhcchhcCCCEeEEEE-CCCCC
Confidence 778776444333222235554 99985
No 58
>PRK10909 rsmD 16S rRNA m(2)G966-methyltransferase; Provisional
Probab=77.85 E-value=4.2 Score=42.16 Aligned_cols=96 Identities=7% Similarity=0.142 Sum_probs=47.7
Q ss_pred ccCCeEEeeccCcchhhHHHHHHHH--HcCCccc-------ccCCCCCCCCCCCccccccccccCCCCCCCCCceeeecC
Q 003658 700 RSGDTIVDFCCGANDFSCMMKVKLE--QMGKSCS-------FRNYDLIQPKNDFSFEKRDWMTVRPEELPDGSQLIMGLN 770 (805)
Q Consensus 700 ~~~d~~~d~~~g~~~~~~~~~~~~~--~~~~~~~-------~~n~d~~~~~~~~~f~~~~w~~~~~~~l~~g~~li~gl~ 770 (805)
.+|..|+|++||+..|+-.+-.+.- -++-..+ -+|.....- ++..|...|+...-+. ..+..=++-+|
T Consensus 52 ~~~~~vLDl~~GsG~l~l~~lsr~a~~V~~vE~~~~a~~~a~~Nl~~~~~-~~v~~~~~D~~~~l~~--~~~~fDlV~~D 128 (199)
T PRK10909 52 IVDARCLDCFAGSGALGLEALSRYAAGATLLEMDRAVAQQLIKNLATLKA-GNARVVNTNALSFLAQ--PGTPHNVVFVD 128 (199)
T ss_pred cCCCEEEEcCCCccHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHHHhCC-CcEEEEEchHHHHHhh--cCCCceEEEEC
Confidence 5789999999999999975422210 1111111 123322221 2356666776553222 12334455679
Q ss_pred CCcchh-hhhHHHHhhhhhccCCcEEEEe
Q 003658 771 PPFGVK-ASLANKFISQALKFKPKLIVLI 798 (805)
Q Consensus 771 ppfg~~-~~~a~kf~~~~~~f~p~~~~li 798 (805)
|||... ...+...+...--..|.=||+|
T Consensus 129 PPy~~g~~~~~l~~l~~~~~l~~~~iv~v 157 (199)
T PRK10909 129 PPFRKGLLEETINLLEDNGWLADEALIYV 157 (199)
T ss_pred CCCCCChHHHHHHHHHHCCCcCCCcEEEE
Confidence 997432 1122233333211356655554
No 59
>PF07669 Eco57I: Eco57I restriction-modification methylase; InterPro: IPR011639 This entry contains restriction modification methylases, which in the case of endonuclease Eco57I is found adjacent to the DNA cleavage domain, which recognises asymmetric DNA sequence 5'-CTGAAG [, ]. The methylase causes specific methylation on A-5 on one strand, the other strand being methylated by the Eco57IB methylase []. ; GO: 0003677 DNA binding, 0003824 catalytic activity, 0006304 DNA modification
Probab=77.51 E-value=1.8 Score=40.27 Aligned_cols=36 Identities=31% Similarity=0.630 Sum_probs=28.6
Q ss_pred eeeecCCCcchhhhhHH-------------HHhhhhhccCCcEEEEecCC
Q 003658 765 LIMGLNPPFGVKASLAN-------------KFISQALKFKPKLIVLIVPQ 801 (805)
Q Consensus 765 li~gl~ppfg~~~~~a~-------------kf~~~~~~f~p~~~~li~p~ 801 (805)
.|+| |||++....+.+ -||.+|++.-.-.+.+|+|.
T Consensus 5 ~VIG-NPPY~~~~~~~~~~~~~~~~~dlY~~Fie~~~~ll~G~~~~I~P~ 53 (106)
T PF07669_consen 5 VVIG-NPPYIKIKSLSKKKKKKKKKSDLYILFIEKSLNLLNGYLSFITPN 53 (106)
T ss_pred EEEE-CCCChhhccccchhhcccccCcHHHHHHHHHHHHhCCeEEEEeCh
Confidence 7899 999987653221 29999988888899999996
No 60
>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]
Probab=76.59 E-value=2.2 Score=45.77 Aligned_cols=59 Identities=19% Similarity=0.381 Sum_probs=43.7
Q ss_pred hhHhhHHHHhhccccccccccccccccccCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHH
Q 003658 650 EILCQIFQWKRKLDVYLAPFLHGMRYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 650 ~~l~q~~~~~~~l~~~l~p~~~g~~y~s~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
.+-.++..+-+... +--|||.|.+-...|.+..... +|+.|+|.|||..++.-++.+.-
T Consensus 15 ~vF~~ia~~YD~~n----------~~~S~g~~~~Wr~~~i~~~~~~-----~g~~vLDva~GTGd~a~~~~k~~ 73 (238)
T COG2226 15 KVFDKVAKKYDLMN----------DLMSFGLHRLWRRALISLLGIK-----PGDKVLDVACGTGDMALLLAKSV 73 (238)
T ss_pred HHHHhhHHHHHhhc----------ccccCcchHHHHHHHHHhhCCC-----CCCEEEEecCCccHHHHHHHHhc
Confidence 34555666655544 3348999999988887754432 99999999999999988887763
No 61
>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional
Probab=74.45 E-value=16 Score=37.97 Aligned_cols=65 Identities=22% Similarity=0.306 Sum_probs=44.3
Q ss_pred hhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHHHcCCcccccCCCCCC--CCCCCccccccccc
Q 003658 685 VEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQMGKSCSFRNYDLIQ--PKNDFSFEKRDWMT 753 (805)
Q Consensus 685 ~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~~~~~~~~~n~d~~~--~~~~~~f~~~~w~~ 753 (805)
..||.||.+++. ++.+|++|||++||...|+..+-++. |..+..--.|+.+ +..+..|..-|..+
T Consensus 36 ~~kl~~~~~~~~-~~~~~~~VLDlG~GtG~~t~~l~~~~---~~~~~V~aVDi~~~~~~~~v~~i~~D~~~ 102 (209)
T PRK11188 36 WFKLDEIQQSDK-LFKPGMTVVDLGAAPGGWSQYAVTQI---GDKGRVIACDILPMDPIVGVDFLQGDFRD 102 (209)
T ss_pred HHhhHHHHHHhc-cCCCCCEEEEEcccCCHHHHHHHHHc---CCCceEEEEecccccCCCCcEEEecCCCC
Confidence 348888988864 57899999999999999998777653 3334444455543 12235566666655
No 62
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=73.26 E-value=1.9 Score=38.35 Aligned_cols=33 Identities=21% Similarity=0.585 Sum_probs=27.2
Q ss_pred CcccccccccCCCCCCCCCceeeccCCCcCCCCccchhcc
Q 003658 276 EHQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSK 315 (805)
Q Consensus 276 qh~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~ 315 (805)
...|.+|++. .+-.+.|....|.+.||+.|...
T Consensus 36 ~~~C~~C~~~-------~Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 36 KLKCSICKKK-------GGACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCCCcCCCCC-------CCeEEEEeCCCCCcEEChHHHcc
Confidence 4579999865 24688999999999999999764
No 63
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=73.24 E-value=2.6 Score=43.81 Aligned_cols=45 Identities=18% Similarity=0.446 Sum_probs=35.3
Q ss_pred ecccccccCcccccccccCCCCCCCCCceeeccCCCcCCCCccchhc
Q 003658 268 LCQNCVYQEHQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVS 314 (805)
Q Consensus 268 ~C~eC~~gqh~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~ 314 (805)
.|.-|..+...|-+|...+.+-......+.+| ..|+..||..|..
T Consensus 144 ~C~lC~~kGfiCe~C~~~~~IfPF~~~~~~~C--~~C~~v~H~~C~~ 188 (202)
T PF13901_consen 144 SCELCQQKGFICEICNSDDIIFPFQIDTTVRC--PKCKSVFHKSCFR 188 (202)
T ss_pred HhHHHHhCCCCCccCCCCCCCCCCCCCCeeeC--CcCccccchhhcC
Confidence 67888877788889976654433344689999 8999999999976
No 64
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=70.88 E-value=3.2 Score=52.57 Aligned_cols=66 Identities=24% Similarity=0.456 Sum_probs=46.1
Q ss_pred cccccccccCCCCCCCCCceeeccCCCcCCCCccchhcccCCCCchhHHHHHHHHhhcCCceecCCcccccCcCCccccc
Q 003658 277 HQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCPVHKCFVCQQSEDMNV 356 (805)
Q Consensus 277 h~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~~p~~~~~~~eL~krV~~g~~F~CPlH~C~~C~~~edk~~ 356 (805)
..|.+|.+-... +....+.| +.|+..+|..|.+..+-|+ ..| .|..|-++..
T Consensus 220 ~~C~iC~~~~~~---n~n~ivfC--D~Cnl~VHq~Cygi~~ipe---------------g~W-----lCr~Cl~s~~--- 271 (1051)
T KOG0955|consen 220 AVCCICLDGECQ---NSNVIVFC--DGCNLAVHQECYGIPFIPE---------------GQW-----LCRRCLQSPQ--- 271 (1051)
T ss_pred ccceeecccccC---CCceEEEc--CCCcchhhhhccCCCCCCC---------------CcE-----eehhhccCcC---
Confidence 358888764432 23567889 9999999999998444332 334 6788988764
Q ss_pred cccceeecccccccccc
Q 003658 357 EDLQLAICRRCPKAYHR 373 (805)
Q Consensus 357 ~~~qL~~C~RCPkAYH~ 373 (805)
..+.|.-||.+=|.
T Consensus 272 ---~~v~c~~cp~~~gA 285 (1051)
T KOG0955|consen 272 ---RPVRCLLCPSKGGA 285 (1051)
T ss_pred ---cccceEeccCCCCc
Confidence 34889999876554
No 65
>KOG3420 consensus Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=70.39 E-value=4.6 Score=40.97 Aligned_cols=107 Identities=25% Similarity=0.338 Sum_probs=58.8
Q ss_pred chhhhHHHHHHhhcceec--cCCeEEeeccCcchhh--HHHHHHHHHcCCcccccCCCCCCCCCCCcccccc-cc--ccC
Q 003658 683 TKVEKLKEIVDRLHWYVR--SGDTIVDFCCGANDFS--CMMKVKLEQMGKSCSFRNYDLIQPKNDFSFEKRD-WM--TVR 755 (805)
Q Consensus 683 t~~ekl~~i~~~l~~~~~--~~d~~~d~~~g~~~~~--~~~~~~~~~~~~~~~~~n~d~~~~~~~~~f~~~~-w~--~~~ 755 (805)
|.|+-..-.+.-.|-+.- +|--+.|++||-...| .-|-+.=.=.|-+..--...++ ..|-..||-.+ .+ ++.
T Consensus 28 T~p~iAasM~~~Ih~TygdiEgkkl~DLgcgcGmLs~a~sm~~~e~vlGfDIdpeALEIf-~rNaeEfEvqidlLqcdil 106 (185)
T KOG3420|consen 28 TRPHIAASMLYTIHNTYGDIEGKKLKDLGCGCGMLSIAFSMPKNESVLGFDIDPEALEIF-TRNAEEFEVQIDLLQCDIL 106 (185)
T ss_pred CcHHHHHHHHHHHHhhhccccCcchhhhcCchhhhHHHhhcCCCceEEeeecCHHHHHHH-hhchHHhhhhhheeeeecc
Confidence 556655555666666553 5666999999987665 2222111111111111111111 24445554332 11 223
Q ss_pred CCCCCCCCceeeecCCCcchhhhhH-HHHhhhhhcc
Q 003658 756 PEELPDGSQLIMGLNPPFGVKASLA-NKFISQALKF 790 (805)
Q Consensus 756 ~~~l~~g~~li~gl~ppfg~~~~~a-~kf~~~~~~f 790 (805)
-.++..|-.-.--.|||||-+-.-| -+|+++||+.
T Consensus 107 dle~~~g~fDtaviNppFGTk~~~aDm~fv~~al~~ 142 (185)
T KOG3420|consen 107 DLELKGGIFDTAVINPPFGTKKKGADMEFVSAALKV 142 (185)
T ss_pred chhccCCeEeeEEecCCCCcccccccHHHHHHHHHH
Confidence 3456667777778899999775544 4799999874
No 66
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.09 E-value=2.3 Score=47.89 Aligned_cols=49 Identities=18% Similarity=0.405 Sum_probs=33.6
Q ss_pred cccccccccCCCCCCCCCceeeccCCCcCCCCccchhcccCCCCchhHHHHHHHHhhcCCceecCCcccccCcCCcc
Q 003658 277 HQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCPVHKCFVCQQSED 353 (805)
Q Consensus 277 h~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~~p~~~~~~~eL~krV~~g~~F~CPlH~C~~C~~~ed 353 (805)
..|.+|-+.-. .++.++= -.|.+.||..|+.+|+.. + +|+|.+|++.-.
T Consensus 230 ~~CaIClEdY~-----~GdklRi--LPC~H~FH~~CIDpWL~~--------------------~-r~~CPvCK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDYE-----KGDKLRI--LPCSHKFHVNCIDPWLTQ--------------------T-RTFCPVCKRDIR 278 (348)
T ss_pred ceEEEeecccc-----cCCeeeE--ecCCCchhhccchhhHhh--------------------c-CccCCCCCCcCC
Confidence 46888865322 2333332 689999999999999732 1 578999999554
No 67
>PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=69.80 E-value=7.7 Score=40.77 Aligned_cols=70 Identities=21% Similarity=0.430 Sum_probs=41.8
Q ss_pred eccCCeEEeeccCcchhhHHHHHHHHHcCCcccccCCCCCC-------------CCCCCccccccccccCCCCCCCCC-c
Q 003658 699 VRSGDTIVDFCCGANDFSCMMKVKLEQMGKSCSFRNYDLIQ-------------PKNDFSFEKRDWMTVRPEELPDGS-Q 764 (805)
Q Consensus 699 ~~~~d~~~d~~~g~~~~~~~~~~~~~~~~~~~~~~n~d~~~-------------~~~~~~f~~~~w~~~~~~~l~~g~-~ 764 (805)
..++..|+|++||+..+...+...+. .+.+--.|+.+ ..+...|...||..- ++.+. -
T Consensus 106 ~~~~~~vLDiG~GsG~~~~~la~~~~----~~~v~~iDis~~~l~~a~~n~~~~~~~~i~~~~~d~~~~----~~~~~fD 177 (275)
T PRK09328 106 LKEPLRVLDLGTGSGAIALALAKERP----DAEVTAVDISPEALAVARRNAKHGLGARVEFLQGDWFEP----LPGGRFD 177 (275)
T ss_pred ccCCCEEEEEcCcHHHHHHHHHHHCC----CCEEEEEECCHHHHHHHHHHHHhCCCCcEEEEEccccCc----CCCCcee
Confidence 35778999999999999888776541 12222222221 124567777777542 22333 3
Q ss_pred eeeecCCCcchhh
Q 003658 765 LIMGLNPPFGVKA 777 (805)
Q Consensus 765 li~gl~ppfg~~~ 777 (805)
+|+. ||||....
T Consensus 178 ~Iv~-npPy~~~~ 189 (275)
T PRK09328 178 LIVS-NPPYIPEA 189 (275)
T ss_pred EEEE-CCCcCCcc
Confidence 5555 99997543
No 68
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=68.57 E-value=1.3 Score=34.19 Aligned_cols=35 Identities=26% Similarity=0.705 Sum_probs=16.9
Q ss_pred CceeecCcccccccccccccCccccccccCCcccccCCCCceeccccc
Q 003658 226 GDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCV 273 (805)
Q Consensus 226 GeLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~ 273 (805)
..||.|+ .|.-.+|..| -|+...+ ....|+|.-|+
T Consensus 2 n~ll~C~-~C~v~VH~~C----------YGv~~~~--~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCD-NCNVAVHQSC----------YGVSEVP--DGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-S-SS--EEEHHH----------HT-SS----SS-----HHH-
T ss_pred CceEEeC-CCCCcCChhh----------CCcccCC--CCCcEECCcCC
Confidence 3589999 5999999996 5664433 23469998774
No 69
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=68.29 E-value=2.8 Score=42.85 Aligned_cols=37 Identities=27% Similarity=0.622 Sum_probs=28.5
Q ss_pred ccccCcCCccccccccceeeccccccccccccCCCCcc
Q 003658 344 KCFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPTEIT 381 (805)
Q Consensus 344 ~C~~C~~~edk~~~~~qL~~C~RCPkAYH~kCLP~g~~ 381 (805)
.|.+|...+++ ...++|+-|--|..|||..||-.-+.
T Consensus 1 ~C~~C~~~g~~-~~kG~Lv~CQGCs~sYHk~CLG~Rs~ 37 (175)
T PF15446_consen 1 TCDTCGYEGDD-RNKGPLVYCQGCSSSYHKACLGPRSQ 37 (175)
T ss_pred CcccccCCCCC-ccCCCeEEcCccChHHHhhhcCCccc
Confidence 48899765432 24679999999999999999965444
No 70
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=67.86 E-value=3.6 Score=34.86 Aligned_cols=34 Identities=29% Similarity=0.744 Sum_probs=26.3
Q ss_pred cccccccccCCCCCCCCCceeeccCCCcCCCCccchhccc
Q 003658 277 HQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKL 316 (805)
Q Consensus 277 h~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~ 316 (805)
..|.+|++.-. .+.+++.| +.||.-||..|..+.
T Consensus 6 ~~C~~Cg~~~~----~~dDiVvC--p~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 6 CKCPVCGKKFK----DGDDIVVC--PECGAPYHRDCWEKA 39 (54)
T ss_pred ccChhhCCccc----CCCCEEEC--CCCCCcccHHHHhhC
Confidence 35888987532 35689999 999999999997543
No 71
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=67.44 E-value=1.5 Score=57.11 Aligned_cols=53 Identities=21% Similarity=0.568 Sum_probs=39.2
Q ss_pred ccCCCcccccccCCCC---ceeecCcccccccccccccCccccccccCCcccccCCCCceeccccccc
Q 003658 211 KDENYFAVCAICDDGG---DVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQ 275 (805)
Q Consensus 211 edd~~d~vC~IC~~gG---eLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~g 275 (805)
+.......|.+|...+ +++.|++ |.+.||..|+. ..++.. +.+.|+|+.|...
T Consensus 1103 ~~s~~~~~c~~cr~k~~~~~m~lc~~-c~~~~h~~C~r--------p~~~~~---~~~dW~C~~c~~e 1158 (1404)
T KOG1245|consen 1103 DRSAVNALCKVCRRKKQDEKMLLCDE-CLSGFHLFCLR--------PALSSV---PPGDWMCPSCRKE 1158 (1404)
T ss_pred ccccchhhhhhhhhcccchhhhhhHh-hhhhHHHHhhh--------hhhccC---CcCCccCCccchh
Confidence 3445577899998765 4999995 99999999753 233333 3678999999853
No 72
>PRK05785 hypothetical protein; Provisional
Probab=66.23 E-value=7.3 Score=40.81 Aligned_cols=47 Identities=21% Similarity=0.380 Sum_probs=33.9
Q ss_pred cccccCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHH
Q 003658 674 RYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 674 ~y~s~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
+..|||++.- --.++++.+..+..++.+|+|++||..++...+.++.
T Consensus 27 ~~~s~g~~~~---wr~~~~~~l~~~~~~~~~VLDlGcGtG~~~~~l~~~~ 73 (226)
T PRK05785 27 RFISFNQDVR---WRAELVKTILKYCGRPKKVLDVAAGKGELSYHFKKVF 73 (226)
T ss_pred hhccCCCcHH---HHHHHHHHHHHhcCCCCeEEEEcCCCCHHHHHHHHhc
Confidence 4567887732 1234555665566678999999999999999887763
No 73
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=66.03 E-value=3.8 Score=35.81 Aligned_cols=39 Identities=23% Similarity=0.512 Sum_probs=16.1
Q ss_pred cccccccccCCCCCCCCCceeeccCCCcCCCCccchhcccC
Q 003658 277 HQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLL 317 (805)
Q Consensus 277 h~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~ 317 (805)
..|.+|......+ .....+.|....|++.||..||..|+
T Consensus 3 ~~C~IC~~~~~~~--~~~p~~~C~n~~C~~~fH~~CL~~wf 41 (70)
T PF11793_consen 3 LECGICYSYRLDD--GEIPDVVCPNPSCGKKFHLLCLSEWF 41 (70)
T ss_dssp -S-SSS--SS-TT-------B--S-TT----B-SGGGHHHH
T ss_pred CCCCcCCcEecCC--CCcCceEcCCcccCCHHHHHHHHHHH
Confidence 3578887543211 12346889999999999999999886
No 74
>PF02475 Met_10: Met-10+ like-protein; InterPro: IPR003402 This entry represents the Trm5 family. Trm5 specifically methylates the N1 position of guanosine-37 in various tRNAs [, , ]. Another members of this family, tRNA wybutosine-synthesizing protein 2 (Tyw2) and its homologues, are S-adenosyl-L-methionine-dependent transferases that act as a component of the wybutosine biosynthesis pathway [, ]. tRNA wybutosine-synthesizing protein 2 was originally thought to be a methyltransferase [].; GO: 0016740 transferase activity; PDB: 3A27_A 2ZZN_B 2YX1_A 2ZZM_A 3AY0_B 3K6R_A 3A26_A 3A25_A.
Probab=65.15 E-value=3.1 Score=43.33 Aligned_cols=28 Identities=25% Similarity=0.489 Sum_probs=19.5
Q ss_pred hhcceeccCCeEEeeccCcchhhHHHHH
Q 003658 694 RLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (805)
Q Consensus 694 ~l~~~~~~~d~~~d~~~g~~~~~~~~~~ 721 (805)
|+--.+.+|++|+|++||-.-|+-.+-+
T Consensus 94 Ri~~~v~~~e~VlD~faGIG~f~l~~ak 121 (200)
T PF02475_consen 94 RIANLVKPGEVVLDMFAGIGPFSLPIAK 121 (200)
T ss_dssp HHHTC--TT-EEEETT-TTTTTHHHHHH
T ss_pred HHHhcCCcceEEEEccCCccHHHHHHhh
Confidence 3334589999999999999999988765
No 75
>COG0286 HsdM Type I restriction-modification system methyltransferase subunit [Defense mechanisms]
Probab=65.13 E-value=7.3 Score=45.72 Aligned_cols=49 Identities=22% Similarity=0.269 Sum_probs=43.5
Q ss_pred ccCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHHHcC
Q 003658 677 SFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQMG 727 (805)
Q Consensus 677 s~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~~~ 727 (805)
+.|.+||+.+-.+=||+-|-. .++++|.|.+||+..|-....+.+.+..
T Consensus 164 ~~GEfyTP~~v~~liv~~l~~--~~~~~i~DpacGsgg~l~~a~~~~~~~~ 212 (489)
T COG0286 164 EAGEFYTPREVSELIVELLDP--EPRNSIYDPACGSGGMLLQAAKYLKRHQ 212 (489)
T ss_pred CCCccCChHHHHHHHHHHcCC--CCCCeecCCCCchhHHHHHHHHHHHhhc
Confidence 789999999988889998887 8999999999999999988888886643
No 76
>TIGR00536 hemK_fam HemK family putative methylases. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. Both E. coli and H. influenzae have two members rather than one. The members from the Mycoplasmas have an additional C-terminal domain.
Probab=65.03 E-value=3.2 Score=44.79 Aligned_cols=69 Identities=17% Similarity=0.256 Sum_probs=39.4
Q ss_pred CeEEeeccCcchhhHHHHHHHHH---cCCccc-------ccCCCCCCCCCCCccccccccccCCCCCCC-CCceeeecCC
Q 003658 703 DTIVDFCCGANDFSCMMKVKLEQ---MGKSCS-------FRNYDLIQPKNDFSFEKRDWMTVRPEELPD-GSQLIMGLNP 771 (805)
Q Consensus 703 d~~~d~~~g~~~~~~~~~~~~~~---~~~~~~-------~~n~d~~~~~~~~~f~~~~w~~~~~~~l~~-g~~li~gl~p 771 (805)
..|+|++||+..+...+...... ++-+.+ -+|.....-.+...|...||+.. ++. .=-+|++ ||
T Consensus 116 ~~vLDlG~GsG~i~l~la~~~~~~~v~avDis~~al~~a~~n~~~~~~~~~v~~~~~d~~~~----~~~~~fDlIvs-NP 190 (284)
T TIGR00536 116 LHILDLGTGSGCIALALAYEFPNAEVIAVDISPDALAVAEENAEKNQLEHRVEFIQSNLFEP----LAGQKIDIIVS-NP 190 (284)
T ss_pred CEEEEEeccHhHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEECchhcc----CcCCCccEEEE-CC
Confidence 68999999999998777665321 000000 01111111124577888898763 332 2346666 99
Q ss_pred Ccchh
Q 003658 772 PFGVK 776 (805)
Q Consensus 772 pfg~~ 776 (805)
||-..
T Consensus 191 Pyi~~ 195 (284)
T TIGR00536 191 PYIDE 195 (284)
T ss_pred CCCCc
Confidence 98643
No 77
>TIGR03533 L3_gln_methyl protein-(glutamine-N5) methyltransferase, ribosomal protein L3-specific. Members of this protein family methylate ribosomal protein L3 on a glutamine side chain. This family is related to HemK, a protein-glutamine methyltranferase for peptide chain release factors.
Probab=64.20 E-value=4.5 Score=43.92 Aligned_cols=72 Identities=19% Similarity=0.311 Sum_probs=41.2
Q ss_pred ccCCeEEeeccCcchhhHHHHHHHHH---cCCccc-------ccCCCCCCCCCCCccccccccccCCCCCCCCC-ceeee
Q 003658 700 RSGDTIVDFCCGANDFSCMMKVKLEQ---MGKSCS-------FRNYDLIQPKNDFSFEKRDWMTVRPEELPDGS-QLIMG 768 (805)
Q Consensus 700 ~~~d~~~d~~~g~~~~~~~~~~~~~~---~~~~~~-------~~n~d~~~~~~~~~f~~~~w~~~~~~~l~~g~-~li~g 768 (805)
.++..|+|++||+..+...+.++... ++-+.+ -+|.....-.+...|...|+++. ++.+. -+|+.
T Consensus 120 ~~~~~vLDlG~GsG~i~~~la~~~~~~~v~avDis~~al~~A~~n~~~~~~~~~i~~~~~D~~~~----~~~~~fD~Iv~ 195 (284)
T TIGR03533 120 EPVKRILDLCTGSGCIAIACAYAFPEAEVDAVDISPDALAVAEINIERHGLEDRVTLIQSDLFAA----LPGRKYDLIVS 195 (284)
T ss_pred CCCCEEEEEeCchhHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEECchhhc----cCCCCccEEEE
Confidence 45678999999999999888765311 111110 11211111124567888887642 33332 46665
Q ss_pred cCCCcchh
Q 003658 769 LNPPFGVK 776 (805)
Q Consensus 769 l~ppfg~~ 776 (805)
||||...
T Consensus 196 -NPPy~~~ 202 (284)
T TIGR03533 196 -NPPYVDA 202 (284)
T ss_pred -CCCCCCc
Confidence 9998643
No 78
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=62.87 E-value=5 Score=47.70 Aligned_cols=50 Identities=24% Similarity=0.199 Sum_probs=32.7
Q ss_pred chHHhhccCCCCccccc--CCccccccceecccchhhHH--------HHH--HHHHHhhCCC
Q 003658 589 NEEEFMKSHIVPITHAH--HSKHLLEKSITLGLVEGSVK--------AVR--AALEMLDGGC 638 (805)
Q Consensus 589 ~~~~~~~~~~~~~t~~~--~~~~~~~~~i~~g~~e~sv~--------a~~--~~l~~l~~g~ 638 (805)
+.||+.+..++|-++.. .+..-+|+.+-.|+--+.|. +-| --|.||-.|.
T Consensus 447 s~eDi~k~sk~p~~~~pdpas~~~~e~~~w~~~ps~~V~~~~~~~R~~~R~~eql~Kl~sgi 508 (670)
T KOG1044|consen 447 SSEDIIKFSKFPAAQAPDPASTPEIETDHWPGKPSFAVPGPEMKRRSLGRQEEQLMKLNSGL 508 (670)
T ss_pred cccchhhhhcCCcccCCCCCCCCcccccCCCCCCcccccCchhhhhhccchhhhhhhccchh
Confidence 38999999999988553 33333567777777666665 333 3466777663
No 79
>TIGR02143 trmA_only tRNA (uracil-5-)-methyltransferase. This family consists exclusively of proteins believed to act as tRNA (uracil-5-)-methyltransferase. All members of far are proteobacterial. The seed alignment was taken directly from pfam05958 in Pfam 12.0, but higher cutoffs are used to select only functionally equivalent proteins. Homologous proteins excluded by the higher cutoff scores of this model include other uracil methyltransferases, such as RumA, active on rRNA.
Probab=62.68 E-value=8.6 Score=43.11 Aligned_cols=91 Identities=14% Similarity=0.250 Sum_probs=47.5
Q ss_pred CCeEEeeccCcchhhHHHHHHHHH-cCC-------cccccCCCCCCCCCCCccccccccccCCC-----CCC--CC----
Q 003658 702 GDTIVDFCCGANDFSCMMKVKLEQ-MGK-------SCSFRNYDLIQPKNDFSFEKRDWMTVRPE-----ELP--DG---- 762 (805)
Q Consensus 702 ~d~~~d~~~g~~~~~~~~~~~~~~-~~~-------~~~~~n~d~~~~~~~~~f~~~~w~~~~~~-----~l~--~g---- 762 (805)
++.|+|++||+..|+-.+.++... +|- ..--+|..+-.-. +..|...|....-+. .++ .|
T Consensus 198 ~~~vlDl~~G~G~~sl~la~~~~~v~~vE~~~~av~~a~~n~~~~~~~-~v~~~~~d~~~~~~~~~~~~~~~~~~~~~~~ 276 (353)
T TIGR02143 198 KGDLLELYCGNGNFSLALAQNFRRVLATEIAKPSVNAAQYNIAANNID-NVQIIRMSAEEFTQAMNGVREFRRLKGIDLK 276 (353)
T ss_pred CCcEEEEeccccHHHHHHHHhCCEEEEEECCHHHHHHHHHHHHHcCCC-cEEEEEcCHHHHHHHHhhccccccccccccc
Confidence 457999999999999988765210 000 0001222111111 355666665443221 110 11
Q ss_pred --CceeeecCCCcchhhhhHHHHhhhhhccCCcEEEEe
Q 003658 763 --SQLIMGLNPPFGVKASLANKFISQALKFKPKLIVLI 798 (805)
Q Consensus 763 --~~li~gl~ppfg~~~~~a~kf~~~~~~f~p~~~~li 798 (805)
..=++-|||| ++-++.++++-... |+-||.|
T Consensus 277 ~~~~d~v~lDPP---R~G~~~~~l~~l~~--~~~ivYv 309 (353)
T TIGR02143 277 SYNCSTIFVDPP---RAGLDPDTCKLVQA--YERILYI 309 (353)
T ss_pred cCCCCEEEECCC---CCCCcHHHHHHHHc--CCcEEEE
Confidence 1135567999 46677788776666 4545444
No 80
>COG0293 FtsJ 23S rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=62.39 E-value=8.6 Score=40.53 Aligned_cols=54 Identities=22% Similarity=0.288 Sum_probs=44.4
Q ss_pred hhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHHHcCC--cccccCCCCCC
Q 003658 685 VEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQMGK--SCSFRNYDLIQ 739 (805)
Q Consensus 685 ~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~~~~--~~~~~n~d~~~ 739 (805)
..||+||.+|- -.+.+|+.|||+++.=..||+...+++...|+ .++.-+-+.|+
T Consensus 30 a~KL~el~~k~-~i~~~~~~ViDLGAAPGgWsQva~~~~~~~~~ivavDi~p~~~~~ 85 (205)
T COG0293 30 AYKLLELNEKF-KLFKPGMVVVDLGAAPGGWSQVAAKKLGAGGKIVAVDILPMKPIP 85 (205)
T ss_pred HHHHHHHHHhc-CeecCCCEEEEcCCCCCcHHHHHHHHhCCCCcEEEEECcccccCC
Confidence 56999999998 88999999999999999999999999888764 33444444444
No 81
>PRK14967 putative methyltransferase; Provisional
Probab=61.38 E-value=12 Score=38.62 Aligned_cols=34 Identities=15% Similarity=0.377 Sum_probs=26.5
Q ss_pred hhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHH
Q 003658 686 EKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (805)
Q Consensus 686 ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~ 721 (805)
+.|.+++.++ .+.+|+.|+|++||...++..+.+
T Consensus 23 ~~l~~~l~~~--~~~~~~~vLDlGcG~G~~~~~la~ 56 (223)
T PRK14967 23 QLLADALAAE--GLGPGRRVLDLCTGSGALAVAAAA 56 (223)
T ss_pred HHHHHHHHhc--ccCCCCeEEEecCCHHHHHHHHHH
Confidence 4566666654 367899999999999999887765
No 82
>PRK11805 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=61.11 E-value=4.5 Score=44.49 Aligned_cols=64 Identities=20% Similarity=0.417 Sum_probs=39.0
Q ss_pred CeEEeeccCcchhhHHHHHHHHHcCCcccccCCCCC--------------CCCCCCccccccccccCCCCCCCCC-ceee
Q 003658 703 DTIVDFCCGANDFSCMMKVKLEQMGKSCSFRNYDLI--------------QPKNDFSFEKRDWMTVRPEELPDGS-QLIM 767 (805)
Q Consensus 703 d~~~d~~~g~~~~~~~~~~~~~~~~~~~~~~n~d~~--------------~~~~~~~f~~~~w~~~~~~~l~~g~-~li~ 767 (805)
.+|+|++||+..++..+..+.. ....--.|+. .-.+...|...||.+. +|.++ .+|+
T Consensus 135 ~~VLDlG~GsG~iai~la~~~p----~~~V~avDis~~al~~A~~n~~~~~l~~~i~~~~~D~~~~----l~~~~fDlIv 206 (307)
T PRK11805 135 TRILDLCTGSGCIAIACAYAFP----DAEVDAVDISPDALAVAEINIERHGLEDRVTLIESDLFAA----LPGRRYDLIV 206 (307)
T ss_pred CEEEEEechhhHHHHHHHHHCC----CCEEEEEeCCHHHHHHHHHHHHHhCCCCcEEEEECchhhh----CCCCCccEEE
Confidence 6899999999999988866521 1111112221 1124567888887652 33333 4666
Q ss_pred ecCCCcch
Q 003658 768 GLNPPFGV 775 (805)
Q Consensus 768 gl~ppfg~ 775 (805)
. ||||-.
T Consensus 207 s-NPPyi~ 213 (307)
T PRK11805 207 S-NPPYVD 213 (307)
T ss_pred E-CCCCCC
Confidence 6 999854
No 83
>TIGR03587 Pse_Me-ase pseudaminic acid biosynthesis-associated methylase. Members of this small clade are methyltransferases of the pfam08241 family and are observed within operons for the biosynthesis of pseudaminic acid, a component of exopolysaccharide and flagellin glycosyl modifications. Notable among these genomes is Pseudomonas fluorescens PfO-1. Possibly one of the two hydroxyl groups of pseudaminic acid, at positions 4 and 8 is converted to a methoxy group by this enzyme
Probab=58.20 E-value=11 Score=39.06 Aligned_cols=51 Identities=12% Similarity=0.036 Sum_probs=43.7
Q ss_pred cccccccCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 672 GMRYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 672 g~~y~s~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
|.+|+.-+|+..-....-+.+.++...+.+++.|+|+-||...+...+.+.
T Consensus 14 g~~~~~rn~~~~~~~~~~~~~~~~l~~~~~~~~VLDiGCG~G~~~~~L~~~ 64 (204)
T TIGR03587 14 GKEYIDRNSRQSLVAAKLAMFARALNRLPKIASILELGANIGMNLAALKRL 64 (204)
T ss_pred cchhhhccccHHHHHHHHHHHHHHHHhcCCCCcEEEEecCCCHHHHHHHHh
Confidence 668999999887777777777777778889999999999999999988765
No 84
>TIGR00095 RNA methyltransferase, RsmD family. This model represents a family of uncharacterized bacterial proteins. Members are present in nearly every complete bacterial genome, always in a single copy. PSI-BLAST analysis shows homology to several families of SAM-dependent methyltransferases, including ribosomal RNA adenine dimethylases.
Probab=57.78 E-value=12 Score=38.33 Aligned_cols=37 Identities=14% Similarity=0.163 Sum_probs=25.3
Q ss_pred hhhHHH-HHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 685 VEKLKE-IVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 685 ~ekl~~-i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
.++++| +..-|.-+ .+|..|+|++||+..|.-+.-.+
T Consensus 33 ~~~vrea~f~~l~~~-~~g~~vLDLfaGsG~lglea~sr 70 (189)
T TIGR00095 33 TRVVRELFFNILRPE-IQGAHLLDVFAGSGLLGEEALSR 70 (189)
T ss_pred hHHHHHHHHHHHHHh-cCCCEEEEecCCCcHHHHHHHhC
Confidence 345554 44444333 46889999999999998776554
No 85
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=57.61 E-value=13 Score=45.55 Aligned_cols=69 Identities=23% Similarity=0.328 Sum_probs=36.7
Q ss_pred CchhHhhHHHHhhcccccccccccccc-----ccccCcccchhhhH-HHHHHhhcceeccCCeEEeeccCcchhhHHH
Q 003658 648 PPEILCQIFQWKRKLDVYLAPFLHGMR-----YTSFGRHFTKVEKL-KEIVDRLHWYVRSGDTIVDFCCGANDFSCMM 719 (805)
Q Consensus 648 ~p~~l~q~~~~~~~l~~~l~p~~~g~~-----y~s~~rhft~~ekl-~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~ 719 (805)
.|++.-.+..-++.+-+||- +.|.. |-.+..--.-.|.| ..|+..-.| ..+|+.+||..||+.+|..+-
T Consensus 134 ~pdv~i~~~~~~~~~~l~ld--~sg~~L~rRgyr~~~~~Apl~etlAaa~l~~a~w-~~~~~~l~DP~CGSGTilIEA 208 (702)
T PRK11783 134 QPDIRINARLNKGEATISLD--LSGESLHQRGYRQATGEAPLKENLAAAILLRSGW-PQEGTPLLDPMCGSGTLLIEA 208 (702)
T ss_pred CCCEEEEEEEeCCEEEEEEE--CCCCchhhccCccCCCCCCCcHHHHHHHHHHcCC-CCCCCeEEccCCCccHHHHHH
Confidence 45554444444555555554 23332 32222222223333 334433445 357899999999999998654
No 86
>PLN02672 methionine S-methyltransferase
Probab=56.63 E-value=17 Score=46.79 Aligned_cols=146 Identities=17% Similarity=0.181 Sum_probs=77.2
Q ss_pred hHHHHHHHHHHhhCCCChhhhhhcCCchhHhhHHHHhhc---------------cccccccccccccccccCccc-----
Q 003658 623 SVKAVRAALEMLDGGCDIEDAKAVCPPEILCQIFQWKRK---------------LDVYLAPFLHGMRYTSFGRHF----- 682 (805)
Q Consensus 623 sv~a~~~~l~~l~~g~~~~~aka~c~p~~l~q~~~~~~~---------------l~~~l~p~~~g~~y~s~~rhf----- 682 (805)
.-.|.|..|+.|++-.+--+|.+. |..|.+--.. =.++|.|.- |.+ -=+|+.|
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-G~~-~F~~l~~~V~p~ 94 (1082)
T PLN02672 22 AYGAFKGVLERLEDPTTRSDARKL-----LSAVEKRVAASEAGEDCFATYHFRIHDLVLDDYE-GFR-NRKKLTMMEIPS 94 (1082)
T ss_pred HHHHHHHHHHHhcCccccHHHHHH-----HHHHHHHhcccCcccchhhhcceEEeeEEEcCCC-CeE-EecCCceeeCCC
Confidence 457888889999988776666543 3333332211 124555543 332 1223333
Q ss_pred --chhhhHHHHHHhhcc---eeccCCeEEeeccCcchhhHHHHHHHHH---cCCccc-------ccCCCC-------C--
Q 003658 683 --TKVEKLKEIVDRLHW---YVRSGDTIVDFCCGANDFSCMMKVKLEQ---MGKSCS-------FRNYDL-------I-- 738 (805)
Q Consensus 683 --t~~ekl~~i~~~l~~---~~~~~d~~~d~~~g~~~~~~~~~~~~~~---~~~~~~-------~~n~d~-------~-- 738 (805)
-+-+-.+..|+.|.. ..-.|..|+|++||+...+-.+.++... ++-+.+ -+|-.. .
T Consensus 95 VLIPRpeTE~lve~L~~~~~~~~~~~~VLDlG~GSG~Iai~La~~~~~~~v~avDis~~Al~~A~~Na~~n~l~~~~~~~ 174 (1082)
T PLN02672 95 IFIPEDWSFTFYEGLNRHPDSIFRDKTVAELGCGNGWISIAIAEKWLPSKVYGLDINPRAVKVAWINLYLNALDDDGLPV 174 (1082)
T ss_pred cccCchhHHHHHHHHHhcccccCCCCEEEEEecchHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCcccccccc
Confidence 222344444444322 2223568999999999999888776421 111111 111111 0
Q ss_pred ------CCCCCCccccccccccCCCCCCCCCceeeecCCCcchhh
Q 003658 739 ------QPKNDFSFEKRDWMTVRPEELPDGSQLIMGLNPPFGVKA 777 (805)
Q Consensus 739 ------~~~~~~~f~~~~w~~~~~~~l~~g~~li~gl~ppfg~~~ 777 (805)
...+...|...||.+.-+. ....=-+|.+ |||+=..+
T Consensus 175 ~~~~~~~l~~rV~f~~sDl~~~~~~-~~~~fDlIVS-NPPYI~~~ 217 (1082)
T PLN02672 175 YDGEGKTLLDRVEFYESDLLGYCRD-NNIELDRIVG-CIPQILNP 217 (1082)
T ss_pred cccccccccccEEEEECchhhhccc-cCCceEEEEE-CCCcCCCc
Confidence 0124689999999864321 1001358888 99986544
No 87
>TIGR00080 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt.
Probab=55.40 E-value=15 Score=37.72 Aligned_cols=45 Identities=9% Similarity=0.290 Sum_probs=35.9
Q ss_pred cCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHH
Q 003658 678 FGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLE 724 (805)
Q Consensus 678 ~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~ 724 (805)
+|++++.+.-...+++.|. +++|+.|+|+.||+..++..|-+...
T Consensus 56 ~~~~~~~p~~~~~~~~~l~--~~~~~~VLDiG~GsG~~a~~la~~~~ 100 (215)
T TIGR00080 56 YGQTISAPHMVAMMTELLE--LKPGMKVLEIGTGSGYQAAVLAEIVG 100 (215)
T ss_pred CCCEechHHHHHHHHHHhC--CCCcCEEEEECCCccHHHHHHHHHhC
Confidence 3677777766667777664 78999999999999999988877643
No 88
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=55.03 E-value=14 Score=40.31 Aligned_cols=99 Identities=15% Similarity=0.272 Sum_probs=67.0
Q ss_pred cccCcccchhh-hHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHHH----------------cCCcccccCCCCC
Q 003658 676 TSFGRHFTKVE-KLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQ----------------MGKSCSFRNYDLI 738 (805)
Q Consensus 676 ~s~~rhft~~e-kl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~----------------~~~~~~~~n~d~~ 738 (805)
.+||.||..-. -+..||+... +++||+|++.=+|-...-..|-++... .-. .+.|+.+|
T Consensus 6 K~~GQnFL~d~~v~~kIv~~a~--~~~~d~VlEIGpG~GaLT~~Ll~~~~~v~aiEiD~~l~~~L~~~~~--~~~n~~vi 81 (259)
T COG0030 6 KRLGQNFLIDKNVIDKIVEAAN--ISPGDNVLEIGPGLGALTEPLLERAARVTAIEIDRRLAEVLKERFA--PYDNLTVI 81 (259)
T ss_pred CCcccccccCHHHHHHHHHhcC--CCCCCeEEEECCCCCHHHHHHHhhcCeEEEEEeCHHHHHHHHHhcc--cccceEEE
Confidence 58999998766 5678888764 566999999999999887766554222 111 45666666
Q ss_pred CCCCCCccccccccccCCCCCCCCCceeeecCCCcchhhhhHHHHhhhhhccCCc
Q 003658 739 QPKNDFSFEKRDWMTVRPEELPDGSQLIMGLNPPFGVKASLANKFISQALKFKPK 793 (805)
Q Consensus 739 ~~~~~~~f~~~~w~~~~~~~l~~g~~li~gl~ppfg~~~~~a~kf~~~~~~f~p~ 793 (805)
. .|-|.+...+|- +...|.| |.||++ +..++-|.++..+.
T Consensus 82 ~---------~DaLk~d~~~l~-~~~~vVa-NlPY~I----sspii~kll~~~~~ 121 (259)
T COG0030 82 N---------GDALKFDFPSLA-QPYKVVA-NLPYNI----SSPILFKLLEEKFI 121 (259)
T ss_pred e---------CchhcCcchhhc-CCCEEEE-cCCCcc----cHHHHHHHHhccCc
Confidence 5 344555555544 5568888 999995 45555555555544
No 89
>PRK14966 unknown domain/N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase fusion protein; Provisional
Probab=54.65 E-value=16 Score=42.47 Aligned_cols=36 Identities=8% Similarity=0.215 Sum_probs=25.8
Q ss_pred hHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 687 KLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 687 kl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
-++.+++.+.-.+.++..|+|++||+..++..+..+
T Consensus 237 eTE~LVe~aL~~l~~~~rVLDLGcGSG~IaiaLA~~ 272 (423)
T PRK14966 237 ETEHLVEAVLARLPENGRVWDLGTGSGAVAVTVALE 272 (423)
T ss_pred cHHHHHHHhhhccCCCCEEEEEeChhhHHHHHHHHh
Confidence 345555554444567889999999999998766543
No 90
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=53.22 E-value=5.6 Score=39.82 Aligned_cols=32 Identities=28% Similarity=0.587 Sum_probs=24.2
Q ss_pred eecCCcccccCcCCccccccccceeecccccccccc-ccCC
Q 003658 338 FTCPVHKCFVCQQSEDMNVEDLQLAICRRCPKAYHR-KCLP 377 (805)
Q Consensus 338 F~CPlH~C~~C~~~edk~~~~~qL~~C~RCPkAYH~-kCLP 377 (805)
|.=++|+|.+|+-.+ ...|..|...|+. .|+.
T Consensus 114 ~KP~r~fCaVCG~~S--------~ysC~~CG~kyCsv~C~~ 146 (156)
T KOG3362|consen 114 FKPLRKFCAVCGYDS--------KYSCVNCGTKYCSVRCLK 146 (156)
T ss_pred CCCcchhhhhcCCCc--------hhHHHhcCCceeechhhh
Confidence 343468999999543 4679999999998 5764
No 91
>PRK13944 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=51.00 E-value=19 Score=36.89 Aligned_cols=44 Identities=11% Similarity=0.203 Sum_probs=34.9
Q ss_pred cCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHH
Q 003658 678 FGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 678 ~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
+|++++.+.-+..+.+.|. +.+|+.|+|+-||+..++.+|.+.+
T Consensus 51 ~~~~~~~p~~~~~~~~~l~--~~~~~~VLDiG~GsG~~~~~la~~~ 94 (205)
T PRK13944 51 AGATISAPHMVAMMCELIE--PRPGMKILEVGTGSGYQAAVCAEAI 94 (205)
T ss_pred CCCEechHHHHHHHHHhcC--CCCCCEEEEECcCccHHHHHHHHhc
Confidence 5677777777777777664 5789999999999999988776654
No 92
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=50.50 E-value=8.6 Score=32.65 Aligned_cols=32 Identities=31% Similarity=0.822 Sum_probs=24.3
Q ss_pred ccccCcCCccccccccceeeccccccccccccCCC
Q 003658 344 KCFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPT 378 (805)
Q Consensus 344 ~C~~C~~~edk~~~~~qL~~C~RCPkAYH~kCLP~ 378 (805)
.|..|+..-. .+..+++|..|.+-||+.|-..
T Consensus 7 ~C~~Cg~~~~---~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 7 KCPVCGKKFK---DGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cChhhCCccc---CCCCEEECCCCCCcccHHHHhh
Confidence 4778887542 2347999999999999999643
No 93
>PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=48.79 E-value=19 Score=37.30 Aligned_cols=45 Identities=9% Similarity=0.338 Sum_probs=38.2
Q ss_pred ccCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHH
Q 003658 677 SFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 677 s~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
.+|++.+.|.-+..+++.|. +.+|++|+|+.||+..++.+|.+.+
T Consensus 54 ~~g~~~~~p~~~~~~~~~l~--~~~g~~VLdIG~GsG~~t~~la~~~ 98 (212)
T PRK13942 54 GYGQTISAIHMVAIMCELLD--LKEGMKVLEIGTGSGYHAAVVAEIV 98 (212)
T ss_pred CCCCEeCcHHHHHHHHHHcC--CCCcCEEEEECCcccHHHHHHHHhc
Confidence 46888899998888888885 6899999999999999988877654
No 94
>PF01555 N6_N4_Mtase: DNA methylase; InterPro: IPR002941 This domain is found in DNA methylases. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. This family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases. N-4 cytosine-specific DNA methylases (2.1.1.113 from EC) [] are enzymes that specifically methylate the amino group at the C-4 position of cytosines in DNA. Such enzymes are found as components of type II restriction-modification systems in prokaryotes. Such enzymes recognise a specific sequence in DNA and methylate a cytosine in that sequence. By this action they protect DNA from cleavage by type II restriction enzymes that recognise the same sequence. N-6 adenine-specific DNA methylases (2.1.1.72 from EC) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. Such enzymes are found in the three existing types of bacterial restriction-modification systems (in type I system the A-Mtase is the product of the hsdM gene, and in type III it is the product of the mod gene). All of these enzymes recognise a specific sequence in DNA and methylate an adenine in that sequence.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2ZIF_A 2ZIE_A 2ZIG_A 1NW6_A 1NW8_A 1NW7_A 1NW5_A 1EG2_A 1BOO_A 1G60_B ....
Probab=47.99 E-value=12 Score=37.35 Aligned_cols=49 Identities=24% Similarity=0.266 Sum_probs=25.0
Q ss_pred cccccccccccccC----cccc-hhhhHHHHHHhhcceeccCCeEEeeccCcchhh
Q 003658 666 LAPFLHGMRYTSFG----RHFT-KVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFS 716 (805)
Q Consensus 666 l~p~~~g~~y~s~~----rhft-~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~ 716 (805)
..+.+...++.+.| .|-| +|.+|.|-+ +.++-.+||+|+|+.+||.+=.
T Consensus 153 ~~~~~~~~~~~~~~~~~~~h~~~kP~~l~~~l--I~~~t~~gdiVlDpF~GSGTT~ 206 (231)
T PF01555_consen 153 PFSIIPPSRKNSKGNTKGKHPTQKPVELIERL--IKASTNPGDIVLDPFAGSGTTA 206 (231)
T ss_dssp E-SEEETTSTT--CHH----TT-S-HHHHHHH--HHHHS-TT-EEEETT-TTTHHH
T ss_pred ccccccccccccccccccceeecCCHHHHHHH--HHhhhccceeeehhhhccChHH
Confidence 34455666666553 4544 344433221 3467899999999999998744
No 95
>PF13489 Methyltransf_23: Methyltransferase domain; PDB: 3JWJ_A 3JWH_B 2AOV_B 2AOT_A 1JQD_B 2AOX_A 1JQE_A 2AOU_B 2AOW_A 3DLI_C ....
Probab=47.30 E-value=21 Score=33.61 Aligned_cols=36 Identities=19% Similarity=0.506 Sum_probs=29.8
Q ss_pred hHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 687 KLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 687 kl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
.+.+++.++..+..++..|+|+-||...|...|.+.
T Consensus 8 ~~~~~~~~~~~~~~~~~~vLDiGcG~G~~~~~l~~~ 43 (161)
T PF13489_consen 8 AYADLLERLLPRLKPGKRVLDIGCGTGSFLRALAKR 43 (161)
T ss_dssp CHHHHHHHHHTCTTTTSEEEEESSTTSHHHHHHHHT
T ss_pred HHHHHHHHHhcccCCCCEEEEEcCCCCHHHHHHHHh
Confidence 455677777777899999999999999999999554
No 96
>PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional
Probab=47.21 E-value=65 Score=36.24 Aligned_cols=21 Identities=24% Similarity=0.510 Sum_probs=18.4
Q ss_pred CCeEEeeccCcchhhHHHHHH
Q 003658 702 GDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 702 ~d~~~d~~~g~~~~~~~~~~~ 722 (805)
+..|+|+.||+..++..+.++
T Consensus 197 ~g~VLDlGCG~G~ls~~la~~ 217 (342)
T PRK09489 197 KGKVLDVGCGAGVLSAVLARH 217 (342)
T ss_pred CCeEEEeccCcCHHHHHHHHh
Confidence 457999999999999988776
No 97
>PRK14968 putative methyltransferase; Provisional
Probab=46.61 E-value=48 Score=32.38 Aligned_cols=38 Identities=11% Similarity=0.162 Sum_probs=26.2
Q ss_pred chhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 683 TKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 683 t~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
|+.+-..-+++.+. ..+|+.|+|+.||...+...+-++
T Consensus 7 ~p~~~~~~l~~~~~--~~~~~~vLd~G~G~G~~~~~l~~~ 44 (188)
T PRK14968 7 EPAEDSFLLAENAV--DKKGDRVLEVGTGSGIVAIVAAKN 44 (188)
T ss_pred CcchhHHHHHHhhh--ccCCCEEEEEccccCHHHHHHHhh
Confidence 33443444444443 278999999999999998877654
No 98
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=44.51 E-value=16 Score=31.54 Aligned_cols=32 Identities=31% Similarity=0.783 Sum_probs=24.9
Q ss_pred CCceeccccccc-CcccccccccCCCCCCCCCceeeccCCCcC
Q 003658 264 VPNFLCQNCVYQ-EHQCFACGMLGSSDKSSSQEVFPCVSATCG 305 (805)
Q Consensus 264 ~~~w~C~eC~~g-qh~CfiCgklGssd~~s~~eV~kCsv~~CG 305 (805)
...|.|++|-.- ...|..|.+++ ..++| +.||
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~~--------~~Y~C--P~CG 55 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQS--------NPYTC--PKCG 55 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhcC--------CceEC--CCCC
Confidence 468999999654 67899998764 56788 7777
No 99
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=44.20 E-value=5.9 Score=30.95 Aligned_cols=33 Identities=24% Similarity=0.609 Sum_probs=22.1
Q ss_pred ccccccccCCCCCCCCCceeeccCCCcCCCCccchhcccC
Q 003658 278 QCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLL 317 (805)
Q Consensus 278 ~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~ 317 (805)
.|.+|.+.-. .+..++.. .||+.||..|+..|+
T Consensus 2 ~C~IC~~~~~----~~~~~~~l---~C~H~fh~~Ci~~~~ 34 (44)
T PF13639_consen 2 ECPICLEEFE----DGEKVVKL---PCGHVFHRSCIKEWL 34 (44)
T ss_dssp CETTTTCBHH----TTSCEEEE---TTSEEEEHHHHHHHH
T ss_pred CCcCCChhhc----CCCeEEEc---cCCCeeCHHHHHHHH
Confidence 4677754321 13455544 499999999998875
No 100
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=43.59 E-value=28 Score=37.25 Aligned_cols=51 Identities=16% Similarity=0.362 Sum_probs=36.5
Q ss_pred cccccccc---------ccCcccchh---hhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHH
Q 003658 669 FLHGMRYT---------SFGRHFTKV---EKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (805)
Q Consensus 669 ~~~g~~y~---------s~~rhft~~---ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~ 721 (805)
||.-.+|| .||..|-.+ +-..+++++| .+.+|..|+|+.||...+...+-+
T Consensus 10 ~~~~~~y~~~~~~~~e~~~g~~~~~~gg~~~~~~~l~~l--~l~~~~~VLDiGcG~G~~a~~la~ 72 (263)
T PTZ00098 10 YLENNQYSDEGIKAYEFIFGEDYISSGGIEATTKILSDI--ELNENSKVLDIGSGLGGGCKYINE 72 (263)
T ss_pred hhhccccccccchhHHHHhCCCCCCCCchHHHHHHHHhC--CCCCCCEEEEEcCCCChhhHHHHh
Confidence 55555666 356555555 4567777775 578999999999999988776643
No 101
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=41.90 E-value=23 Score=38.64 Aligned_cols=27 Identities=30% Similarity=0.690 Sum_probs=22.4
Q ss_pred CCceeeccCCCcCC-CCccchhcccCCC
Q 003658 293 SQEVFPCVSATCGQ-FYHPECVSKLLHP 319 (805)
Q Consensus 293 ~~eV~kCsv~~CGr-fYHp~CL~~~~~p 319 (805)
-++|+.|-.++|.+ .||..||+.--.|
T Consensus 231 yGqMVaCDn~nCkrEWFH~~CVGLk~pP 258 (271)
T COG5034 231 YGQMVACDNANCKREWFHLECVGLKEPP 258 (271)
T ss_pred cccceecCCCCCchhheeccccccCCCC
Confidence 57999999999995 7899999865444
No 102
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=41.66 E-value=14 Score=43.01 Aligned_cols=29 Identities=21% Similarity=0.462 Sum_probs=18.5
Q ss_pred cccccccCCC----CceeecCccccccccccccc
Q 003658 216 FAVCAICDDG----GDVTFCDGRCLRSFHATITA 245 (805)
Q Consensus 216 d~vC~IC~~g----GeLL~CdG~C~RsFH~~Cl~ 245 (805)
-+.|.+|-.- -..|.=- .|.-+||..|+.
T Consensus 175 LPTCpVCLERMD~s~~gi~t~-~c~Hsfh~~cl~ 207 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTI-LCNHSFHCSCLM 207 (493)
T ss_pred CCCcchhHhhcCccccceeee-ecccccchHHHh
Confidence 5779999531 1122222 588999999864
No 103
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=41.22 E-value=17 Score=36.66 Aligned_cols=26 Identities=15% Similarity=0.396 Sum_probs=18.7
Q ss_pred cccccccCccccccccCCcccccCCCCceeccccccc
Q 003658 239 FHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQ 275 (805)
Q Consensus 239 FH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~g 275 (805)
||+.|+.+ .|+.. |.+.|+|+.|..+
T Consensus 2 ~H~~CL~P--------pl~~~---P~g~W~Cp~C~~~ 27 (148)
T cd04718 2 FHLCCLRP--------PLKEV---PEGDWICPFCEVE 27 (148)
T ss_pred cccccCCC--------CCCCC---CCCCcCCCCCcCC
Confidence 89997643 44433 5799999999853
No 104
>PF01209 Ubie_methyltran: ubiE/COQ5 methyltransferase family; InterPro: IPR004033 A number of methyltransferases have been shown to share regions of similarities []. Apart from the ubiquinone/menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the ubiE gene of Escherichia coli), the ubiquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the COQ5 gene of Saccharomyces cerevisiae) and the menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the MENH gene of Bacillus subtilis), this family also includes methyltransferases involved in biotin and sterol biosynthesis and in phosphatidylethanolamine methylation.; GO: 0008168 methyltransferase activity; PDB: 1VL5_C.
Probab=41.04 E-value=12 Score=39.67 Aligned_cols=44 Identities=27% Similarity=0.508 Sum_probs=19.9
Q ss_pred cccccCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 674 RYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 674 ~y~s~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
+--|||.|----.++.+++ -+.+|+.|+|+|||..+++..+-++
T Consensus 25 ~~ls~g~~~~wr~~~~~~~-----~~~~g~~vLDv~~GtG~~~~~l~~~ 68 (233)
T PF01209_consen 25 DLLSFGQDRRWRRKLIKLL-----GLRPGDRVLDVACGTGDVTRELARR 68 (233)
T ss_dssp ------------SHHHHHH-----T--S--EEEEET-TTSHHHHHHGGG
T ss_pred cccCCcHHHHHHHHHHhcc-----CCCCCCEEEEeCCChHHHHHHHHHH
Confidence 3358887754444555443 3689999999999999998877543
No 105
>PF01728 FtsJ: FtsJ-like methyltransferase; InterPro: IPR002877 RrmJ (FtsJ) is a well conserved heat shock protein present in prokaryotes, archaea, and eukaryotes. RrmJ is responsible for methylating 23 S rRNA at position U2552 in the aminoacyl (A)1-site of the ribosome []. U2552 is one of the five universally conserved A-loop residues and has been shown to be methylated at the ribose 2'-OH group in the majority of organisms investigated so far. This suggests that this modification plays an important role in the A-loop function. RrmJ recognises its methylation target only when the 23 S rRNA is present in 50 S ribosomal subunits. This suggests that the RrmJ-mediated methylation must occur late in the maturation process of the ribosome. This is in contrast to other known 23 S rRNA modifications that occur in earlier maturation steps. The 1.5 A crystal structure of RrmJ in complex with its cofactor S-adenosylmethionine revealed that RrmJ has a methyltransferase fold. The active site of RrmJ appears to be formed by a catalytic triad consisting of two lysine residues and the negatively charged aspartate residue. Another highly conserved glutamate residue that is present in the active site of RrmJ appears to play only a minor role in the methyltransfer reaction in vivo []. ; GO: 0003676 nucleic acid binding, 0008168 methyltransferase activity, 0032259 methylation; PDB: 3GCZ_A 2PLW_A 2NYU_A 2OXT_C 3EMD_A 3ELY_A 3ELW_A 3ELU_A 3ELD_A 3EMB_A ....
Probab=40.56 E-value=18 Score=35.94 Aligned_cols=38 Identities=21% Similarity=0.293 Sum_probs=31.1
Q ss_pred hhHHHHHHhhcceec-cCCeEEeeccCcchhhHHHHHHH
Q 003658 686 EKLKEIVDRLHWYVR-SGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 686 ekl~~i~~~l~~~~~-~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
.||.||.++..++-. .+.+|||+||+-..|+..+-+++
T Consensus 7 ~KL~ei~~~~~~~~~~~~~~vlDlG~aPGGws~~~~~~~ 45 (181)
T PF01728_consen 7 FKLYEIDEKFKIFKPGKGFTVLDLGAAPGGWSQVLLQRG 45 (181)
T ss_dssp HHHHHHHHTTSSS-TTTTEEEEEET-TTSHHHHHHHTST
T ss_pred HHHHHHHHHCCCCCcccccEEEEcCCcccceeeeeeecc
Confidence 499999999985533 45889999999999999998886
No 106
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=40.03 E-value=20 Score=42.64 Aligned_cols=52 Identities=21% Similarity=0.211 Sum_probs=37.8
Q ss_pred ccCCCcccccccCCCCceeecCcccccccccccccCccccccccCCcccccCCCCceeccccc
Q 003658 211 KDENYFAVCAICDDGGDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCV 273 (805)
Q Consensus 211 edd~~d~vC~IC~~gGeLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~ 273 (805)
...+.+.+|+-|.-+|..|.|+ .|.|+||-.|.-+.. ........|.|+.|.
T Consensus 55 ~~~N~d~~cfechlpg~vl~c~-vc~Rs~h~~c~sp~~----------q~r~~s~p~~~p~p~ 106 (588)
T KOG3612|consen 55 PSSNIDPFCFECHLPGAVLKCI-VCHRSFHENCQSPDP----------QKRNYSVPSDKPQPY 106 (588)
T ss_pred cccCCCcccccccCCcceeeee-hhhccccccccCcch----------hhccccccccCCccc
Confidence 4556789999999999999999 799999999753211 111124578787554
No 107
>PRK00312 pcm protein-L-isoaspartate O-methyltransferase; Reviewed
Probab=38.82 E-value=1e+02 Score=31.52 Aligned_cols=71 Identities=14% Similarity=0.243 Sum_probs=45.4
Q ss_pred CchhHhhHHHHhhcccccccccccccccc------ccCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHH
Q 003658 648 PPEILCQIFQWKRKLDVYLAPFLHGMRYT------SFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (805)
Q Consensus 648 ~p~~l~q~~~~~~~l~~~l~p~~~g~~y~------s~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~ 721 (805)
.|.++..+..+-+..- +++.+.-..|. .+|++.+.++-...+.+.|. +.+|+.|+|+.||+..++.+|.+
T Consensus 23 ~~~~~~a~~~~~r~~f--~p~~~~~~ay~d~~~~~~~~~~~~~p~~~~~l~~~l~--~~~~~~VLeiG~GsG~~t~~la~ 98 (212)
T PRK00312 23 DERVLEAIEATPRELF--VPEAFKHKAYENRALPIGCGQTISQPYMVARMTELLE--LKPGDRVLEIGTGSGYQAAVLAH 98 (212)
T ss_pred CHHHHHHHHcCCHhHc--CCchHHhcCccCCCccCCCCCeeCcHHHHHHHHHhcC--CCCCCEEEEECCCccHHHHHHHH
Confidence 4566666665544422 22222222232 45666778887666776664 57899999999999998887755
Q ss_pred H
Q 003658 722 K 722 (805)
Q Consensus 722 ~ 722 (805)
.
T Consensus 99 ~ 99 (212)
T PRK00312 99 L 99 (212)
T ss_pred H
Confidence 3
No 108
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=38.24 E-value=7.4 Score=34.20 Aligned_cols=17 Identities=35% Similarity=0.995 Sum_probs=14.8
Q ss_pred CCcCCCCccchhcccCC
Q 003658 302 ATCGQFYHPECVSKLLH 318 (805)
Q Consensus 302 ~~CGrfYHp~CL~~~~~ 318 (805)
..||+.||..|+..|+.
T Consensus 48 ~~C~H~FH~~Ci~~Wl~ 64 (73)
T PF12678_consen 48 GPCGHIFHFHCISQWLK 64 (73)
T ss_dssp ETTSEEEEHHHHHHHHT
T ss_pred cccCCCEEHHHHHHHHh
Confidence 56999999999998863
No 109
>COG2520 Predicted methyltransferase [General function prediction only]
Probab=38.06 E-value=8.7 Score=43.37 Aligned_cols=29 Identities=31% Similarity=0.531 Sum_probs=23.2
Q ss_pred hhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 694 RLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 694 ~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
|+--.+.+|++|+|+.+|-.-|+-.+-++
T Consensus 181 Rva~~v~~GE~V~DmFAGVGpfsi~~Ak~ 209 (341)
T COG2520 181 RVAELVKEGETVLDMFAGVGPFSIPIAKK 209 (341)
T ss_pred HHHhhhcCCCEEEEccCCcccchhhhhhc
Confidence 34456778999999999999998766555
No 110
>KOG2187 consensus tRNA uracil-5-methyltransferase and related tRNA-modifying enzymes [Translation, ribosomal structure and biogenesis]
Probab=37.48 E-value=61 Score=38.72 Aligned_cols=126 Identities=24% Similarity=0.406 Sum_probs=78.4
Q ss_pred cccccccccccccc-ccCcccchh----hhHHHHHHhhcceeccCC-eEEeeccCcchhhHHHHHHHHHcC---------
Q 003658 663 DVYLAPFLHGMRYT-SFGRHFTKV----EKLKEIVDRLHWYVRSGD-TIVDFCCGANDFSCMMKVKLEQMG--------- 727 (805)
Q Consensus 663 ~~~l~p~~~g~~y~-s~~rhft~~----ekl~~i~~~l~~~~~~~d-~~~d~~~g~~~~~~~~~~~~~~~~--------- 727 (805)
+.||-=-|.|-|++ |.|-.|-.- |+|-.+|.- |.-+++| +++|+|||+..|+--+-++-..+=
T Consensus 341 ~~~I~E~l~~ltF~iSp~AFFQ~Nt~~aevLys~i~e--~~~l~~~k~llDv~CGTG~iglala~~~~~ViGvEi~~~aV 418 (534)
T KOG2187|consen 341 DPYITESLLGLTFRISPGAFFQTNTSAAEVLYSTIGE--WAGLPADKTLLDVCCGTGTIGLALARGVKRVIGVEISPDAV 418 (534)
T ss_pred ccEEEeecCCeEEEECCchhhccCcHHHHHHHHHHHH--HhCCCCCcEEEEEeecCCceehhhhccccceeeeecChhhc
Confidence 56777777888887 888888643 344444432 4444544 589999999999977765532211
Q ss_pred ----C---cccccCCCCCCCCCCCccccccccccCCCCCCCCCceeeecCCCcchhhhhHHHHhhhhhccC-CcEEEEec
Q 003658 728 ----K---SCSFRNYDLIQPKNDFSFEKRDWMTVRPEELPDGSQLIMGLNPPFGVKASLANKFISQALKFK-PKLIVLIV 799 (805)
Q Consensus 728 ----~---~~~~~n~d~~~~~~~~~f~~~~w~~~~~~~l~~g~~li~gl~ppfg~~~~~a~kf~~~~~~f~-p~~~~li~ 799 (805)
+ .=.--|=+.|+-+ --|=|+.--+..-.+.+|++-+|||= +-+=.+||..-+.++ |+.|+.|+
T Consensus 419 ~dA~~nA~~NgisNa~Fi~gq------aE~~~~sl~~~~~~~~~~v~iiDPpR---~Glh~~~ik~l~~~~~~~rlvyvS 489 (534)
T KOG2187|consen 419 EDAEKNAQINGISNATFIVGQ------AEDLFPSLLTPCCDSETLVAIIDPPR---KGLHMKVIKALRAYKNPRRLVYVS 489 (534)
T ss_pred chhhhcchhcCccceeeeecc------hhhccchhcccCCCCCceEEEECCCc---ccccHHHHHHHHhccCccceEEEE
Confidence 1 1112244444431 01122222222223566899999984 558889999999999 99888775
No 111
>PF10237 N6-adenineMlase: Probable N6-adenine methyltransferase; InterPro: IPR019369 This family of proteins, which are of approximately 200 residues in length, contain a highly conserved Glu-Phe-Trp (QFW) motif close to the N terminus and an Asp/Asn-Pro-Pro-Tyr/Phe motif in the centre. This latter motif is characteristic of N-6 adenine-specific DNA methylases and could be involved in substrate binding or in the catalytic activity (, ).
Probab=36.75 E-value=28 Score=35.41 Aligned_cols=38 Identities=39% Similarity=0.680 Sum_probs=25.9
Q ss_pred HHcCCcccccCCCCCCCCCCCccccccccccCCCCCCCCCceeeecCCCcch
Q 003658 724 EQMGKSCSFRNYDLIQPKNDFSFEKRDWMTVRPEELPDGSQLIMGLNPPFGV 775 (805)
Q Consensus 724 ~~~~~~~~~~n~d~~~~~~~~~f~~~~w~~~~~~~l~~g~~li~gl~ppfg~ 775 (805)
..-|.. .|.-||.-.|.. =|.+| .|+..++-.||||-.
T Consensus 61 ~~~~~~-~F~fyD~~~p~~------------~~~~l-~~~~d~vv~DPPFl~ 98 (162)
T PF10237_consen 61 EQFGGD-EFVFYDYNEPEE------------LPEEL-KGKFDVVVIDPPFLS 98 (162)
T ss_pred HhcCCc-ceEECCCCChhh------------hhhhc-CCCceEEEECCCCCC
Confidence 334444 566788877652 24556 889999999999943
No 112
>PTZ00146 fibrillarin; Provisional
Probab=34.67 E-value=39 Score=37.55 Aligned_cols=58 Identities=16% Similarity=0.230 Sum_probs=40.0
Q ss_pred ccc--ccccccccccCccc--chhh---------hHH-HHHHhhc-ceeccCCeEEeeccCcchhhHHHHHHH
Q 003658 666 LAP--FLHGMRYTSFGRHF--TKVE---------KLK-EIVDRLH-WYVRSGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 666 l~p--~~~g~~y~s~~rhf--t~~e---------kl~-~i~~~l~-~~~~~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
|.| -+||.+..+++-.- ++.| ||- -|+.-|- .++.+|++|+|++||...|+..+-+..
T Consensus 82 ~~pg~~vygek~~~~~~~~~~~~~eyR~w~p~rSKlaa~i~~g~~~l~IkpG~~VLDLGaG~G~~t~~lAdiV 154 (293)
T PTZ00146 82 MVPGESVYGEKRISVEDAEGGEKIEYRVWNPFRSKLAAAIIGGVANIPIKPGSKVLYLGAASGTTVSHVSDLV 154 (293)
T ss_pred CCCCcccccceEEeeccCCCCCcceeeeeCCcccHHHHHHHCCcceeccCCCCEEEEeCCcCCHHHHHHHHHh
Confidence 455 56777776665222 2323 666 4544444 468999999999999999998888765
No 113
>KOG4217 consensus Nuclear receptors of the nerve growth factor-induced protein B type [Transcription]
Probab=34.46 E-value=13 Score=43.42 Aligned_cols=60 Identities=27% Similarity=0.619 Sum_probs=38.1
Q ss_pred cCCCcccccccCCCCc-----eeecCcccccccccccccCccccccccCCcccccCCCCceecccccc
Q 003658 212 DENYFAVCAICDDGGD-----VTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVY 274 (805)
Q Consensus 212 dd~~d~vC~IC~~gGe-----LL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~ 274 (805)
+...+..|++|++... .-.|+| |...|-.+...+....| |+-..-+++...+-.|..|++
T Consensus 265 ~~~~e~~CAVCgDnAaCqHYGvRTCEG-CKGFFKRTVQKnaKYvC--lanKnCPVDKRrRnRCQyCRf 329 (605)
T KOG4217|consen 265 SLSAEGLCAVCGDNAACQHYGVRTCEG-CKGFFKRTVQKNAKYVC--LANKNCPVDKRRRNRCQYCRF 329 (605)
T ss_pred CCCccceeeecCChHHhhhcCcccccc-chHHHHHHHhcCCeeEe--ecCCCCCcchhhhhhchhhhH
Confidence 4455889999998631 568997 99999888544444444 443333444444556666664
No 114
>TIGR00438 rrmJ cell division protein FtsJ.
Probab=34.28 E-value=46 Score=33.41 Aligned_cols=36 Identities=19% Similarity=0.455 Sum_probs=30.1
Q ss_pred hHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHH
Q 003658 687 KLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 687 kl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
+|.++.+++. .+++|+.|+|+.||...++..+-++.
T Consensus 19 ~~~~~~~~~~-~i~~g~~VLDiG~GtG~~~~~l~~~~ 54 (188)
T TIGR00438 19 KLLQLNQKFK-LIKPGDTVLDLGAAPGGWSQVAVEQV 54 (188)
T ss_pred HHHHHHHHhc-ccCCCCEEEEecCCCCHHHHHHHHHh
Confidence 7778777765 45789999999999999999887765
No 115
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=33.60 E-value=26 Score=30.46 Aligned_cols=32 Identities=34% Similarity=0.896 Sum_probs=25.4
Q ss_pred CCceeccccc-ccCcccccccccCCCCCCCCCceeeccCCCcC
Q 003658 264 VPNFLCQNCV-YQEHQCFACGMLGSSDKSSSQEVFPCVSATCG 305 (805)
Q Consensus 264 ~~~w~C~eC~-~gqh~CfiCgklGssd~~s~~eV~kCsv~~CG 305 (805)
...|.|++|- .-...|..|.++| ..++| ++||
T Consensus 25 ~v~F~CPnCGe~~I~Rc~~CRk~g--------~~Y~C--p~CG 57 (61)
T COG2888 25 AVKFPCPNCGEVEIYRCAKCRKLG--------NPYRC--PKCG 57 (61)
T ss_pred eeEeeCCCCCceeeehhhhHHHcC--------CceEC--CCcC
Confidence 4589999997 4567899998875 57888 7787
No 116
>PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed
Probab=33.19 E-value=50 Score=33.84 Aligned_cols=28 Identities=11% Similarity=0.178 Sum_probs=23.0
Q ss_pred hcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 695 LHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 695 l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
+-+|-+++..|+|+.||...++..+.++
T Consensus 34 ~~~~~~~~~~VLDiGcGtG~~~~~la~~ 61 (202)
T PRK00121 34 AELFGNDAPIHLEIGFGKGEFLVEMAKA 61 (202)
T ss_pred HHHcCCCCCeEEEEccCCCHHHHHHHHH
Confidence 4455668899999999999999988665
No 117
>PHA02929 N1R/p28-like protein; Provisional
Probab=33.02 E-value=31 Score=37.23 Aligned_cols=17 Identities=18% Similarity=0.544 Sum_probs=14.7
Q ss_pred CCCcCCCCccchhcccC
Q 003658 301 SATCGQFYHPECVSKLL 317 (805)
Q Consensus 301 v~~CGrfYHp~CL~~~~ 317 (805)
...||+.||..|+..|+
T Consensus 197 l~~C~H~FC~~CI~~Wl 213 (238)
T PHA02929 197 LSNCNHVFCIECIDIWK 213 (238)
T ss_pred cCCCCCcccHHHHHHHH
Confidence 36899999999998775
No 118
>TIGR02469 CbiT precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit. This model recognizes the CbiT methylase which is responsible, in part (along with CbiE), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiE subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL.
Probab=33.00 E-value=64 Score=29.01 Aligned_cols=35 Identities=20% Similarity=0.273 Sum_probs=25.6
Q ss_pred hhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 686 EKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 686 ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
+....+++.+ ++.+++.|+|+.||...+...+-++
T Consensus 6 ~~~~~~~~~~--~~~~~~~vldlG~G~G~~~~~l~~~ 40 (124)
T TIGR02469 6 EVRALTLSKL--RLRPGDVLWDIGAGSGSITIEAARL 40 (124)
T ss_pred HHHHHHHHHc--CCCCCCEEEEeCCCCCHHHHHHHHH
Confidence 3333444444 5678899999999999998887655
No 119
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=32.54 E-value=39 Score=24.87 Aligned_cols=29 Identities=28% Similarity=0.567 Sum_probs=22.9
Q ss_pred cccccCcCCccccccccc-eeeccccccccccccC
Q 003658 343 HKCFVCQQSEDMNVEDLQ-LAICRRCPKAYHRKCL 376 (805)
Q Consensus 343 H~C~~C~~~edk~~~~~q-L~~C~RCPkAYH~kCL 376 (805)
++|.+|.+..+. . +..|..|.-..|..|.
T Consensus 1 ~~C~~C~~~~~~-----~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 1 FWCDVCRRKIDG-----FYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCCcCC-----CEeEEeCCCCCeEcCccC
Confidence 468889775542 3 8999999999999884
No 120
>KOG1169 consensus Diacylglycerol kinase [Lipid transport and metabolism; Signal transduction mechanisms]
Probab=32.15 E-value=27 Score=42.48 Aligned_cols=138 Identities=22% Similarity=0.374 Sum_probs=78.1
Q ss_pred cccccCCCC--ceeecCcccccccccccccCccccccc---cCCccccc--------CC---CCceecccccccCccccc
Q 003658 218 VCAICDDGG--DVTFCDGRCLRSFHATITAGKNALCQS---LGYTQAQI--------DA---VPNFLCQNCVYQEHQCFA 281 (805)
Q Consensus 218 vC~IC~~gG--eLL~CdG~C~RsFH~~Cl~g~~s~C~s---Lglt~~ev--------~~---~~~w~C~eC~~gqh~Cfi 281 (805)
+|.+|...- .-+-|+ .|.-..|..|..+..+.|.. +|+...-. .+ ...-+|..|. ..|..
T Consensus 46 ~~~~~~~~~~~~~~~~~-~~g~~~~~~~~~~~~s~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~c~~c~---~~c~~ 121 (634)
T KOG1169|consen 46 VCCVCLWSEMAPSVDCD-VDGGVSHEECVSGAASDCPLLVLLGFENQRHKTDGDHVWRPKHLWKPAYCFVCP---KSCGS 121 (634)
T ss_pred hhhhhhhccccccccee-ccccchhhhhhcccccchHHHHHHHhhhhhhhccCceeccCCCCCCCceEEecc---ccccc
Confidence 999998732 267888 59999999998776665632 22211100 01 1233444444 35666
Q ss_pred ccccCCCCCCCCCceeeccCCCcCCCCccchhcccCCCCchhHHHHHHHHhh--cCCceecCCc-c--------cccCcC
Q 003658 282 CGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERIA--AGESFTCPVH-K--------CFVCQQ 350 (805)
Q Consensus 282 CgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~~p~~~~~~~eL~krV~--~g~~F~CPlH-~--------C~~C~~ 350 (805)
|+..+ ...+.| .-|++.-|..|+.....- +..... ..+...++.+ . |..|..
T Consensus 122 ~~~~~-------~~g~~C--~~C~~~vh~~C~~~~~~~--------~~~~~~~~~~r~~v~~~~~~~~~~~~~~~~~~~~ 184 (634)
T KOG1169|consen 122 CGVGI-------KQGLCC--DWCGRTVHERCVRRADPE--------CQCKCDLGRLRKIVLDHPWVKGNAGEAKCDQCLK 184 (634)
T ss_pred hhhcc-------cCceee--ccccchHHHHHHhhcCcc--------cccccccccccceeecCcccccccCCccchhhhc
Confidence 66543 346889 899999999999765311 000000 1122222221 1 223332
Q ss_pred CccccccccceeeccccccccccccCC
Q 003658 351 SEDMNVEDLQLAICRRCPKAYHRKCLP 377 (805)
Q Consensus 351 ~edk~~~~~qL~~C~RCPkAYH~kCLP 377 (805)
.-. .....+..+|..|..++|..|..
T Consensus 185 ~~~-~~~~~~~~~c~~~~~~~h~~~~~ 210 (634)
T KOG1169|consen 185 SVK-ADQGLTGPRCGWCQIRVHDKCKS 210 (634)
T ss_pred ccc-ccccccccccceeeeeeecchHH
Confidence 211 12344577999999999999975
No 121
>COG2890 HemK Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]
Probab=32.11 E-value=47 Score=36.28 Aligned_cols=84 Identities=15% Similarity=0.120 Sum_probs=42.7
Q ss_pred hHHHHHHhhcceeccCC-eEEeeccCcchhhHHHHHHHHH---cCCcccc-------cCCCCCCCCCCCccccccccccC
Q 003658 687 KLKEIVDRLHWYVRSGD-TIVDFCCGANDFSCMMKVKLEQ---MGKSCSF-------RNYDLIQPKNDFSFEKRDWMTVR 755 (805)
Q Consensus 687 kl~~i~~~l~~~~~~~d-~~~d~~~g~~~~~~~~~~~~~~---~~~~~~~-------~n~d~~~~~~~~~f~~~~w~~~~ 755 (805)
-++.+|+.+.-.+...+ +|+|+|||+.--.--+..+... ++-+.+- .|-....- .++.|-..||+.--
T Consensus 95 dTe~Lve~~l~~~~~~~~~ilDlGTGSG~iai~la~~~~~~~V~a~Dis~~Al~~A~~Na~~~~l-~~~~~~~~dlf~~~ 173 (280)
T COG2890 95 DTELLVEAALALLLQLDKRILDLGTGSGAIAIALAKEGPDAEVIAVDISPDALALARENAERNGL-VRVLVVQSDLFEPL 173 (280)
T ss_pred chHHHHHHHHHhhhhcCCcEEEecCChHHHHHHHHhhCcCCeEEEEECCHHHHHHHHHHHHHcCC-ccEEEEeeeccccc
Confidence 34445544322233333 7999999999888777766432 1111111 11111111 22445555887643
Q ss_pred CCCCCCCCceeeecCCCcchh
Q 003658 756 PEELPDGSQLIMGLNPPFGVK 776 (805)
Q Consensus 756 ~~~l~~g~~li~gl~ppfg~~ 776 (805)
++ .=.+|.. ||||=..
T Consensus 174 ~~----~fDlIVs-NPPYip~ 189 (280)
T COG2890 174 RG----KFDLIVS-NPPYIPA 189 (280)
T ss_pred CC----ceeEEEe-CCCCCCC
Confidence 33 3335555 9998544
No 122
>PRK07402 precorrin-6B methylase; Provisional
Probab=31.94 E-value=68 Score=32.38 Aligned_cols=41 Identities=17% Similarity=0.251 Sum_probs=32.2
Q ss_pred CcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHH
Q 003658 679 GRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (805)
Q Consensus 679 ~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~ 721 (805)
|.-.|+.+--.-+++.|. +.+|++|+|+.||+..+...+.+
T Consensus 20 ~~p~t~~~v~~~l~~~l~--~~~~~~VLDiG~G~G~~~~~la~ 60 (196)
T PRK07402 20 GIPLTKREVRLLLISQLR--LEPDSVLWDIGAGTGTIPVEAGL 60 (196)
T ss_pred CCCCCHHHHHHHHHHhcC--CCCCCEEEEeCCCCCHHHHHHHH
Confidence 434777777777777774 47899999999999999887753
No 123
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=31.50 E-value=18 Score=30.72 Aligned_cols=9 Identities=67% Similarity=1.789 Sum_probs=7.8
Q ss_pred EeeccCcch
Q 003658 706 VDFCCGAND 714 (805)
Q Consensus 706 ~d~~~g~~~ 714 (805)
+|||||.|.
T Consensus 24 IDfCCgG~~ 32 (56)
T PF04405_consen 24 IDFCCGGNR 32 (56)
T ss_pred CcccCCCCc
Confidence 899999974
No 124
>PRK15001 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional
Probab=31.39 E-value=42 Score=38.44 Aligned_cols=114 Identities=17% Similarity=0.194 Sum_probs=59.5
Q ss_pred ccccccCcccchh--h-hHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHH---HcCCccccc-------CCCCCC
Q 003658 673 MRYTSFGRHFTKV--E-KLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLE---QMGKSCSFR-------NYDLIQ 739 (805)
Q Consensus 673 ~~y~s~~rhft~~--e-kl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~---~~~~~~~~~-------n~d~~~ 739 (805)
..+++..--|..- + -.+=..+.|... .+..|+|+.||+...+..+.++.- =++-+-+.. |+..-.
T Consensus 199 ~~~~~~~gVFs~~~LD~GtrllL~~lp~~--~~~~VLDLGCGtGvi~i~la~~~P~~~V~~vD~S~~Av~~A~~N~~~n~ 276 (378)
T PRK15001 199 WTIHNHANVFSRTGLDIGARFFMQHLPEN--LEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDESPMAVASSRLNVETNM 276 (378)
T ss_pred EEEEecCCccCCCCcChHHHHHHHhCCcc--cCCeEEEEeccccHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcC
Confidence 3344555556532 2 122233334332 246899999999999988877631 112222221 221111
Q ss_pred CC--CCCccccccccccCCCCCCCCC-ceeeecCCCcchhh----hhHHHHhhhhhcc-CCc
Q 003658 740 PK--NDFSFEKRDWMTVRPEELPDGS-QLIMGLNPPFGVKA----SLANKFISQALKF-KPK 793 (805)
Q Consensus 740 ~~--~~~~f~~~~w~~~~~~~l~~g~-~li~gl~ppfg~~~----~~a~kf~~~~~~f-~p~ 793 (805)
+. ....|...|.++ .++.++ .+|+. ||||.... .+|.+|+..|... +|.
T Consensus 277 ~~~~~~v~~~~~D~l~----~~~~~~fDlIls-NPPfh~~~~~~~~ia~~l~~~a~~~LkpG 333 (378)
T PRK15001 277 PEALDRCEFMINNALS----GVEPFRFNAVLC-NPPFHQQHALTDNVAWEMFHHARRCLKIN 333 (378)
T ss_pred cccCceEEEEEccccc----cCCCCCEEEEEE-CcCcccCccCCHHHHHHHHHHHHHhcccC
Confidence 11 245666666553 233333 46665 99996542 5688888776532 443
No 125
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=31.33 E-value=31 Score=36.96 Aligned_cols=25 Identities=4% Similarity=0.100 Sum_probs=20.5
Q ss_pred eeccCCeEEeeccCcchhhHHHHHH
Q 003658 698 YVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 698 ~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
.+++|++|+|+|||...++..|-+.
T Consensus 68 ~~~~g~~VLDl~ag~G~kt~~la~~ 92 (264)
T TIGR00446 68 EPDPPERVLDMAAAPGGKTTQISAL 92 (264)
T ss_pred CCCCcCEEEEECCCchHHHHHHHHH
Confidence 4689999999999999888666444
No 126
>TIGR02752 MenG_heptapren 2-heptaprenyl-1,4-naphthoquinone methyltransferase. MenG is a generic term for a methyltransferase that catalyzes the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone methyltransferase, and are found together in operons with the two subunits of the heptaprenyl diphosphate synthase in Bacillus subtilis and related species.
Probab=31.19 E-value=42 Score=34.38 Aligned_cols=43 Identities=33% Similarity=0.648 Sum_probs=29.6
Q ss_pred cccCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHH
Q 003658 676 TSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 676 ~s~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
.|++++..-. ++++..+ .+.+|++|+|+.||...+...|.+..
T Consensus 25 ~~~~~~~~~~---~~~l~~l--~~~~~~~vLDiGcG~G~~~~~la~~~ 67 (231)
T TIGR02752 25 ISFQRHKKWR---KDTMKRM--NVQAGTSALDVCCGTADWSIALAEAV 67 (231)
T ss_pred hcCCchHHHH---HHHHHhc--CCCCCCEEEEeCCCcCHHHHHHHHHh
Confidence 4555544333 3344443 46789999999999999998887653
No 127
>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]
Probab=30.92 E-value=50 Score=36.56 Aligned_cols=34 Identities=26% Similarity=0.520 Sum_probs=29.8
Q ss_pred hHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 687 KLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 687 kl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
|++.|.++|+ |++|++++|+=||-...+..|-++
T Consensus 60 k~~~~~~kl~--L~~G~~lLDiGCGWG~l~~~aA~~ 93 (283)
T COG2230 60 KLDLILEKLG--LKPGMTLLDIGCGWGGLAIYAAEE 93 (283)
T ss_pred HHHHHHHhcC--CCCCCEEEEeCCChhHHHHHHHHH
Confidence 9999999998 899999999999988877766554
No 128
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=30.15 E-value=25 Score=41.46 Aligned_cols=71 Identities=14% Similarity=0.257 Sum_probs=40.0
Q ss_pred cCCeEEeeccCcchhhHHHHHHHH---HcCCcccc-------cCCCCCCCCCCCccccccccccCCCCCCCCC-ceeeec
Q 003658 701 SGDTIVDFCCGANDFSCMMKVKLE---QMGKSCSF-------RNYDLIQPKNDFSFEKRDWMTVRPEELPDGS-QLIMGL 769 (805)
Q Consensus 701 ~~d~~~d~~~g~~~~~~~~~~~~~---~~~~~~~~-------~n~d~~~~~~~~~f~~~~w~~~~~~~l~~g~-~li~gl 769 (805)
++..|+|++||+..+...+..++. -++-+.+- +|.....-.+...|...||++. ++.+. -+|+ .
T Consensus 138 ~~~~VLDlG~GsG~iai~la~~~p~~~v~avDis~~al~~A~~N~~~~~l~~~v~~~~~D~~~~----~~~~~fDlIv-s 212 (506)
T PRK01544 138 KFLNILELGTGSGCIAISLLCELPNANVIATDISLDAIEVAKSNAIKYEVTDRIQIIHSNWFEN----IEKQKFDFIV-S 212 (506)
T ss_pred CCCEEEEccCchhHHHHHHHHHCCCCeEEEEECCHHHHHHHHHHHHHcCCccceeeeecchhhh----CcCCCccEEE-E
Confidence 456899999999999987765431 11111111 1111011124567888888752 33333 3555 4
Q ss_pred CCCcchh
Q 003658 770 NPPFGVK 776 (805)
Q Consensus 770 ~ppfg~~ 776 (805)
||||-..
T Consensus 213 NPPYi~~ 219 (506)
T PRK01544 213 NPPYISH 219 (506)
T ss_pred CCCCCCc
Confidence 9998753
No 129
>cd00315 Cyt_C5_DNA_methylase Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Probab=30.14 E-value=1.2e+02 Score=32.90 Aligned_cols=82 Identities=21% Similarity=0.351 Sum_probs=51.9
Q ss_pred eEEeeccCcchhhHHHHHHHHHcCCcccc-------------cCCCCCCCCCCCccccccccccCCCCCCCCCceeeecC
Q 003658 704 TIVDFCCGANDFSCMMKVKLEQMGKSCSF-------------RNYDLIQPKNDFSFEKRDWMTVRPEELPDGSQLIMGLN 770 (805)
Q Consensus 704 ~~~d~~~g~~~~~~~~~~~~~~~~~~~~~-------------~n~d~~~~~~~~~f~~~~w~~~~~~~l~~g~~li~gl~ 770 (805)
+++|++||...++.-++. .|-.+-+ +||. +. +...|.-++.+.+++..-.+|+| .
T Consensus 2 ~v~dLFsG~Gg~~~gl~~----~G~~~v~a~e~~~~a~~~~~~N~~-----~~--~~~~Di~~~~~~~~~~~~D~l~~-g 69 (275)
T cd00315 2 RVIDLFAGIGGFRLGLEK----AGFEIVAANEIDKSAAETYEANFP-----NK--LIEGDITKIDEKDFIPDIDLLTG-G 69 (275)
T ss_pred cEEEEccCcchHHHHHHH----cCCEEEEEEeCCHHHHHHHHHhCC-----CC--CccCccccCchhhcCCCCCEEEe-C
Confidence 589999999999877754 3433322 2331 11 33456666677664333446666 4
Q ss_pred CC---c----------chhhhhHHHHhhhhhccCCcEEEE
Q 003658 771 PP---F----------GVKASLANKFISQALKFKPKLIVL 797 (805)
Q Consensus 771 pp---f----------g~~~~~a~kf~~~~~~f~p~~~~l 797 (805)
|| | +.++.|...|++-+-.++|+++++
T Consensus 70 pPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~P~~~v~ 109 (275)
T cd00315 70 FPCQPFSIAGKRKGFEDTRGTLFFEIIRILKEKKPKYFLL 109 (275)
T ss_pred CCChhhhHHhhcCCCCCchHHHHHHHHHHHHhcCCCEEEE
Confidence 43 3 235557778999999999998876
No 130
>TIGR00406 prmA ribosomal protein L11 methyltransferase. Ribosomal protein L11 methyltransferase is an S-adenosyl-L-methionine-dependent methyltransferase required for the modification of ribosomal protein L11. This protein is found in bacteria and (with a probable transit peptide) in Arabidopsis.
Probab=30.10 E-value=55 Score=35.53 Aligned_cols=39 Identities=23% Similarity=0.226 Sum_probs=27.3
Q ss_pred CcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHH
Q 003658 679 GRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (805)
Q Consensus 679 ~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~ 721 (805)
|.|-|..-.|+ -|..++.+|++|+|+.||+..++..+.+
T Consensus 141 G~h~tt~l~l~----~l~~~~~~g~~VLDvGcGsG~lai~aa~ 179 (288)
T TIGR00406 141 GTHPTTSLCLE----WLEDLDLKDKNVIDVGCGSGILSIAALK 179 (288)
T ss_pred CCCHHHHHHHH----HHHhhcCCCCEEEEeCCChhHHHHHHHH
Confidence 46666544333 3444678999999999999988866653
No 131
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=29.70 E-value=42 Score=37.24 Aligned_cols=35 Identities=29% Similarity=0.368 Sum_probs=30.3
Q ss_pred hHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHH
Q 003658 687 KLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 687 kl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
-|.|+++.|. +++|+++||..||...++..+-+++
T Consensus 7 ll~Evl~~L~--~~pg~~vlD~TlG~GGhS~~il~~~ 41 (296)
T PRK00050 7 LLDEVVDALA--IKPDGIYVDGTFGGGGHSRAILERL 41 (296)
T ss_pred cHHHHHHhhC--CCCCCEEEEeCcCChHHHHHHHHhC
Confidence 5788998886 5799999999999999999887664
No 132
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=29.27 E-value=19 Score=27.88 Aligned_cols=17 Identities=35% Similarity=0.870 Sum_probs=13.1
Q ss_pred ceeeccccccccccccC
Q 003658 360 QLAICRRCPKAYHRKCL 376 (805)
Q Consensus 360 qL~~C~RCPkAYH~kCL 376 (805)
+|+.|.+|..+.|..|-
T Consensus 3 ~ll~C~~C~v~VH~~CY 19 (36)
T PF13831_consen 3 PLLFCDNCNVAVHQSCY 19 (36)
T ss_dssp EEEE-SSS--EEEHHHH
T ss_pred ceEEeCCCCCcCChhhC
Confidence 79999999999999996
No 133
>PRK13699 putative methylase; Provisional
Probab=28.68 E-value=37 Score=35.93 Aligned_cols=22 Identities=9% Similarity=0.224 Sum_probs=17.9
Q ss_pred cceeccCCeEEeeccCcchhhH
Q 003658 696 HWYVRSGDTIVDFCCGANDFSC 717 (805)
Q Consensus 696 ~~~~~~~d~~~d~~~g~~~~~~ 717 (805)
.-|-++||+|+|+.|||.+.--
T Consensus 158 ~~~s~~g~~vlDpf~Gsgtt~~ 179 (227)
T PRK13699 158 ESFTHPNAIVLDPFAGSGSTCV 179 (227)
T ss_pred HHhCCCCCEEEeCCCCCCHHHH
Confidence 3567899999999999987543
No 134
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=28.31 E-value=25 Score=32.40 Aligned_cols=17 Identities=29% Similarity=0.755 Sum_probs=14.9
Q ss_pred CCcCCCCccchhcccCC
Q 003658 302 ATCGQFYHPECVSKLLH 318 (805)
Q Consensus 302 ~~CGrfYHp~CL~~~~~ 318 (805)
..|++.||..|+.+++.
T Consensus 50 g~C~H~FH~hCI~kWl~ 66 (85)
T PF12861_consen 50 GKCSHNFHMHCILKWLS 66 (85)
T ss_pred ccCccHHHHHHHHHHHc
Confidence 46999999999999874
No 135
>PRK08287 cobalt-precorrin-6Y C(15)-methyltransferase; Validated
Probab=28.21 E-value=93 Score=31.12 Aligned_cols=42 Identities=17% Similarity=0.223 Sum_probs=33.0
Q ss_pred CcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 679 GRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 679 ~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
.+..|+.+--..+++.|. +.+|++|+|+.||+..+...+.++
T Consensus 11 ~~~~~~~~~r~~~~~~l~--~~~~~~vLDiG~G~G~~~~~la~~ 52 (187)
T PRK08287 11 KVPMTKEEVRALALSKLE--LHRAKHLIDVGAGTGSVSIEAALQ 52 (187)
T ss_pred CCCCchHHHHHHHHHhcC--CCCCCEEEEECCcCCHHHHHHHHH
Confidence 466787776666777775 458999999999999998877654
No 136
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.68 E-value=33 Score=39.01 Aligned_cols=29 Identities=31% Similarity=0.542 Sum_probs=21.7
Q ss_pred ccccccCCC---CceeecCcccccccccccccC
Q 003658 217 AVCAICDDG---GDVTFCDGRCLRSFHATITAG 246 (805)
Q Consensus 217 ~vC~IC~~g---GeLL~CdG~C~RsFH~~Cl~g 246 (805)
+.|+||-+. |+.|.== +|.-.||..|.+.
T Consensus 230 ~~CaIClEdY~~GdklRiL-PC~H~FH~~CIDp 261 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRIL-PCSHKFHVNCIDP 261 (348)
T ss_pred ceEEEeecccccCCeeeEe-cCCCchhhccchh
Confidence 799999764 6644443 7889999998654
No 137
>PF05413 Peptidase_C34: Putative closterovirus papain-like endopeptidase; InterPro: IPR008744 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This signature is found in the RNA-direct RNA polymerase of apple chlorotic leaf spot virus and cherry mottle virus.; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0005524 ATP binding, 0019079 viral genome replication
Probab=27.56 E-value=23 Score=32.41 Aligned_cols=15 Identities=47% Similarity=1.088 Sum_probs=13.2
Q ss_pred hCCCChhhhhhcCCc
Q 003658 635 DGGCDIEDAKAVCPP 649 (805)
Q Consensus 635 ~~g~~~~~aka~c~p 649 (805)
..|||++||||+|+.
T Consensus 41 NkGCsidD~k~iC~~ 55 (92)
T PF05413_consen 41 NKGCSIDDLKAICEK 55 (92)
T ss_pred cCCCCHHHHHHHHhh
Confidence 379999999999974
No 138
>PRK11524 putative methyltransferase; Provisional
Probab=27.24 E-value=49 Score=35.86 Aligned_cols=34 Identities=24% Similarity=0.318 Sum_probs=23.2
Q ss_pred cccchhhhHHHHHHhh-cceeccCCeEEeeccCcchh
Q 003658 680 RHFTKVEKLKEIVDRL-HWYVRSGDTIVDFCCGANDF 715 (805)
Q Consensus 680 rhft~~ekl~~i~~~l-~~~~~~~d~~~d~~~g~~~~ 715 (805)
.|-| +|=+++++++ ..+=++||+|+|+++||.+=
T Consensus 188 ~HPt--~kP~~L~erlI~~~S~~GD~VLDPF~GSGTT 222 (284)
T PRK11524 188 NHPT--QKPEALLKRIILASSNPGDIVLDPFAGSFTT 222 (284)
T ss_pred cCcc--cChHHHHHHHHHHhCCCCCEEEECCCCCcHH
Confidence 3655 3444445552 34559999999999999863
No 139
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=27.07 E-value=27 Score=39.61 Aligned_cols=28 Identities=29% Similarity=0.761 Sum_probs=22.0
Q ss_pred CcccccccCCC--C---ceeecCccccccccccc
Q 003658 215 YFAVCAICDDG--G---DVTFCDGRCLRSFHATI 243 (805)
Q Consensus 215 ~d~vC~IC~~g--G---eLL~CdG~C~RsFH~~C 243 (805)
.+..|.+|++- | -||.|+ +|...|..+-
T Consensus 14 l~ElCPVCGDkVSGYHYGLLTCE-SCKGFFKRTV 46 (475)
T KOG4218|consen 14 LGELCPVCGDKVSGYHYGLLTCE-SCKGFFKRTV 46 (475)
T ss_pred cccccccccCccccceeeeeehh-hhhhHHHHHh
Confidence 35789999974 3 399999 7999887764
No 140
>KOG3285 consensus Spindle assembly checkpoint protein [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=27.04 E-value=55 Score=34.20 Aligned_cols=47 Identities=30% Similarity=0.367 Sum_probs=34.7
Q ss_pred eecCCCCeeEeEee---------eeeecccc-cCCCCcceEEEecccCCCccceeeeE
Q 003658 20 FLDQNEESISFSVL---------PLQWDGCD-IVGSSEMQVFLHGNIGDGPWNFNEQV 67 (805)
Q Consensus 20 f~d~~~~~v~fs~l---------p~~~~~~~-~~~~~~~~v~l~g~~d~gl~~v~~~v 67 (805)
|.--=+++.+|.+| |..|.+|. .+-.+...|.||++. .++.+|--+|
T Consensus 141 fLP~Le~~ctFdvLiyTdkD~~vP~~W~eS~~~~I~n~e~VqlrsFs-T~~HKVdt~V 197 (203)
T KOG3285|consen 141 FLPLLEEICTFDVLIYTDKDTEVPEKWDESGPKLIQNPEAVQLRSFS-TSIHKVDTQV 197 (203)
T ss_pred ecccccceeEEEEEEEeCCCccCCcchhcCCCeEecChhhEEEeecc-ccceeecceE
Confidence 44445667777765 99999987 446677789999998 7777776554
No 141
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=26.93 E-value=31 Score=30.22 Aligned_cols=33 Identities=24% Similarity=0.593 Sum_probs=12.2
Q ss_pred ccccCcCCccccccccceeecc--ccccccccccCC
Q 003658 344 KCFVCQQSEDMNVEDLQLAICR--RCPKAYHRKCLP 377 (805)
Q Consensus 344 ~C~~C~~~edk~~~~~qL~~C~--RCPkAYH~kCLP 377 (805)
.|..|...... +.+...+.|. +|...||..||-
T Consensus 4 ~C~IC~~~~~~-~~~~p~~~C~n~~C~~~fH~~CL~ 38 (70)
T PF11793_consen 4 ECGICYSYRLD-DGEIPDVVCPNPSCGKKFHLLCLS 38 (70)
T ss_dssp S-SSS--SS-T-T-----B--S-TT----B-SGGGH
T ss_pred CCCcCCcEecC-CCCcCceEcCCcccCCHHHHHHHH
Confidence 47788875431 2234567897 999999999993
No 142
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=26.48 E-value=37 Score=39.74 Aligned_cols=35 Identities=23% Similarity=0.476 Sum_probs=22.4
Q ss_pred ccccccccCCCCCCCCCceeeccCCCcCCCCccchhcccCC
Q 003658 278 QCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLH 318 (805)
Q Consensus 278 ~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~~ 318 (805)
.|-+|-+.-.+ +. ..++ ...|.+.||-.|+..|..
T Consensus 177 TCpVCLERMD~--s~-~gi~---t~~c~Hsfh~~cl~~w~~ 211 (493)
T KOG0804|consen 177 TCPVCLERMDS--ST-TGIL---TILCNHSFHCSCLMKWWD 211 (493)
T ss_pred CcchhHhhcCc--cc-ccee---eeecccccchHHHhhccc
Confidence 46677554322 22 2333 257999999999998863
No 143
>COG1041 Predicted DNA modification methylase [DNA replication, recombination, and repair]
Probab=26.44 E-value=1.3e+02 Score=34.40 Aligned_cols=91 Identities=22% Similarity=0.442 Sum_probs=51.9
Q ss_pred eccCCeEEeeccCcchhhHHH-------------HHHHHHcCCcccccCCCCCCCCCCCcccccccccc-CCCCCCCCCc
Q 003658 699 VRSGDTIVDFCCGANDFSCMM-------------KVKLEQMGKSCSFRNYDLIQPKNDFSFEKRDWMTV-RPEELPDGSQ 764 (805)
Q Consensus 699 ~~~~d~~~d~~~g~~~~~~~~-------------~~~~~~~~~~~~~~n~d~~~~~~~~~f~~~~w~~~-~~~~l~~g~~ 764 (805)
|.+|+.|+|..||...|.-.- .++++. ..-+++-|- + .+|.| +++ +.+.||=.++
T Consensus 195 v~~G~~vlDPFcGTGgiLiEagl~G~~viG~Did~~mv~g--ak~Nl~~y~-i---~~~~~-----~~~~Da~~lpl~~~ 263 (347)
T COG1041 195 VKRGELVLDPFCGTGGILIEAGLMGARVIGSDIDERMVRG--AKINLEYYG-I---EDYPV-----LKVLDATNLPLRDN 263 (347)
T ss_pred cccCCEeecCcCCccHHHHhhhhcCceEeecchHHHHHhh--hhhhhhhhC-c---CceeE-----EEecccccCCCCCC
Confidence 789999999999999985332 222222 122222221 1 11111 344 5555554443
Q ss_pred --eeeecCCCcchhh--------hhHHHHhhhhhccC-C-cEEEEecC
Q 003658 765 --LIMGLNPPFGVKA--------SLANKFISQALKFK-P-KLIVLIVP 800 (805)
Q Consensus 765 --li~gl~ppfg~~~--------~~a~kf~~~~~~f~-p-~~~~li~p 800 (805)
=-+--+||+|..+ .|-.+|++.|.+-= + -.+++.+|
T Consensus 264 ~vdaIatDPPYGrst~~~~~~l~~Ly~~~le~~~evLk~gG~~vf~~p 311 (347)
T COG1041 264 SVDAIATDPPYGRSTKIKGEGLDELYEEALESASEVLKPGGRIVFAAP 311 (347)
T ss_pred ccceEEecCCCCcccccccccHHHHHHHHHHHHHHHhhcCcEEEEecC
Confidence 2345599999988 45566677666543 3 24666666
No 144
>TIGR01712 phage_N6A_met phage N-6-adenine-methyltransferase. This is a model for a phage-borne DNA N-6-adenine-methyltransferase.
Probab=26.30 E-value=51 Score=33.91 Aligned_cols=34 Identities=21% Similarity=0.490 Sum_probs=23.6
Q ss_pred eeecCCCcchhhhhHHHHhhhhhcc---CCcEEEEecCCCC
Q 003658 766 IMGLNPPFGVKASLANKFISQALKF---KPKLIVLIVPQET 803 (805)
Q Consensus 766 i~gl~ppfg~~~~~a~kf~~~~~~f---~p~~~~li~p~~~ 803 (805)
-+=+||||+ -+..||.||.++ +=..+|..+|..|
T Consensus 64 ~vf~NPPYS----~~~~~v~kaae~~~~~g~~~VmLlpa~t 100 (166)
T TIGR01712 64 AVWLNPPYS----RPDIFVNKTAWFTEARQAAEVILIEADL 100 (166)
T ss_pred eEEecCCCC----cHHHHHHHHHHHHHhhCCeEEEEEecCC
Confidence 344699998 347999999765 1135677777665
No 145
>PF05869 Dam: DNA N-6-adenine-methyltransferase (Dam); InterPro: IPR008593 This family consists of several bacterial and phage DNA N-6-adenine-methyltransferase (Dam) like sequences [].; GO: 0003677 DNA binding, 0009007 site-specific DNA-methyltransferase (adenine-specific) activity, 0032775 DNA methylation on adenine
Probab=26.25 E-value=66 Score=33.29 Aligned_cols=87 Identities=20% Similarity=0.372 Sum_probs=47.4
Q ss_pred ccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHHHHcCCcccccCCCCCCCCCCCccccccccccCCCCCC
Q 003658 681 HFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQMGKSCSFRNYDLIQPKNDFSFEKRDWMTVRPEELP 760 (805)
Q Consensus 681 hft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~~~~~~~~~n~d~~~~~~~~~f~~~~w~~~~~~~l~ 760 (805)
--|+++-+..+-..+++| -+|.|+...+ . .|. +-|. ...|. =..||-..-.
T Consensus 14 W~TP~~lf~~l~~~fg~f------~LD~aa~~~N-a------------~~~-~y~T--~~~Dg---L~~~W~~~~~---- 64 (181)
T PF05869_consen 14 WQTPPELFDALNREFGPF------DLDPAASDEN-A------------KCP-RYYT--EEDDG---LAQDWSAELM---- 64 (181)
T ss_pred CcCCHHHHHHHHHHhCCc------cccccCCCCC-h------------hhh-hhcC--ccccH---hhhhhhhccc----
Confidence 357888788888888874 4788875432 1 121 1111 11222 3445643211
Q ss_pred CCCceeeecCCCcchhhhhHHHHhhhhhccC---CcEEEEecCCCC
Q 003658 761 DGSQLIMGLNPPFGVKASLANKFISQALKFK---PKLIVLIVPQET 803 (805)
Q Consensus 761 ~g~~li~gl~ppfg~~~~~a~kf~~~~~~f~---p~~~~li~p~~~ 803 (805)
| -| =+||||+.. ...||.||.+-. =..++|+.|..+
T Consensus 65 -g--~v-f~NPPYs~~---i~~wv~Ka~~e~~~g~~~VvLL~~~~~ 103 (181)
T PF05869_consen 65 -G--RV-FCNPPYSRG---IGPWVEKAIEEYERGNQTVVLLPPADT 103 (181)
T ss_pred -c--eE-EecCchhhh---HHHHHHHHHHHHHhCCcEEEEEeccCC
Confidence 2 23 359999952 667777776532 134667766544
No 146
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=26.06 E-value=54 Score=26.40 Aligned_cols=34 Identities=29% Similarity=0.390 Sum_probs=24.3
Q ss_pred cccccCcCCccccccccceeeccccccccccccCCC
Q 003658 343 HKCFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPT 378 (805)
Q Consensus 343 H~C~~C~~~edk~~~~~qL~~C~RCPkAYH~kCLP~ 378 (805)
-+|..|+..=-. ...+-++|..|...+|.+|++.
T Consensus 12 ~~C~~C~~~i~g--~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 12 TYCDVCGKFIWG--LGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp EB-TTSSSBECS--SSSCEEEETTTT-EEETTGGCT
T ss_pred CCCcccCcccCC--CCCCeEEECCCCChHhhhhhhh
Confidence 368888885311 2357889999999999999865
No 147
>PF14881 Tubulin_3: Tubulin domain
Probab=25.99 E-value=44 Score=34.36 Aligned_cols=47 Identities=19% Similarity=0.383 Sum_probs=39.5
Q ss_pred cccchhhhHHHHHHh-hcceeccCCe------EEeeccCcchhhHHHHHHHHHc
Q 003658 680 RHFTKVEKLKEIVDR-LHWYVRSGDT------IVDFCCGANDFSCMMKVKLEQM 726 (805)
Q Consensus 680 rhft~~ekl~~i~~~-l~~~~~~~d~------~~d~~~g~~~~~~~~~~~~~~~ 726 (805)
..|...++..++.|+ ||+||++=|. |+|...|-..|.--|-+.|.+.
T Consensus 48 ~~f~~~~~~~d~~D~~lR~f~EECD~lQGfQ~~~d~d~gwgGfas~~Le~L~DE 101 (180)
T PF14881_consen 48 ELFKSLDYEEDFFDRDLRFFLEECDSLQGFQVLTDVDDGWGGFASSLLEHLRDE 101 (180)
T ss_pred HHHhhhhhhhHHHHHHHHHHHHHcccccceEEEecCCCchHhHHHHHHHHHHHH
Confidence 357777788999997 9999999998 7999999999988887887763
No 148
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=25.26 E-value=35 Score=37.46 Aligned_cols=59 Identities=31% Similarity=0.628 Sum_probs=36.3
Q ss_pred CCCcccccccCC-----CCceeecCcccccccccccccCc---cccccccCCcccccCCCCceecccccc-cCccccccc
Q 003658 213 ENYFAVCAICDD-----GGDVTFCDGRCLRSFHATITAGK---NALCQSLGYTQAQIDAVPNFLCQNCVY-QEHQCFACG 283 (805)
Q Consensus 213 d~~d~vC~IC~~-----gGeLL~CdG~C~RsFH~~Cl~g~---~s~C~sLglt~~ev~~~~~w~C~eC~~-gqh~CfiCg 283 (805)
.+.+.+|.-|+. ||.+..|. -|.... |.+.. +..|+-| ..++|.|..|.. ||+.|..|+
T Consensus 122 pl~da~C~EC~R~vw~hGGrif~Cs-fC~~fl---CEDDQFEHQAsCQvL--------e~E~~KC~SCNrlGq~sCLRCK 189 (314)
T PF06524_consen 122 PLQDAVCIECERGVWDHGGRIFKCS-FCDNFL---CEDDQFEHQASCQVL--------ESETFKCQSCNRLGQYSCLRCK 189 (314)
T ss_pred cCCCcEeeeeecccccCCCeEEEee-cCCCee---eccchhhhhhhhhhh--------hcccccccccccccchhhhhee
Confidence 566888999975 58888888 566433 22210 0123211 246788888854 777777775
No 149
>TIGR00762 DegV EDD domain protein, DegV family. This family of proteins is related to DegV of Bacillus subtilis and includes paralogous sets in several species (B. subtilis, Deinococcus radiodurans, Mycoplasma pneumoniae) that are closer in percent identity to each than to most homologs from other species. This suggests both recent paralogy and diversity of function. DegV itself is encoded immediately downstream of DegU, a transcriptional regulator of degradation, but is itself uncharacterized. Crystallography suggested a lipid-binding site, while comparison of the crystal structure to dihydroxyacetone kinase and to a mannose transporter EIIA domain suggests a conserved domain, EDD, with phosphotransferase activity.
Probab=24.99 E-value=2.7e+02 Score=30.04 Aligned_cols=94 Identities=17% Similarity=0.294 Sum_probs=59.0
Q ss_pred HHHHHHHHHHhhCCCChhhhhhcCCchhHhhHHHHhhccccc---------------------------cccccc--ccc
Q 003658 624 VKAVRAALEMLDGGCDIEDAKAVCPPEILCQIFQWKRKLDVY---------------------------LAPFLH--GMR 674 (805)
Q Consensus 624 v~a~~~~l~~l~~g~~~~~aka~c~p~~l~q~~~~~~~l~~~---------------------------l~p~~~--g~~ 674 (805)
-..|..|.+|+++|.+++|+ +.+|..++++-.+| |-|+|. .-.
T Consensus 122 g~~v~~a~~~~~~G~s~~eI--------~~~l~~~~~~~~~~f~v~~L~~L~~gGRis~~~~~~g~lL~ikPIi~~~~G~ 193 (275)
T TIGR00762 122 GLLVLEAAKLAEEGKSLEEI--------LAKLEELRERTKLYFVVDTLEYLVKGGRISKAAALIGSLLNIKPILTVDDGK 193 (275)
T ss_pred HHHHHHHHHHHHcCCCHHHH--------HHHHHHHHhhcEEEEEECcHHHHHhcCCccHHHHHHHHhhcceeEEEEeCCE
Confidence 34677788999999998876 34444444444444 234442 245
Q ss_pred ccccCcccchhhhHHHHHHhhcceeccCC-eEEe-eccCcchhhHHHHHHHHH
Q 003658 675 YTSFGRHFTKVEKLKEIVDRLHWYVRSGD-TIVD-FCCGANDFSCMMKVKLEQ 725 (805)
Q Consensus 675 y~s~~rhft~~ekl~~i~~~l~~~~~~~d-~~~d-~~~g~~~~~~~~~~~~~~ 725 (805)
...+|+..+..--++++++.+.-++..++ -.+. ..+|..+=...+++.|.+
T Consensus 194 i~~~~k~Rg~kka~~~l~~~~~~~~~~~~~~~i~i~~~~~~e~~~~l~~~l~~ 246 (275)
T TIGR00762 194 LVPIEKVRGRKKAIKKLVELVKEDIKDGKPKRVAIIHADAEEEAEELKEKLKE 246 (275)
T ss_pred EEEeeccccHHHHHHHHHHHHHHhhccCCCcEEEEEeCCCHHHHHHHHHHHHh
Confidence 66788888887778888888776665443 2333 345554455566666665
No 150
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=24.80 E-value=45 Score=39.05 Aligned_cols=42 Identities=21% Similarity=0.753 Sum_probs=32.8
Q ss_pred CceecccccccCcccccccccCCCCCCCCCceeeccCCCcCCCCccchhcc
Q 003658 265 PNFLCQNCVYQEHQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSK 315 (805)
Q Consensus 265 ~~w~C~eC~~gqh~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~ 315 (805)
.+-+|..|. |.+|.+... ..++--.+.| ..||+.-|..|--.
T Consensus 122 ~~gFC~~C~-----C~iC~kfD~--~~n~~~Wi~C--d~CgH~cH~dCALr 163 (446)
T PF07227_consen 122 EPGFCRRCM-----CCICSKFDD--NKNTCSWIGC--DVCGHWCHLDCALR 163 (446)
T ss_pred CCCccccCC-----ccccCCccc--CCCCeeEEec--cCCCceehhhhhcc
Confidence 345788898 999998643 3356678999 78999999999643
No 151
>PRK04266 fibrillarin; Provisional
Probab=24.63 E-value=87 Score=33.15 Aligned_cols=27 Identities=4% Similarity=0.154 Sum_probs=23.0
Q ss_pred ceeccCCeEEeeccCcchhhHHHHHHH
Q 003658 697 WYVRSGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 697 ~~~~~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
--+.+|+.|+|++||...++..+-+..
T Consensus 68 l~i~~g~~VlD~G~G~G~~~~~la~~v 94 (226)
T PRK04266 68 FPIKKGSKVLYLGAASGTTVSHVSDIV 94 (226)
T ss_pred CCCCCCCEEEEEccCCCHHHHHHHHhc
Confidence 357899999999999999988887654
No 152
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.26 E-value=28 Score=40.07 Aligned_cols=29 Identities=31% Similarity=0.888 Sum_probs=22.9
Q ss_pred CCcCCCCccchhcccCCCCchhHHHHHHHHhhcCCceecCC-cccccCcC
Q 003658 302 ATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCPV-HKCFVCQQ 350 (805)
Q Consensus 302 ~~CGrfYHp~CL~~~~~p~~~~~~~eL~krV~~g~~F~CPl-H~C~~C~~ 350 (805)
..||+.||..|+..|.. .||. ..|..|..
T Consensus 24 ~~cGhifh~~cl~qwfe--------------------~~Ps~R~cpic~i 53 (465)
T KOG0827|consen 24 GTCGHIFHTTCLTQWFE--------------------GDPSNRGCPICQI 53 (465)
T ss_pred cchhhHHHHHHHHHHHc--------------------cCCccCCCCceee
Confidence 67999999999988852 4666 47888883
No 153
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=23.95 E-value=26 Score=39.18 Aligned_cols=64 Identities=20% Similarity=0.417 Sum_probs=37.7
Q ss_pred cccccccCCC----CceeecCcccccccccccccCccccccccCCcccccCCCCceecccccccCcccccccccCCCCCC
Q 003658 216 FAVCAICDDG----GDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQEHQCFACGMLGSSDKS 291 (805)
Q Consensus 216 d~vC~IC~~g----GeLL~CdG~C~RsFH~~Cl~g~~s~C~sLglt~~ev~~~~~w~C~eC~~gqh~CfiCgklGssd~~ 291 (805)
-.+|.-|+-+ |.||-|+ |..|++ |.- . ...-+|+.|......=..|.
T Consensus 90 VHfCd~Cd~PI~IYGRmIPCk-------HvFCl~-----CAr--~-------~~dK~Cp~C~d~VqrIeq~~-------- 140 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPCK-------HVFCLE-----CAR--S-------DSDKICPLCDDRVQRIEQIM-------- 140 (389)
T ss_pred eEeecccCCcceeeecccccc-------hhhhhh-----hhh--c-------CccccCcCcccHHHHHHHhc--------
Confidence 4679999875 7888766 455443 311 1 12457888876543333332
Q ss_pred CCCceeeccCCC-cCCCCc
Q 003658 292 SSQEVFPCVSAT-CGQFYH 309 (805)
Q Consensus 292 s~~eV~kCsv~~-CGrfYH 309 (805)
-+.+|.|+... |-|.|-
T Consensus 141 -~g~iFmC~~~~GC~RTyL 158 (389)
T KOG2932|consen 141 -MGGIFMCAAPHGCLRTYL 158 (389)
T ss_pred -ccceEEeecchhHHHHHh
Confidence 25799996444 665553
No 154
>PRK06202 hypothetical protein; Provisional
Probab=23.83 E-value=67 Score=33.29 Aligned_cols=39 Identities=18% Similarity=0.194 Sum_probs=29.4
Q ss_pred ccCCeEEeeccCcchhhHHHHHHHHHcCCcccccCCCCC
Q 003658 700 RSGDTIVDFCCGANDFSCMMKVKLEQMGKSCSFRNYDLI 738 (805)
Q Consensus 700 ~~~d~~~d~~~g~~~~~~~~~~~~~~~~~~~~~~n~d~~ 738 (805)
..+..|+|+.||...++..+-+.+.+.|....+--.|+.
T Consensus 59 ~~~~~iLDlGcG~G~~~~~L~~~~~~~g~~~~v~gvD~s 97 (232)
T PRK06202 59 DRPLTLLDIGCGGGDLAIDLARWARRDGLRLEVTAIDPD 97 (232)
T ss_pred CCCcEEEEeccCCCHHHHHHHHHHHhCCCCcEEEEEcCC
Confidence 577899999999999998887766655555555555554
No 155
>TIGR00497 hsdM type I restriction system adenine methylase (hsdM). Function: methylation of specific adenine residues; required for both restriction and modification activities. The ECOR124/3 I enzyme recognizes 5'GAA(N7)RTCG. for E.coli see (J. Mol. Biol. 257: 960-969 (1996)).
Probab=23.83 E-value=45 Score=39.15 Aligned_cols=47 Identities=17% Similarity=0.134 Sum_probs=34.7
Q ss_pred ccccccccCcccchhhhHHHHHHhhcceeccCCeEEeeccCcchhhH
Q 003658 671 HGMRYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSC 717 (805)
Q Consensus 671 ~g~~y~s~~rhft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~ 717 (805)
-|.-||+-|-+||+.+-+.-+++-+-.--.++..|-|+|||+..|-.
T Consensus 187 a~e~~t~~g~~~Tp~~Iv~l~~~~~~~~~dp~~~~~Dp~~Gsg~~L~ 233 (501)
T TIGR00497 187 AQNAGKSGGEFFTPQDISELLARIAIGKKDTVDDVYDMACGSGSLLL 233 (501)
T ss_pred HHhcCCcCceeeCcHHHHHHHHHHhccCCCCCCcccccccchHHHHH
Confidence 46678999999998875544444333323478899999999999874
No 156
>PF02353 CMAS: Mycolic acid cyclopropane synthetase; InterPro: IPR003333 This entry represents mycolic acid cyclopropane synthases and related enzymes, including CmaA1, CmaA2 (cyclopropane mycolic acid synthase A1 and A2) and MmaA1-4 (methoxymycolic acid synthase A1-4). All are thought to be S-adenosyl-L-methionine (SAM) utilising methyltransferases []. Mycolic acid cyclopropane synthase or cyclopropane-fatty-acyl-phospholipid synthase (CFA synthase) 2.1.1.79 from EC catalyses the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid -> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid. The major mycolic acid produced by Mycobacterium tuberculosis contains two cis-cyclopropanes in the meromycolate chain. Cyclopropanation may contribute to the structural integrity of the cell wall complex [].; GO: 0008610 lipid biosynthetic process; PDB: 3HA5_A 2FK8_A 3HA7_A 3HA3_A 2FK7_A 1KPG_D 1KP9_B 1KPH_D 3VC2_E 3VC1_D ....
Probab=23.67 E-value=77 Score=34.55 Aligned_cols=34 Identities=24% Similarity=0.532 Sum_probs=25.9
Q ss_pred hHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 687 KLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 687 kl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
|+.-|+++| -|++|++|+|+=||-..++..|-++
T Consensus 50 k~~~~~~~~--~l~~G~~vLDiGcGwG~~~~~~a~~ 83 (273)
T PF02353_consen 50 KLDLLCEKL--GLKPGDRVLDIGCGWGGLAIYAAER 83 (273)
T ss_dssp HHHHHHTTT--T--TT-EEEEES-TTSHHHHHHHHH
T ss_pred HHHHHHHHh--CCCCCCEEEEeCCCccHHHHHHHHH
Confidence 667777777 4899999999999999999988877
No 157
>PF05958 tRNA_U5-meth_tr: tRNA (Uracil-5-)-methyltransferase; InterPro: IPR010280 This family consists of (uracil-5-)-methyltransferases 2.1.1.35 from EC from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalysed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity []. This protein family also contains the 23SrRNA methyltransferases, first proposed to be RNA methyltransferases by homology to the TrmA family. The member from Escherichia coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA [].; GO: 0008173 RNA methyltransferase activity, 0006396 RNA processing; PDB: 2VS1_A 2JJQ_A 2BH2_A 1UWV_A 3BT7_B.
Probab=23.33 E-value=68 Score=36.08 Aligned_cols=50 Identities=18% Similarity=0.363 Sum_probs=26.9
Q ss_pred ccccccCcccchh--hhHHHHHHhhcceecc-CCeEEeeccCcchhhHHHHHH
Q 003658 673 MRYTSFGRHFTKV--EKLKEIVDRLHWYVRS-GDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 673 ~~y~s~~rhft~~--ekl~~i~~~l~~~~~~-~d~~~d~~~g~~~~~~~~~~~ 722 (805)
.+|.-.-..|.++ +-.+.+++...-++.. ++.|+|++||..+|+-.|-++
T Consensus 165 ~~~~~~~~sFfQvN~~~~~~l~~~~~~~l~~~~~~vlDlycG~G~fsl~la~~ 217 (352)
T PF05958_consen 165 LSFRISPGSFFQVNPEQNEKLYEQALEWLDLSKGDVLDLYCGVGTFSLPLAKK 217 (352)
T ss_dssp EEEEEETTS---SBHHHHHHHHHHHHHHCTT-TTEEEEES-TTTCCHHHHHCC
T ss_pred eEEEECCCcCccCcHHHHHHHHHHHHHHhhcCCCcEEEEeecCCHHHHHHHhh
Confidence 3444222345443 3444455543334443 347999999999999887543
No 158
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=23.12 E-value=1.2e+02 Score=26.08 Aligned_cols=48 Identities=19% Similarity=0.273 Sum_probs=37.3
Q ss_pred hhHHHHHHHhhhccCC-CCchHHhhccCCCCcccccCCccccccceecccchhhHHHHHHHHHHhhCCCChh
Q 003658 571 AEMEKELLALIKDSTS-SFNEEEFMKSHIVPITHAHHSKHLLEKSITLGLVEGSVKAVRAALEMLDGGCDIE 641 (805)
Q Consensus 571 ~~~e~r~~~~~~~~~~-~~~~~~~~~~~~~~~t~~~~~~~~~~~~i~~g~~e~sv~a~~~~l~~l~~g~~~~ 641 (805)
.+++.+||.++++... .+|..++-+..-++. .+|+.+|..|++-|-|+
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~-----------------------~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNLGLPK-----------------------KEVNRVLYSLEKKGKVC 53 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCH-----------------------HHHHHHHHHHHHCCCEE
Confidence 5679999999999866 599999988877655 35677788777776653
No 159
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=22.83 E-value=66 Score=29.58 Aligned_cols=29 Identities=31% Similarity=0.814 Sum_probs=21.0
Q ss_pred CCcccccccCCCCc-----eeecCccccccccccc
Q 003658 214 NYFAVCAICDDGGD-----VTFCDGRCLRSFHATI 243 (805)
Q Consensus 214 ~~d~vC~IC~~gGe-----LL~CdG~C~RsFH~~C 243 (805)
.....|.||++... .+.|.| |.-.|.-..
T Consensus 4 ~~~~~C~VCg~~~~g~hyGv~sC~a-Ck~FFRR~v 37 (90)
T cd07168 4 ESPKLCSICEDKATGLHYGIITCEG-CKGFFKRTV 37 (90)
T ss_pred ccCCCCcccCCcCcceEECceehhh-hhHhhhhhh
Confidence 34567999987532 678995 888887763
No 160
>COG4798 Predicted methyltransferase [General function prediction only]
Probab=22.74 E-value=44 Score=35.67 Aligned_cols=49 Identities=16% Similarity=0.250 Sum_probs=42.9
Q ss_pred cceeccCCeEEeeccCcchhhHHHHHHHHHcCCcccccCCCCCCCCCCC
Q 003658 696 HWYVRSGDTIVDFCCGANDFSCMMKVKLEQMGKSCSFRNYDLIQPKNDF 744 (805)
Q Consensus 696 ~~~~~~~d~~~d~~~g~~~~~~~~~~~~~~~~~~~~~~n~d~~~~~~~~ 744 (805)
-|=|.+|+||||+.-|...|-+++..-+-..|+--.|-+.++.-+++++
T Consensus 43 FaGlkpg~tVid~~PGgGy~TrI~s~~vgp~G~Vy~~~p~e~~~~~~~~ 91 (238)
T COG4798 43 FAGLKPGATVIDLIPGGGYFTRIFSPAVGPKGKVYAYVPAELTKFAKRE 91 (238)
T ss_pred EeccCCCCEEEEEecCCccHhhhhchhcCCceeEEEecchhhcccccch
Confidence 3679999999999999999999999999888987788888887777665
No 161
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=22.69 E-value=1e+02 Score=34.85 Aligned_cols=33 Identities=18% Similarity=0.502 Sum_probs=25.8
Q ss_pred cCcCCccc--cccccceeeccccccccc-cccCCCC
Q 003658 347 VCQQSEDM--NVEDLQLAICRRCPKAYH-RKCLPTE 379 (805)
Q Consensus 347 ~C~~~edk--~~~~~qL~~C~RCPkAYH-~kCLP~g 379 (805)
+|....++ ...++-|++|.-|+-||| ..|+|.-
T Consensus 132 ~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~~~ 167 (345)
T KOG2752|consen 132 KCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQAK 167 (345)
T ss_pred EecCCCCCccccccceeeeEEeccchhcccccCccc
Confidence 56665554 345778999999999999 8899874
No 162
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=22.60 E-value=1.2e+02 Score=30.86 Aligned_cols=39 Identities=28% Similarity=0.474 Sum_probs=29.2
Q ss_pred cchhhhHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 682 FTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 682 ft~~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
+|+.|.-.-++.++. +.+|+.|+|+.||+..|+..+-+.
T Consensus 23 ~t~~~~r~~~l~~l~--~~~~~~vlDlG~GtG~~s~~~a~~ 61 (198)
T PRK00377 23 MTKEEIRALALSKLR--LRKGDMILDIGCGTGSVTVEASLL 61 (198)
T ss_pred CCHHHHHHHHHHHcC--CCCcCEEEEeCCcCCHHHHHHHHH
Confidence 787775333445554 679999999999999998876554
No 163
>TIGR02081 metW methionine biosynthesis protein MetW. This protein is found alongside MetX, of the enzyme that acylates homoserine as a first step toward methionine biosynthesis, in many species. It appears to act in methionine biosynthesis but is not fully characterized.
Probab=22.22 E-value=89 Score=31.50 Aligned_cols=31 Identities=19% Similarity=0.626 Sum_probs=23.6
Q ss_pred HHHHHHhhcceeccCCeEEeeccCcchhhHHHHHH
Q 003658 688 LKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 688 l~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
|.++.+. +.+|++|+|+.||...+...+.+.
T Consensus 4 ~~~i~~~----i~~~~~iLDiGcG~G~~~~~l~~~ 34 (194)
T TIGR02081 4 LESILNL----IPPGSRVLDLGCGDGELLALLRDE 34 (194)
T ss_pred HHHHHHh----cCCCCEEEEeCCCCCHHHHHHHhc
Confidence 4445544 458999999999999998877543
No 164
>PF09445 Methyltransf_15: RNA cap guanine-N2 methyltransferase; InterPro: IPR019012 RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe (Fission yeast) trimethylguanosine synthase (Tgs1) and Giardia lamblia (Giardia intestinalis) Tgs2, catalyse the methylation step(s) for the conversion of the 7-monomethylguanosine (m(7)G) caps of snRNAs and snoRNAs to a 2,2,7-trimethylguanosine (m(2,2,7)G) cap structure [, , ]. Trimethylguanosine synthase is specific for guanine, and N7 methylation must precede N2 methylation. This enzyme is required for pre-mRNA splicing, pre-rRNA processing and small ribosomal subunit synthesis. As such, this enzyme plays a role in transcriptional regulation. ; GO: 0008168 methyltransferase activity, 0001510 RNA methylation, 0009452 RNA capping; PDB: 3EGI_B 3GDH_A.
Probab=21.84 E-value=13 Score=37.75 Aligned_cols=72 Identities=18% Similarity=0.356 Sum_probs=35.3
Q ss_pred CeEEeeccCcchhhHHHHHHHHH--------cCCcccccCCCCCCCCCCCccccccccccCCCCCCCCC-ceeeecCCCc
Q 003658 703 DTIVDFCCGANDFSCMMKVKLEQ--------MGKSCSFRNYDLIQPKNDFSFEKRDWMTVRPEELPDGS-QLIMGLNPPF 773 (805)
Q Consensus 703 d~~~d~~~g~~~~~~~~~~~~~~--------~~~~~~~~n~d~~~~~~~~~f~~~~w~~~~~~~l~~g~-~li~gl~ppf 773 (805)
++|+|++||...+.--+-+.-.. +-..|--.|-.+.--.+...|-.-||+++-+. +..+. .=++=|.||.
T Consensus 1 ~~vlD~fcG~GGNtIqFA~~~~~Viaidid~~~~~~a~hNa~vYGv~~~I~~i~gD~~~~~~~-~~~~~~~D~vFlSPPW 79 (163)
T PF09445_consen 1 TTVLDAFCGVGGNTIQFARTFDRVIAIDIDPERLECAKHNAEVYGVADNIDFICGDFFELLKR-LKSNKIFDVVFLSPPW 79 (163)
T ss_dssp SEEEETT-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHGGG-B------SEEEE---B
T ss_pred CEEEEeccCcCHHHHHHHHhCCeEEEEECCHHHHHHHHHHHHHcCCCCcEEEEeCCHHHHHhh-ccccccccEEEECCCC
Confidence 47999999987765555443211 11122233434443356788999999998665 22222 1233458999
Q ss_pred ch
Q 003658 774 GV 775 (805)
Q Consensus 774 g~ 775 (805)
|-
T Consensus 80 GG 81 (163)
T PF09445_consen 80 GG 81 (163)
T ss_dssp SS
T ss_pred CC
Confidence 84
No 165
>KOG1098 consensus Putative SAM-dependent rRNA methyltransferase SPB1 [RNA processing and modification; General function prediction only]
Probab=21.78 E-value=46 Score=40.61 Aligned_cols=31 Identities=13% Similarity=0.410 Sum_probs=25.3
Q ss_pred hhhHHHHHHhhcceeccCCeEEeeccCcchhh
Q 003658 685 VEKLKEIVDRLHWYVRSGDTIVDFCCGANDFS 716 (805)
Q Consensus 685 ~ekl~~i~~~l~~~~~~~d~~~d~~~g~~~~~ 716 (805)
..||.+|..+. =|++++-.++|+||+-..|.
T Consensus 29 aFKLlQln~ky-~fl~~a~~vlDLcaAPG~W~ 59 (780)
T KOG1098|consen 29 AFKLLQLNKKY-KFLEKAHVVLDLCAAPGGWL 59 (780)
T ss_pred HHHHHHHHHHh-ccccccchheeeccCCcHHH
Confidence 34899999988 68999999999999755433
No 166
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=21.66 E-value=48 Score=27.16 Aligned_cols=37 Identities=24% Similarity=0.566 Sum_probs=20.7
Q ss_pred ccccccccCCCCCCCCCceeeccCCCcCCCCccchhcccC
Q 003658 278 QCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLL 317 (805)
Q Consensus 278 ~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~ 317 (805)
+|.+|...+. + ...-+..|.-..--+++|..|+..|+
T Consensus 1 ~CrIC~~~~~-~--~~~l~~PC~C~G~~~~vH~~Cl~~W~ 37 (49)
T smart00744 1 ICRICHDEGD-E--GDPLVSPCRCKGSLKYVHQECLERWI 37 (49)
T ss_pred CccCCCCCCC-C--CCeeEeccccCCchhHHHHHHHHHHH
Confidence 3677765221 1 11223445222223899999999886
No 167
>COG3028 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.23 E-value=73 Score=33.13 Aligned_cols=33 Identities=30% Similarity=0.441 Sum_probs=28.4
Q ss_pred hHHHHHHHHHHhhCCCChhhhhhcCCchhHhhHHHHhhcc
Q 003658 623 SVKAVRAALEMLDGGCDIEDAKAVCPPEILCQIFQWKRKL 662 (805)
Q Consensus 623 sv~a~~~~l~~l~~g~~~~~aka~c~p~~l~q~~~~~~~l 662 (805)
-|++||+||.+|++-+..+-| -|..|.+|.+.|
T Consensus 94 DvepI~~~Ldkl~~~~~q~~a-------~lHklE~~RdrL 126 (187)
T COG3028 94 DVEPIRAALDKLRNRHNQQVA-------LLHKLEQLRDRL 126 (187)
T ss_pred ChHHHHHHHHHHhhhHHHHHH-------HHHHHHHHHHHH
Confidence 689999999999999887766 688889998765
No 168
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=21.22 E-value=32 Score=39.34 Aligned_cols=27 Identities=41% Similarity=0.870 Sum_probs=21.1
Q ss_pred CcccccccCCC--Cc---eeecCcccccccccc
Q 003658 215 YFAVCAICDDG--GD---VTFCDGRCLRSFHAT 242 (805)
Q Consensus 215 ~d~vC~IC~~g--Ge---LL~CdG~C~RsFH~~ 242 (805)
-..+|+||++- |. -+.|+| |...|-..
T Consensus 18 ~~~~CaICGDkaTGKHYGA~SCdG-CKGFFRRS 49 (432)
T KOG4215|consen 18 VAEFCAICGDKATGKHYGAISCDG-CKGFFRRS 49 (432)
T ss_pred ccchhheeCCcccccccceeecCc-chHHHHHH
Confidence 46789999973 32 789997 98888766
No 169
>KOG4589 consensus Cell division protein FtsJ [Cell cycle control, cell division, chromosome partitioning]
Probab=21.09 E-value=62 Score=34.42 Aligned_cols=36 Identities=28% Similarity=0.437 Sum_probs=32.0
Q ss_pred hHHHHHHhhcceeccCCeEEeeccCcchhhHHHHHHH
Q 003658 687 KLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 687 kl~~i~~~l~~~~~~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
||.||.+| +-++.+||+|+|.=|+-.+||+.-.+|-
T Consensus 56 KLiEindK-y~~l~p~~~VlD~G~APGsWsQVavqr~ 91 (232)
T KOG4589|consen 56 KLIEINDK-YRFLRPEDTVLDCGAAPGSWSQVAVQRV 91 (232)
T ss_pred hheeehhh-ccccCCCCEEEEccCCCChHHHHHHHhh
Confidence 89999887 4578999999999999999999998884
No 170
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=20.82 E-value=48 Score=40.11 Aligned_cols=12 Identities=25% Similarity=0.589 Sum_probs=9.0
Q ss_pred ceecccccccCc
Q 003658 266 NFLCQNCVYQEH 277 (805)
Q Consensus 266 ~w~C~eC~~gqh 277 (805)
.++|++|..+.+
T Consensus 95 ~~lc~~c~~~~~ 106 (715)
T COG1107 95 EGLCPECRRKPK 106 (715)
T ss_pred cccChhHhhCCc
Confidence 348999987766
No 171
>PF13679 Methyltransf_32: Methyltransferase domain
Probab=20.78 E-value=1.2e+02 Score=29.23 Aligned_cols=98 Identities=18% Similarity=0.262 Sum_probs=55.7
Q ss_pred hhhHHHHHHhhcce---eccCCeEEeeccCcchhhHHHHHHHHHcCCcccccCCCCCCC----------------CCCCc
Q 003658 685 VEKLKEIVDRLHWY---VRSGDTIVDFCCGANDFSCMMKVKLEQMGKSCSFRNYDLIQP----------------KNDFS 745 (805)
Q Consensus 685 ~ekl~~i~~~l~~~---~~~~d~~~d~~~g~~~~~~~~~~~~~~~~~~~~~~n~d~~~~----------------~~~~~ 745 (805)
++.+.++++.+.-. ..+..+|||++||-.-.+.++-..|...+..+..--.|.=+. .+.+.
T Consensus 6 i~~~~~~i~~~~~~~~~~~~~~~vvD~GsG~GyLs~~La~~l~~~~~~~~v~~iD~~~~~~~~a~~~~~~~~~~~~~~~~ 85 (141)
T PF13679_consen 6 IERMAELIDSLCDSVGESKRCITVVDLGSGKGYLSRALAHLLCNSSPNLRVLGIDCNESLVESAQKRAQKLGSDLEKRLS 85 (141)
T ss_pred HHHHHHHHHHHHHHhhccCCCCEEEEeCCChhHHHHHHHHHHHhcCCCCeEEEEECCcHHHHHHHHHHHHhcchhhccch
Confidence 44555566655433 467889999999999999999997766543443333332211 12333
Q ss_pred cccccccccCCCCCCCCCceeeecCCCcchhhhhHHHHhhhhhc
Q 003658 746 FEKRDWMTVRPEELPDGSQLIMGLNPPFGVKASLANKFISQALK 789 (805)
Q Consensus 746 f~~~~w~~~~~~~l~~g~~li~gl~ppfg~~~~~a~kf~~~~~~ 789 (805)
|...+.-... -..+..++.||-. =+.|+-.-+..+..
T Consensus 86 ~~~~~~~~~~---~~~~~~~~vgLHa----CG~Ls~~~l~~~~~ 122 (141)
T PF13679_consen 86 FIQGDIADES---SSDPPDILVGLHA----CGDLSDRALRLFIR 122 (141)
T ss_pred hhccchhhhc---ccCCCeEEEEeec----ccchHHHHHHHHHH
Confidence 3332222111 1445556666543 23477777777777
No 172
>PHA02862 5L protein; Provisional
Probab=20.75 E-value=44 Score=33.82 Aligned_cols=36 Identities=14% Similarity=0.330 Sum_probs=25.3
Q ss_pred cccccccccCCCCCCCCCceeeccCCCcCCCCccchhcccCC
Q 003658 277 HQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLH 318 (805)
Q Consensus 277 h~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~~~ 318 (805)
+.|.+|...+. .++..|.-.+--++-|..|+..|..
T Consensus 3 diCWIC~~~~~------e~~~PC~C~GS~K~VHq~CL~~WIn 38 (156)
T PHA02862 3 DICWICNDVCD------ERNNFCGCNEEYKVVHIKCMQLWIN 38 (156)
T ss_pred CEEEEecCcCC------CCcccccccCcchhHHHHHHHHHHh
Confidence 45888876542 2356775455578999999999873
No 173
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=20.27 E-value=31 Score=41.58 Aligned_cols=47 Identities=19% Similarity=0.449 Sum_probs=33.8
Q ss_pred ecccccccCcccccccccCCCCCCCCCceeeccCCCcCCCCccchhccc
Q 003658 268 LCQNCVYQEHQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKL 316 (805)
Q Consensus 268 ~C~eC~~gqh~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~~ 316 (805)
.|.-|...-..|-+|...+.+-......+.+| ..||..||..|....
T Consensus 503 ~C~lC~~~gfiCe~Cq~~~iiyPF~~~~~~rC--~~C~avfH~~C~~r~ 549 (580)
T KOG1829|consen 503 ECDLCTGKGFICELCQHNDIIYPFETRNTRRC--STCLAVFHKKCLRRK 549 (580)
T ss_pred hchhhccCeeeeeeccCCCcccccccccceeH--HHHHHHHHHHHHhcc
Confidence 48888887788888844332212224578999 899999999998643
No 174
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=20.22 E-value=72 Score=36.87 Aligned_cols=25 Identities=24% Similarity=0.498 Sum_probs=20.5
Q ss_pred eccCCeEEeeccCcchhhHHHHHHH
Q 003658 699 VRSGDTIVDFCCGANDFSCMMKVKL 723 (805)
Q Consensus 699 ~~~~d~~~d~~~g~~~~~~~~~~~~ 723 (805)
.++|+.|+|+|||...++..|-+.+
T Consensus 248 ~~~g~~VLDlgaG~G~kt~~la~~~ 272 (445)
T PRK14904 248 PQPGSTVLDLCAAPGGKSTFMAELM 272 (445)
T ss_pred CCCCCEEEEECCCCCHHHHHHHHHh
Confidence 4789999999999998887665543
No 175
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=20.20 E-value=52 Score=29.67 Aligned_cols=30 Identities=30% Similarity=0.768 Sum_probs=0.0
Q ss_pred ccccccccCCCCCCCCCceeeccCCCcCCCCccchhcc
Q 003658 278 QCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSK 315 (805)
Q Consensus 278 ~CfiCgklGssd~~s~~eV~kCsv~~CGrfYHp~CL~~ 315 (805)
.|.+|++. -+..+|.- -.||+.||..|...
T Consensus 80 ~C~vC~k~------l~~~~f~~--~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 80 KCSVCGKP------LGNSVFVV--FPCGHVVHYSCIKR 109 (109)
T ss_pred CccCcCCc------CCCceEEE--eCCCeEEecccccC
No 176
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=20.14 E-value=41 Score=31.11 Aligned_cols=27 Identities=30% Similarity=0.637 Sum_probs=17.3
Q ss_pred ccccccCCCCc---eeecCccccccccccccc
Q 003658 217 AVCAICDDGGD---VTFCDGRCLRSFHATITA 245 (805)
Q Consensus 217 ~vC~IC~~gGe---LL~CdG~C~RsFH~~Cl~ 245 (805)
..|..|.-+|+ |+ -|.|...||..|+.
T Consensus 33 g~Cp~Ck~Pgd~Cplv--~g~C~H~FH~hCI~ 62 (85)
T PF12861_consen 33 GCCPDCKFPGDDCPLV--WGKCSHNFHMHCIL 62 (85)
T ss_pred cCCCCccCCCCCCcee--eccCccHHHHHHHH
Confidence 33444444564 33 45699999999853
No 177
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=20.06 E-value=55 Score=30.58 Aligned_cols=22 Identities=32% Similarity=0.711 Sum_probs=19.0
Q ss_pred CceecccccccCcccccccccC
Q 003658 265 PNFLCQNCVYQEHQCFACGMLG 286 (805)
Q Consensus 265 ~~w~C~eC~~gqh~CfiCgklG 286 (805)
+.-+|+.|.|....|-.||+.-
T Consensus 58 g~~YCq~CAYkkGiCamCGKki 79 (90)
T PF10235_consen 58 GAKYCQTCAYKKGICAMCGKKI 79 (90)
T ss_pred CCccChhhhcccCcccccCCee
Confidence 4578999999999999999753
No 178
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=20.00 E-value=70 Score=36.85 Aligned_cols=24 Identities=17% Similarity=0.354 Sum_probs=20.4
Q ss_pred eccCCeEEeeccCcchhhHHHHHH
Q 003658 699 VRSGDTIVDFCCGANDFSCMMKVK 722 (805)
Q Consensus 699 ~~~~d~~~d~~~g~~~~~~~~~~~ 722 (805)
+++|++|+|+|||...++..|-+.
T Consensus 250 ~~~g~~VLDl~ag~G~kt~~la~~ 273 (434)
T PRK14901 250 PQPGEVILDACAAPGGKTTHIAEL 273 (434)
T ss_pred CCCcCEEEEeCCCCchhHHHHHHH
Confidence 578999999999999888776554
Done!