Query 004169
Match_columns 770
No_of_seqs 204 out of 554
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 18:45:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004169.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004169hhsearch_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 9.3E-21 2E-25 182.2 2.3 131 7-137 1-145 (146)
2 KOG4443 Putative transcription 98.1 1.7E-06 3.7E-11 99.8 3.3 83 277-380 19-102 (694)
3 COG5034 TNG2 Chromatin remodel 97.6 4.5E-05 9.6E-10 80.2 3.9 48 213-274 218-269 (271)
4 KOG4299 PHD Zn-finger protein 97.6 5.8E-05 1.3E-09 87.2 4.2 50 344-412 255-304 (613)
5 KOG4299 PHD Zn-finger protein 97.5 2.6E-05 5.6E-10 90.0 1.2 50 216-275 253-305 (613)
6 PF00628 PHD: PHD-finger; Int 97.5 2.7E-05 6E-10 62.2 0.8 46 218-274 1-50 (51)
7 COG5141 PHD zinc finger-contai 97.5 4.5E-05 9.9E-10 85.7 2.6 89 213-315 190-335 (669)
8 KOG1244 Predicted transcriptio 97.5 3.4E-05 7.3E-10 81.6 1.0 83 213-317 221-315 (336)
9 KOG1973 Chromatin remodeling p 97.5 6.4E-05 1.4E-09 80.4 3.0 51 210-274 215-267 (274)
10 smart00249 PHD PHD zinc finger 97.4 0.00013 2.9E-09 55.6 3.1 44 218-272 1-47 (47)
11 KOG1512 PHD Zn-finger protein 97.3 6.3E-05 1.4E-09 80.0 1.1 82 214-317 256-348 (381)
12 KOG0955 PHD finger protein BR1 97.3 0.00024 5.2E-09 87.2 4.9 142 210-383 213-368 (1051)
13 KOG1244 Predicted transcriptio 97.2 0.00029 6.3E-09 74.7 4.2 96 264-383 222-318 (336)
14 KOG4443 Putative transcription 97.0 0.00027 5.8E-09 82.2 1.9 83 213-317 15-102 (694)
15 KOG0954 PHD finger protein [Ge 96.8 0.00062 1.4E-08 79.9 2.2 157 215-414 270-440 (893)
16 KOG0956 PHD finger protein AF1 96.7 0.00088 1.9E-08 78.2 3.1 84 219-315 8-156 (900)
17 PF15446 zf-PHD-like: PHD/FYVE 96.7 0.0031 6.7E-08 63.2 6.2 26 356-381 119-144 (175)
18 KOG0383 Predicted helicase [Ge 96.6 0.00079 1.7E-08 79.9 1.5 51 212-274 43-93 (696)
19 smart00249 PHD PHD zinc finger 96.1 0.0056 1.2E-07 46.6 3.3 34 344-381 1-34 (47)
20 KOG1473 Nucleosome remodeling 95.7 0.0059 1.3E-07 74.7 2.8 50 212-273 340-389 (1414)
21 KOG0825 PHD Zn-finger protein 95.4 0.0096 2.1E-07 70.7 2.7 47 216-274 215-265 (1134)
22 PF00628 PHD: PHD-finger; Int 95.2 0.015 3.3E-07 46.4 2.8 34 344-381 1-34 (51)
23 KOG1512 PHD Zn-finger protein 94.3 0.026 5.7E-07 60.7 2.4 69 294-378 277-346 (381)
24 KOG1701 Focal adhesion adaptor 94.1 0.007 1.5E-07 68.0 -2.3 87 212-313 271-361 (468)
25 KOG4323 Polycomb-like PHD Zn-f 94.1 0.022 4.8E-07 65.1 1.6 57 210-275 162-224 (464)
26 KOG0383 Predicted helicase [Ge 93.4 0.045 9.8E-07 65.5 2.5 81 234-351 1-96 (696)
27 KOG0825 PHD Zn-finger protein 92.5 0.071 1.5E-06 63.7 2.3 33 344-380 217-250 (1134)
28 PF13832 zf-HC5HC2H_2: PHD-zin 92.2 0.16 3.5E-06 46.7 4.0 84 218-315 2-87 (110)
29 PF13832 zf-HC5HC2H_2: PHD-zin 92.1 0.088 1.9E-06 48.5 2.0 102 278-410 2-110 (110)
30 PRK05785 hypothetical protein; 90.3 0.56 1.2E-05 48.8 6.1 47 674-723 27-73 (226)
31 COG2226 UbiE Methylase involve 89.8 0.27 5.9E-06 52.2 3.4 59 650-723 15-73 (238)
32 PRK14896 ksgA 16S ribosomal RN 87.5 0.62 1.4E-05 49.2 4.2 44 677-722 6-50 (258)
33 PRK00274 ksgA 16S ribosomal RN 86.9 0.84 1.8E-05 48.7 4.8 49 672-722 13-63 (272)
34 PF13771 zf-HC5HC2H: PHD-like 84.6 0.53 1.1E-05 41.7 1.6 33 213-245 33-67 (90)
35 KOG0957 PHD finger protein [Ge 83.9 0.53 1.1E-05 54.3 1.6 52 343-411 545-596 (707)
36 PTZ00338 dimethyladenosine tra 82.8 1.5 3.2E-05 47.8 4.4 49 671-721 6-56 (294)
37 PRK11188 rrmJ 23S rRNA methylt 82.3 1.3 2.8E-05 45.6 3.6 38 685-723 36-73 (209)
38 KOG0957 PHD finger protein [Ge 82.0 0.64 1.4E-05 53.7 1.3 50 215-273 543-596 (707)
39 KOG4323 Polycomb-like PHD Zn-f 81.4 0.79 1.7E-05 52.9 1.8 53 345-412 171-223 (464)
40 KOG1973 Chromatin remodeling p 80.1 1 2.2E-05 48.6 2.1 27 293-319 229-256 (274)
41 TIGR00755 ksgA dimethyladenosi 78.4 2.7 5.8E-05 44.2 4.4 45 676-722 5-50 (253)
42 KOG0956 PHD finger protein AF1 77.4 1 2.2E-05 53.8 1.1 58 212-274 113-179 (900)
43 KOG1245 Chromatin remodeling c 76.4 0.73 1.6E-05 59.6 -0.5 61 212-284 1104-1170(1404)
44 TIGR03587 Pse_Me-ase pseudamin 76.2 2.3 5.1E-05 43.6 3.2 51 672-722 14-64 (204)
45 PF01209 Ubie_methyltran: ubiE 73.8 1.4 3.1E-05 46.3 1.0 43 674-721 25-67 (233)
46 PF13771 zf-HC5HC2H: PHD-like 73.8 2 4.3E-05 38.1 1.7 33 276-315 36-68 (90)
47 PF13831 PHD_2: PHD-finger; PD 73.6 0.96 2.1E-05 34.7 -0.3 35 226-273 2-36 (36)
48 PHA03412 putative methyltransf 71.3 2.9 6.2E-05 44.8 2.5 42 677-722 29-70 (241)
49 PF13901 DUF4206: Domain of un 71.2 3.2 7E-05 42.9 2.8 46 268-315 144-189 (202)
50 TIGR02987 met_A_Alw26 type II 69.7 5.7 0.00012 46.3 4.7 49 677-725 2-55 (524)
51 KOG0955 PHD finger protein BR1 68.2 4 8.7E-05 51.5 3.2 67 277-374 220-286 (1051)
52 PF02384 N6_Mtase: N-6 DNA Met 68.1 5 0.00011 43.1 3.6 46 676-723 23-68 (311)
53 PF15446 zf-PHD-like: PHD/FYVE 67.1 3.1 6.8E-05 42.3 1.7 37 344-381 1-37 (175)
54 PF11793 FANCL_C: FANCL C-term 66.3 3.8 8.2E-05 35.6 1.8 39 277-317 3-41 (70)
55 PRK00312 pcm protein-L-isoaspa 65.4 18 0.0004 36.6 6.9 72 648-721 23-98 (212)
56 TIGR00080 pimt protein-L-isoas 65.2 7.5 0.00016 39.8 4.0 52 671-724 47-100 (215)
57 KOG4628 Predicted E3 ubiquitin 64.7 3.5 7.5E-05 46.3 1.6 92 18-124 24-116 (348)
58 PF13679 Methyltransf_32: Meth 64.1 8.6 0.00019 37.0 4.0 43 684-726 5-50 (141)
59 TIGR00438 rrmJ cell division p 63.8 8.3 0.00018 38.5 4.0 37 687-724 19-55 (188)
60 TIGR02752 MenG_heptapren 2-hep 63.4 6.5 0.00014 40.1 3.2 45 674-723 23-67 (231)
61 PF14446 Prok-RING_1: Prokaryo 63.2 5.2 0.00011 33.7 2.0 33 277-315 6-38 (54)
62 PRK13942 protein-L-isoaspartat 62.8 7.6 0.00016 39.9 3.6 46 676-723 53-98 (212)
63 PTZ00098 phosphoethanolamine N 61.7 9.7 0.00021 40.5 4.3 51 669-721 10-72 (263)
64 cd04718 BAH_plant_2 BAH, or Br 61.7 5 0.00011 40.1 1.9 26 239-275 2-27 (148)
65 KOG1044 Actin-binding LIM Zn-f 60.0 6.1 0.00013 46.8 2.5 51 589-639 447-509 (670)
66 TIGR00446 nop2p NOL1/NOP2/sun 60.0 5.4 0.00012 42.5 2.0 25 698-722 68-92 (264)
67 PF01728 FtsJ: FtsJ-like methy 59.8 5.2 0.00011 39.5 1.7 38 686-723 7-45 (181)
68 COG2230 Cfa Cyclopropane fatty 56.8 11 0.00023 41.5 3.6 37 684-722 57-93 (283)
69 PRK08287 cobalt-precorrin-6Y C 56.4 17 0.00037 36.2 4.7 41 679-721 11-51 (187)
70 PRK13944 protein-L-isoaspartat 56.3 14 0.0003 37.8 4.1 44 678-723 51-94 (205)
71 PF14446 Prok-RING_1: Prokaryo 56.0 6.4 0.00014 33.2 1.3 32 344-378 7-38 (54)
72 PF01555 N6_N4_Mtase: DNA meth 55.1 9.1 0.0002 38.0 2.6 48 664-713 151-203 (231)
73 PF04405 ScdA_N: Domain of Unk 54.7 4.6 0.0001 34.0 0.3 9 706-714 24-32 (56)
74 TIGR02469 CbiT precorrin-6Y C5 51.8 20 0.00044 32.1 4.1 36 685-722 5-40 (124)
75 PLN02233 ubiquinone biosynthes 49.1 19 0.00042 38.2 4.0 25 698-722 70-94 (261)
76 PTZ00146 fibrillarin; Provisio 48.9 11 0.00023 41.6 2.1 26 698-723 129-154 (293)
77 PHA03411 putative methyltransf 48.4 22 0.00048 39.0 4.3 40 678-721 45-84 (279)
78 smart00650 rADc Ribosomal RNA 48.4 17 0.00036 35.7 3.2 33 688-722 2-34 (169)
79 TIGR02081 metW methionine bios 48.3 19 0.00041 36.1 3.6 31 688-722 4-34 (194)
80 PRK08317 hypothetical protein; 47.5 22 0.00049 35.5 4.0 31 691-723 11-41 (241)
81 PRK13168 rumA 23S rRNA m(5)U19 47.1 18 0.0004 41.3 3.7 23 699-721 295-317 (443)
82 PRK07402 precorrin-6B methylas 47.1 27 0.00059 35.0 4.5 40 679-720 20-59 (196)
83 TIGR00479 rumA 23S rRNA (uraci 46.7 19 0.0004 41.0 3.6 38 684-721 273-312 (431)
84 KOG3362 Predicted BBOX Zn-fing 46.4 8.2 0.00018 38.5 0.6 32 338-377 114-146 (156)
85 PRK14967 putative methyltransf 44.1 21 0.00045 36.8 3.2 34 685-720 22-55 (223)
86 PF13639 zf-RING_2: Ring finge 44.0 6.9 0.00015 30.4 -0.2 33 278-317 2-34 (44)
87 PRK14904 16S rRNA methyltransf 43.3 15 0.00033 42.0 2.3 23 699-721 248-270 (445)
88 PF02475 Met_10: Met-10+ like- 43.2 11 0.00025 39.0 1.1 43 661-721 79-121 (200)
89 TIGR02021 BchM-ChlM magnesium 42.6 18 0.0004 36.8 2.5 33 689-721 39-75 (219)
90 PRK14901 16S rRNA methyltransf 42.1 16 0.00034 41.8 2.1 23 699-721 250-272 (434)
91 PF02353 CMAS: Mycolic acid cy 41.9 28 0.0006 37.7 3.9 35 686-722 49-83 (273)
92 PF13489 Methyltransf_23: Meth 41.3 24 0.00051 33.1 2.9 35 688-722 9-43 (161)
93 COG4798 Predicted methyltransf 41.0 13 0.00029 39.2 1.2 49 696-744 43-91 (238)
94 PF12678 zf-rbx1: RING-H2 zinc 41.0 6.8 0.00015 34.2 -0.7 16 302-317 48-63 (73)
95 PRK06202 hypothetical protein; 40.7 24 0.00051 36.4 3.0 25 700-724 59-83 (232)
96 KOG3612 PHD Zn-finger protein 40.7 19 0.00042 42.5 2.6 33 211-244 55-87 (588)
97 PRK00377 cbiT cobalt-precorrin 40.5 37 0.0008 34.3 4.3 37 682-720 23-59 (198)
98 COG0293 FtsJ 23S rRNA methylas 39.8 30 0.00065 36.4 3.6 53 685-741 30-82 (205)
99 PRK00050 16S rRNA m(4)C1402 me 39.8 26 0.00056 38.6 3.3 34 688-723 8-41 (296)
100 PF00398 RrnaAD: Ribosomal RNA 39.3 37 0.00081 36.1 4.3 46 676-723 6-52 (262)
101 PRK14890 putative Zn-ribbon RN 39.2 21 0.00045 30.8 1.9 32 264-305 23-55 (59)
102 PF13659 Methyltransf_26: Meth 38.9 24 0.00052 31.7 2.4 22 702-723 1-22 (117)
103 COG5034 TNG2 Chromatin remodel 38.6 25 0.00054 38.2 2.8 27 293-319 231-258 (271)
104 KOG0804 Cytoplasmic Zn-finger 38.5 17 0.00037 42.1 1.6 29 216-245 175-207 (493)
105 PRK00216 ubiE ubiquinone/menaq 37.2 32 0.0007 34.6 3.3 45 674-723 29-73 (239)
106 TIGR00563 rsmB ribosomal RNA s 36.2 24 0.00052 40.2 2.4 23 699-721 236-258 (426)
107 PLN02336 phosphoethanolamine N 35.4 42 0.0009 38.5 4.2 34 687-722 254-287 (475)
108 TIGR03534 RF_mod_PrmC protein- 35.3 30 0.00066 35.4 2.8 28 695-722 81-108 (251)
109 TIGR00406 prmA ribosomal prote 35.0 43 0.00094 36.1 4.0 38 679-720 141-178 (288)
110 PRK04266 fibrillarin; Provisio 35.0 30 0.00064 36.4 2.7 34 690-723 60-94 (226)
111 KOG4628 Predicted E3 ubiquitin 34.6 24 0.00051 39.9 2.0 29 217-246 230-261 (348)
112 PF12847 Methyltransf_18: Meth 34.2 37 0.00079 30.2 2.8 21 701-721 1-21 (112)
113 PRK03522 rumB 23S rRNA methylu 34.0 31 0.00068 37.6 2.8 33 686-720 159-192 (315)
114 PRK11705 cyclopropane fatty ac 33.3 47 0.001 37.6 4.1 35 686-722 154-188 (383)
115 PHA02929 N1R/p28-like protein; 32.8 33 0.00073 36.8 2.7 16 302-317 198-213 (238)
116 KOG3285 Spindle assembly check 30.9 43 0.00093 34.7 2.9 47 20-67 141-197 (203)
117 PF12861 zf-Apc11: Anaphase-pr 30.5 25 0.00053 32.3 1.1 17 302-318 50-66 (85)
118 cd04813 PA_1 PA_1: Protease-as 30.3 22 0.00048 33.8 0.8 16 670-685 2-17 (117)
119 PRK00107 gidB 16S rRNA methylt 30.3 40 0.00086 34.5 2.6 24 698-721 42-65 (187)
120 KOG4217 Nuclear receptors of t 30.0 17 0.00037 42.3 -0.0 60 212-274 265-329 (605)
121 PRK14903 16S rRNA methyltransf 29.8 31 0.00067 39.6 2.0 23 699-721 235-257 (431)
122 PRK14902 16S rRNA methyltransf 29.8 40 0.00086 38.6 2.8 25 699-723 248-272 (444)
123 COG0286 HsdM Type I restrictio 29.4 59 0.0013 38.1 4.2 49 677-727 164-212 (489)
124 KOG0804 Cytoplasmic Zn-finger 29.4 32 0.00069 40.0 1.9 34 278-317 177-210 (493)
125 PRK00121 trmB tRNA (guanine-N( 29.4 43 0.00093 34.2 2.7 28 695-722 34-61 (202)
126 PF05413 Peptidase_C34: Putati 29.1 15 0.00032 33.5 -0.6 15 635-649 41-55 (92)
127 TIGR03533 L3_gln_methyl protei 28.7 63 0.0014 35.0 4.0 23 700-722 120-142 (284)
128 PF11793 FANCL_C: FANCL C-term 28.6 28 0.0006 30.3 1.0 34 344-378 4-39 (70)
129 PRK11524 putative methyltransf 28.5 45 0.00097 35.9 2.8 32 680-713 188-220 (284)
130 PRK09328 N5-glutamine S-adenos 28.3 63 0.0014 33.8 3.8 25 699-723 106-130 (275)
131 PRK10901 16S rRNA methyltransf 27.6 44 0.00096 38.1 2.7 23 699-721 242-264 (427)
132 TIGR01934 MenG_MenH_UbiE ubiqu 27.4 63 0.0014 32.2 3.5 33 689-723 29-61 (223)
133 PF06524 NOA36: NOA36 protein; 27.2 33 0.00072 37.4 1.5 59 213-283 122-189 (314)
134 PF14881 Tubulin_3: Tubulin do 26.8 38 0.00082 34.6 1.8 52 680-731 48-107 (180)
135 PF03107 C1_2: C1 domain; Int 26.6 59 0.0013 23.8 2.3 29 343-376 1-30 (30)
136 COG2888 Predicted Zn-ribbon RN 26.5 38 0.00082 29.3 1.4 32 264-305 25-57 (61)
137 PF13831 PHD_2: PHD-finger; PD 26.5 23 0.00049 27.3 0.1 19 360-378 3-21 (36)
138 TIGR00762 DegV EDD domain prot 26.2 1.8E+02 0.0039 31.2 6.9 95 624-726 122-247 (275)
139 PLN02244 tocopherol O-methyltr 25.9 70 0.0015 35.5 3.8 24 700-723 117-140 (340)
140 PRK13943 protein-L-isoaspartat 25.5 97 0.0021 34.5 4.8 38 683-722 64-101 (322)
141 PRK01683 trans-aconitate 2-met 25.1 69 0.0015 33.3 3.4 32 689-722 21-52 (258)
142 KOG0827 Predicted E3 ubiquitin 24.8 29 0.00063 39.7 0.6 28 302-349 24-52 (465)
143 smart00550 Zalpha Z-DNA-bindin 24.5 1.3E+02 0.0028 25.8 4.4 49 570-641 4-53 (68)
144 PF03291 Pox_MCEL: mRNA cappin 23.9 32 0.0007 38.4 0.7 19 701-719 62-81 (331)
145 KOG2932 E3 ubiquitin ligase in 23.6 27 0.00059 38.9 0.1 63 216-308 90-157 (389)
146 cd06569 GH20_Sm-chitobiase-lik 23.5 47 0.001 38.6 1.9 24 679-702 15-46 (445)
147 smart00744 RINGv The RING-vari 23.3 48 0.001 27.0 1.4 37 278-317 1-37 (49)
148 PF15656 Tox-HDC: Toxin with a 23.1 61 0.0013 31.5 2.3 26 684-714 89-114 (119)
149 PF12861 zf-Apc11: Anaphase-pr 23.1 34 0.00074 31.4 0.6 30 216-245 32-62 (85)
150 PF00728 Glyco_hydro_20: Glyco 23.0 58 0.0013 35.5 2.5 24 679-702 11-42 (351)
151 PRK10992 iron-sulfur cluster r 23.0 31 0.00068 36.3 0.4 9 706-714 27-35 (220)
152 PRK11036 putative S-adenosyl-L 22.9 84 0.0018 33.0 3.5 32 686-720 32-63 (255)
153 cd07168 NR_DBD_DHR4_like DNA-b 22.6 67 0.0015 29.4 2.4 29 214-243 4-37 (90)
154 KOG1473 Nucleosome remodeling 22.5 19 0.00042 45.7 -1.4 51 216-275 428-479 (1414)
155 PF00130 C1_1: Phorbol esters/ 22.0 73 0.0016 25.5 2.2 34 343-378 12-45 (53)
156 PF07227 DUF1423: Protein of u 21.9 55 0.0012 38.2 2.0 42 265-315 122-163 (446)
157 KOG1734 Predicted RING-contain 21.7 29 0.00064 38.0 -0.1 42 276-317 224-265 (328)
158 PTZ00487 ceramidase; Provision 21.7 73 0.0016 39.3 3.1 72 562-637 93-179 (715)
159 TIGR00138 gidB 16S rRNA methyl 21.6 1E+02 0.0023 31.1 3.8 25 695-720 37-61 (181)
160 PF07649 C1_3: C1-like domain; 21.4 50 0.0011 24.0 1.1 29 278-313 2-30 (30)
161 PHA02862 5L protein; Provision 21.1 47 0.001 33.5 1.1 36 277-318 3-38 (156)
162 cd06568 GH20_SpHex_like A subg 20.9 63 0.0014 35.9 2.2 24 679-702 11-42 (329)
163 cd06570 GH20_chitobiase-like_1 20.7 65 0.0014 35.6 2.3 24 679-702 11-42 (311)
164 TIGR00536 hemK_fam HemK family 20.6 96 0.0021 33.4 3.5 19 703-721 116-134 (284)
165 COG3764 SrtA Sortase (surface 20.6 57 0.0012 34.4 1.7 21 669-689 116-136 (210)
166 PF10367 Vps39_2: Vacuolar sor 20.2 52 0.0011 29.5 1.2 29 216-244 78-107 (109)
167 COG2846 Regulator of cell morp 20.2 37 0.0008 35.8 0.2 8 706-713 27-34 (221)
168 PRK05031 tRNA (uracil-5-)-meth 20.1 84 0.0018 35.3 3.0 41 681-721 183-226 (362)
169 PF09151 DUF1936: Domain of un 20.0 53 0.0012 25.1 1.0 13 293-305 21-33 (36)
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=99.80 E-value=9.3e-21 Score=182.19 Aligned_cols=131 Identities=24% Similarity=0.401 Sum_probs=101.1
Q ss_pred CCCccccccceeEeecCCCCceEeeeeeeeccccccCCCCcceEEE----------eecccCCccceeeeEEEeeeeccC
Q 004169 7 DDDTLTLYVSDYEFLDQNEESISFSVLPLQWDGCDIVGSSEMQVFL----------HGNIGDGPWNFNEQVIAWKFELSY 76 (770)
Q Consensus 7 ~~e~~~~~v~~y~f~d~~~~~v~fs~lp~~~~~~~~~~~~~~~v~l----------~g~~d~gl~~v~~~v~aW~~~l~~ 76 (770)
|++.++..++||+|.|++++||+|+.||++|+...-+.|..+.+++ +|..++|++.++.+|++|.+++..
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 5788899999999999999999999999999998877777788887 799999999999999999999998
Q ss_pred CcceEEEEecCCceeEcCCCchh----HHHHHHHHHHHhhhhhhhccCCccchhHHHHHHHhhcc
Q 004169 77 AQPEIWVLSKQNNWIMLQSPKKS----FKNIVRTILITVHWLYCVKQNPEASRKYIREQMLKVFC 137 (770)
Q Consensus 77 ~~p~i~vls~~~~Wi~L~kPr~~----ye~~ir~vlitv~~LhfvkknPe~s~k~l~~~L~K~fs 137 (770)
..|.+.+++.+.+|++|+||+++ |+.++|++.||++++|+|++||+.+..++|++|.++++
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 66789999999999999999999999999999999864
No 2
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=98.09 E-value=1.7e-06 Score=99.76 Aligned_cols=83 Identities=29% Similarity=0.737 Sum_probs=63.6
Q ss_pred cccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcccCCCCchhHHHHHHHHHhcCCceecCCc-ccccCcCCccCc
Q 004169 277 HQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCPVH-KCFVCQQSEDMN 355 (770)
Q Consensus 277 hqCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~~p~~~~~~~el~krV~~g~~F~CPlH-~C~~C~~~edk~ 355 (770)
+.|++|+-.|.. ..+.++.| ..||.+||+.|+..+.. .++. ...|+||-| .|+.|+..++-
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-----------HAVL-SGGWRCPSCRVCEACGTTGDP- 80 (694)
T ss_pred hhhhhhcccccc---ccCcchhh--hhhcccCCcchhhHHHh-----------HHHh-cCCcccCCceeeeeccccCCc-
Confidence 369999877752 24568889 89999999999987642 2222 345999976 58888876653
Q ss_pred cCccceeeccccccccccccCCCCc
Q 004169 356 VEDLQLAICRRCPKAYHRKCLPTEI 380 (770)
Q Consensus 356 ~~e~qLi~C~RCP~AYH~kCLP~~~ 380 (770)
.++..|.+|..+||.+|+.|..
T Consensus 81 ---~kf~~Ck~cDvsyh~yc~~P~~ 102 (694)
T KOG4443|consen 81 ---KKFLLCKRCDVSYHCYCQKPPN 102 (694)
T ss_pred ---ccccccccccccccccccCCcc
Confidence 3799999999999999996653
No 3
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.61 E-value=4.5e-05 Score=80.17 Aligned_cols=48 Identities=27% Similarity=0.650 Sum_probs=37.6
Q ss_pred CCCcccccccCCC--CceeecCCc-ccc-ccccccccCccccccccCCcccccCCCCcccCccccc
Q 004169 213 ENYFAVCAICDDG--GDVTFCDGR-CLR-SFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVY 274 (770)
Q Consensus 213 d~~d~VC~IC~~g--GeLL~CdG~-C~R-sFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~ 274 (770)
...+.+| +|.++ |+++-|||. |.| |||+.| +||..+ |.+.|+|++|..
T Consensus 218 e~e~lYC-fCqqvSyGqMVaCDn~nCkrEWFH~~C----------VGLk~p---PKG~WYC~eCk~ 269 (271)
T COG5034 218 EGEELYC-FCQQVSYGQMVACDNANCKREWFHLEC----------VGLKEP---PKGKWYCPECKK 269 (271)
T ss_pred cCceeEE-EecccccccceecCCCCCchhheeccc----------cccCCC---CCCcEeCHHhHh
Confidence 3445667 58774 999999986 865 999997 788654 579999999973
No 4
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.55 E-value=5.8e-05 Score=87.22 Aligned_cols=50 Identities=28% Similarity=0.674 Sum_probs=39.2
Q ss_pred ccccCcCCccCccCccceeeccccccccccccCCCCccccccchhhhhhhhhcccCCCceEEEccCCcc
Q 004169 344 KCFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPTEITFSDADENNFQRAWVDLLPNNRILIYCLEHKI 412 (770)
Q Consensus 344 ~C~~C~~~edk~~~e~qLi~C~RCP~AYH~kCLP~~~~f~~~~~e~~~raW~~lL~~~~~LI~C~~H~i 412 (770)
+|..|++.+.- ..++.|+.||.+||..||.|++.-++ +|. .-|+|+.|.+
T Consensus 255 fCsaCn~~~~F----~~~i~CD~Cp~sFH~~CLePPl~~en-------------iP~--g~W~C~ec~~ 304 (613)
T KOG4299|consen 255 FCSACNGSGLF----NDIICCDGCPRSFHQTCLEPPLEPEN-------------IPP--GSWFCPECKI 304 (613)
T ss_pred HHHHhCCcccc----ccceeecCCchHHHHhhcCCCCCccc-------------CCC--CccccCCCee
Confidence 89999998742 35799999999999999999865433 232 2588999986
No 5
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.54 E-value=2.6e-05 Score=90.02 Aligned_cols=50 Identities=30% Similarity=0.689 Sum_probs=40.1
Q ss_pred cccccccCCCCce---eecCCccccccccccccCccccccccCCcccccCCCCcccCcccccc
Q 004169 216 FAVCAICDDGGDV---TFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQ 275 (770)
Q Consensus 216 d~VC~IC~~gGeL---L~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~~ 275 (770)
+++|+.|.+.|.. ||||| |+++||+.|+++. ++...+ |.+.|+|++|..+
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 5699999999876 99997 9999999998752 333333 5689999999843
No 6
>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=97.52 E-value=2.7e-05 Score=62.19 Aligned_cols=46 Identities=28% Similarity=0.748 Sum_probs=33.6
Q ss_pred cccccCC---CCceeecCCccccccccccccCccccccccCCcccccC-CCCcccCccccc
Q 004169 218 VCAICDD---GGDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQID-AVPNFLCQNCVY 274 (770)
Q Consensus 218 VC~IC~~---gGeLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~-~~~~W~C~eC~~ 274 (770)
+|.+|+. .+++|.|+ .|.++||+.| +|++..... +...|+|++|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~-~C~~~~H~~C----------~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCD-SCNRWYHQEC----------VGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBS-TTSCEEETTT----------STSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcC-CCChhhCccc----------CCCChhhccCCCCcEECcCCcC
Confidence 5888987 56799999 5999999997 344332111 234899999974
No 7
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=97.52 E-value=4.5e-05 Score=85.73 Aligned_cols=89 Identities=27% Similarity=0.657 Sum_probs=64.4
Q ss_pred CCCcccccccCCC-----CceeecCCccccccccccccCccccccccCCcccccCCCCcccCccccccCcc---cccccc
Q 004169 213 ENYFAVCAICDDG-----GDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQEHQ---CFACGM 284 (770)
Q Consensus 213 d~~d~VC~IC~~g-----GeLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~~qhq---CfvCgk 284 (770)
|..|+.|++|... ..++.||| |.-+.|..| -|+.-. |.+.|+|..|.++.|+ |.-|-.
T Consensus 190 d~~d~~C~~c~~t~~eN~naiVfCdg-C~i~VHq~C----------YGI~f~---peG~WlCrkCi~~~~~i~~C~fCps 255 (669)
T COG5141 190 DEFDDICTKCTSTHNENSNAIVFCDG-CEICVHQSC----------YGIQFL---PEGFWLCRKCIYGEYQIRCCSFCPS 255 (669)
T ss_pred hhhhhhhHhccccccCCcceEEEecC-cchhhhhhc----------ccceec---CcchhhhhhhcccccceeEEEeccC
Confidence 4678999999765 34999996 999999997 566322 5789999999988653 555522
Q ss_pred cCC-----CCC--------------------------------------------CCCCceeeccCCCcCCcCcchhhcc
Q 004169 285 LGS-----SDK--------------------------------------------SSSQEVFPCVSATCGQFYHPECVSK 315 (770)
Q Consensus 285 lGs-----sd~--------------------------------------------ss~~eV~kCsv~~CGrfYH~~CL~~ 315 (770)
... +|+ --.+.-++|+..+|-+.||..|...
T Consensus 256 ~dGaFkqT~dgrW~H~iCA~~~pelsF~~l~~~dpI~~i~sVs~srwkl~C~iCk~~~GtcIqCs~~nC~~aYHVtCArr 335 (669)
T COG5141 256 SDGAFKQTSDGRWGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFNCTRAYHVTCARR 335 (669)
T ss_pred CCCceeeccCCchHhHhHHHhcchhccccccccchhhhhcccchhhHhheeeEEcccCcceeeecccchhhhhhhhhhhh
Confidence 110 000 0134668999999999999999764
No 8
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.48 E-value=3.4e-05 Score=81.60 Aligned_cols=83 Identities=25% Similarity=0.586 Sum_probs=62.3
Q ss_pred CCCcccccccCCC----------CceeecCCccccccccccccCccccccccCCcccccC--CCCcccCccccccCcccc
Q 004169 213 ENYFAVCAICDDG----------GDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQID--AVPNFLCQNCVYQEHQCF 280 (770)
Q Consensus 213 d~~d~VC~IC~~g----------GeLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~--~~~~W~C~eC~~~qhqCf 280 (770)
.....+|-.|..+ -+|+.|. .|.|+=|+.|+ .+|..-+. ..-.|.|.+|.+ |.
T Consensus 221 a~Pn~YCDFclgdsr~nkkt~~peelvscs-dcgrsghpscl----------qft~nm~~avk~yrwqcieck~----cs 285 (336)
T KOG1244|consen 221 AQPNPYCDFCLGDSRENKKTGMPEELVSCS-DCGRSGHPSCL----------QFTANMIAAVKTYRWQCIECKY----CS 285 (336)
T ss_pred ccCCcccceeccccccccccCCchhhcchh-hcCCCCCcchh----------hhhHHHHHHHHhheeeeeecce----ec
Confidence 4456789999643 3699998 69999999984 34321110 135899999996 99
Q ss_pred cccccCCCCCCCCCceeeccCCCcCCcCcchhhcccC
Q 004169 281 ACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLL 317 (770)
Q Consensus 281 vCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~ 317 (770)
+||-..- ..+++.| ..|.|-||-.|+.+.+
T Consensus 286 icgtsen-----ddqllfc--ddcdrgyhmyclsppm 315 (336)
T KOG1244|consen 286 ICGTSEN-----DDQLLFC--DDCDRGYHMYCLSPPM 315 (336)
T ss_pred cccCcCC-----CceeEee--cccCCceeeEecCCCc
Confidence 9986442 4589999 8999999999998644
No 9
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.47 E-value=6.4e-05 Score=80.39 Aligned_cols=51 Identities=27% Similarity=0.565 Sum_probs=39.8
Q ss_pred cccCCCcccccccCCCCceeecCCc-cc-cccccccccCccccccccCCcccccCCCCcccCccccc
Q 004169 210 DKDENYFAVCAICDDGGDVTFCDGR-CL-RSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVY 274 (770)
Q Consensus 210 d~dd~~d~VC~IC~~gGeLL~CdG~-C~-RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~ 274 (770)
+.+...=-+|. |..+|+++-||+. |+ .|||+.| +||+.+ |.+.|+|+.|..
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 33444445567 7789999999974 99 9999997 788855 468899999984
No 10
>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 KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.35 E-value=6.3e-05 Score=80.00 Aligned_cols=82 Identities=18% Similarity=0.201 Sum_probs=62.6
Q ss_pred CCcccccccCCCC---------ceeecCCccccccccccccCccccccccCCcccccC--CCCcccCccccccCcccccc
Q 004169 214 NYFAVCAICDDGG---------DVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQID--AVPNFLCQNCVYQEHQCFAC 282 (770)
Q Consensus 214 ~~d~VC~IC~~gG---------eLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~--~~~~W~C~eC~~~qhqCfvC 282 (770)
.....|.+|.++- -+|+|. +|.-++|+.|++ ++.+-+. ..-.|.|.+|. .|.+|
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 4456799998763 399999 799999999853 3322111 13479999999 49999
Q ss_pred cccCCCCCCCCCceeeccCCCcCCcCcchhhcccC
Q 004169 283 GMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLL 317 (770)
Q Consensus 283 gklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~ 317 (770)
+++.. ..+++.| ..|.|-||..||+..-
T Consensus 321 ~~P~~-----E~E~~FC--D~CDRG~HT~CVGL~~ 348 (381)
T KOG1512|consen 321 LGPVI-----ESEHLFC--DVCDRGPHTLCVGLQD 348 (381)
T ss_pred CCccc-----chheecc--ccccCCCCcccccccc
Confidence 98753 4588999 8999999999998643
No 12
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=97.27 E-value=0.00024 Score=87.20 Aligned_cols=142 Identities=25% Similarity=0.478 Sum_probs=88.1
Q ss_pred cccCCCcccccccCCCC-----ceeecCCccccccccccccCccccccccCCcccccCCCCcccCccccccC---ccccc
Q 004169 210 DKDENYFAVCAICDDGG-----DVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQE---HQCFA 281 (770)
Q Consensus 210 d~dd~~d~VC~IC~~gG-----eLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~~q---hqCfv 281 (770)
+.++..|.+|.||.++- .+|.||| |.-+.|+.| .|+. ..+.+.|+|..|...+ ..|..
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 35667789999998873 4999996 999999997 5642 2268999999998765 46777
Q ss_pred ccccCCCCCCCCCceeeccCCCcCCcCcchhhcccCCCCchhHHHHHHHHH---hcCCceecCCcccccCcCCccCccCc
Q 004169 282 CGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERI---AAGESFTCPVHKCFVCQQSEDMNVED 358 (770)
Q Consensus 282 CgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~~p~~~~~~~el~krV---~~g~~F~CPlH~C~~C~~~edk~~~e 358 (770)
|-..| .-|+ ...=|+.-|.-|..-.++..... +-+..-| ..-..-+ =.-.|..|+..+ -
T Consensus 279 cp~~~--------gAFk--qt~dgrw~Hv~caiwipev~F~n--t~~~E~I~~i~~i~~aR-wkL~cy~cK~~~-----~ 340 (1051)
T KOG0955|consen 279 CPSKG--------GAFK--QTDDGRWAHVVCAIWIPEVSFAN--TVFLEPIDSIENIPPAR-WKLTCYICKQKG-----L 340 (1051)
T ss_pred ccCCC--------Ccce--eccCCceeeeehhhccccccccc--chhhccccchhcCcHhh-hhceeeeeccCC-----C
Confidence 74332 2222 24568888888865433211100 0000000 0000000 023688998866 1
Q ss_pred cceeec--cccccccccccC-CCCcccc
Q 004169 359 LQLAIC--RRCPKAYHRKCL-PTEITFS 383 (770)
Q Consensus 359 ~qLi~C--~RCP~AYH~kCL-P~~~~f~ 383 (770)
+..++| .+|-+|||..|- .+|+.+.
T Consensus 341 gaciqcs~~~c~~a~hvtca~~agl~m~ 368 (1051)
T KOG0955|consen 341 GACIQCSKANCYTAFHVTCARRAGLYMK 368 (1051)
T ss_pred CcceecchhhhhhhhhhhhHhhcCceEe
Confidence 357788 579999999996 4455443
No 13
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.22 E-value=0.00029 Score=74.75 Aligned_cols=96 Identities=26% Similarity=0.620 Sum_probs=63.2
Q ss_pred CCcccCccccccCcccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcccCCCCchhHHHHHHHHHhcCCceecC-C
Q 004169 264 VPNFLCQNCVYQEHQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCP-V 342 (770)
Q Consensus 264 ~~~W~C~eC~~~qhqCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~~p~~~~~~~el~krV~~g~~F~CP-l 342 (770)
...-||..|.-.+..= ++.|. ..+++-| ..|||.=||.|+.--. .|..-| ..-.|.|= .
T Consensus 222 ~Pn~YCDFclgdsr~n---kkt~~-----peelvsc--sdcgrsghpsclqft~---------nm~~av-k~yrwqciec 281 (336)
T KOG1244|consen 222 QPNPYCDFCLGDSREN---KKTGM-----PEELVSC--SDCGRSGHPSCLQFTA---------NMIAAV-KTYRWQCIEC 281 (336)
T ss_pred cCCcccceeccccccc---cccCC-----chhhcch--hhcCCCCCcchhhhhH---------HHHHHH-Hhheeeeeec
Confidence 3456777776432111 11221 3488899 7999999999986321 121111 11245553 2
Q ss_pred cccccCcCCccCccCccceeeccccccccccccCCCCcccc
Q 004169 343 HKCFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPTEITFS 383 (770)
Q Consensus 343 H~C~~C~~~edk~~~e~qLi~C~RCP~AYH~kCLP~~~~f~ 383 (770)
.+|..|+.++|++ ||+-|+-|.+.||.+||-++.+-.
T Consensus 282 k~csicgtsendd----qllfcddcdrgyhmyclsppm~ep 318 (336)
T KOG1244|consen 282 KYCSICGTSENDD----QLLFCDDCDRGYHMYCLSPPMVEP 318 (336)
T ss_pred ceeccccCcCCCc----eeEeecccCCceeeEecCCCcCCC
Confidence 5899999988764 999999999999999998877643
No 14
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=97.02 E-value=0.00027 Score=82.19 Aligned_cols=83 Identities=23% Similarity=0.551 Sum_probs=62.7
Q ss_pred CCCcccccccCCCC-----ceeecCCccccccccccccCccccccccCCcccccCCCCcccCccccccCcccccccccCC
Q 004169 213 ENYFAVCAICDDGG-----DVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQEHQCFACGMLGS 287 (770)
Q Consensus 213 d~~d~VC~IC~~gG-----eLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~~qhqCfvCgklGs 287 (770)
......|.+|+..| -|+.|. .|...||+.|.. +=++.+.+ ..-|.|+.|.. |-.|+..|.
T Consensus 15 ~~~~~mc~l~~s~G~~~ag~m~ac~-~c~~~yH~~cvt--------~~~~~~~l--~~gWrC~~crv----Ce~c~~~gD 79 (694)
T KOG4443|consen 15 IIVCLMCPLCGSSGKGRAGRLLACS-DCGQKYHPYCVT--------SWAQHAVL--SGGWRCPSCRV----CEACGTTGD 79 (694)
T ss_pred hhhhhhhhhhccccccccCcchhhh-hhcccCCcchhh--------HHHhHHHh--cCCcccCCcee----eeeccccCC
Confidence 34457788998764 499999 799999999743 22333322 35599999994 999997764
Q ss_pred CCCCCCCceeeccCCCcCCcCcchhhcccC
Q 004169 288 SDKSSSQEVFPCVSATCGQFYHPECVSKLL 317 (770)
Q Consensus 288 sd~ss~~eV~kCsv~~CGrfYH~~CL~~~~ 317 (770)
....+.| ..|.-.||-.|+.+..
T Consensus 80 -----~~kf~~C--k~cDvsyh~yc~~P~~ 102 (694)
T KOG4443|consen 80 -----PKKFLLC--KRCDVSYHCYCQKPPN 102 (694)
T ss_pred -----ccccccc--ccccccccccccCCcc
Confidence 3578899 8999999999987653
No 15
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=96.77 E-value=0.00062 Score=79.94 Aligned_cols=157 Identities=21% Similarity=0.465 Sum_probs=92.5
Q ss_pred CcccccccCCC-----CceeecCCccccccccccccCccccccccCCcccccCCCCcccCcccccc-CcccccccccCCC
Q 004169 215 YFAVCAICDDG-----GDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQ-EHQCFACGMLGSS 288 (770)
Q Consensus 215 ~d~VC~IC~~g-----GeLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~~-qhqCfvCgklGss 288 (770)
.+.+|-+|..+ .+|++|| .|.-..|..| .|+.+. |.+.|+|.-|..+ ...|..|=+.|-.
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 56789999776 4699999 7999999997 677654 4699999999987 4689999777643
Q ss_pred CCCCCCceeeccCCCcCCcCcchhhcccCCCCchhHHHHHHHHHhcC-----CceecCCcccccCcCCccCccCccceee
Q 004169 289 DKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAG-----ESFTCPVHKCFVCQQSEDMNVEDLQLAI 363 (770)
Q Consensus 289 d~ss~~eV~kCsv~~CGrfYH~~CL~~~~~p~~~~~~~el~krV~~g-----~~F~CPlH~C~~C~~~edk~~~e~qLi~ 363 (770)
-+++ ..=.++-|..|.--.|.-..+. .+..+=|... ..| .-.|..|+... +.-++
T Consensus 336 mK~~---------~sgT~wAHvsCALwIPEVsie~--~ekmePItkfs~IpesRw---slvC~LCk~k~------GACIq 395 (893)
T KOG0954|consen 336 MKPT---------KSGTKWAHVSCALWIPEVSIEC--PEKMEPITKFSHIPESRW---SLVCNLCKVKS------GACIQ 395 (893)
T ss_pred cccc---------CCCCeeeEeeeeeccceeeccC--HhhcCcccccCCCcHHHH---HHHHHHhcccC------cceEE
Confidence 2221 1222778999854322211111 1111000000 011 13588887743 24455
Q ss_pred c--cccccccccccC-CCCccccccchhhhhhhhhcccCCCceEEEccCCcccc
Q 004169 364 C--RRCPKAYHRKCL-PTEITFSDADENNFQRAWVDLLPNNRILIYCLEHKIIS 414 (770)
Q Consensus 364 C--~RCP~AYH~kCL-P~~~~f~~~~~e~~~raW~~lL~~~~~LI~C~~H~i~~ 414 (770)
| ..|-.+||..|. .+|..+.....++ ..-...-||+.|....
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 3444333222111 1113456778777533
No 16
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=96.74 E-value=0.00088 Score=78.17 Aligned_cols=84 Identities=27% Similarity=0.809 Sum_probs=64.8
Q ss_pred ccccCCC-C----ceeecCCc-cccccccccccCccccccccCCcccccCCCCcccCcccccc-----------------
Q 004169 219 CAICDDG-G----DVTFCDGR-CLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQ----------------- 275 (770)
Q Consensus 219 C~IC~~g-G----eLL~CdG~-C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~~----------------- 275 (770)
|-+|-|- | -|+.|||. |--+.|..| .|| .+| |.+.|+|.-|+..
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 8899663 2 39999995 999999997 676 344 6899999999843
Q ss_pred ------------------------------------------CcccccccccCCCCCCCCCceeeccCCCcCCcCcchhh
Q 004169 276 ------------------------------------------EHQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECV 313 (770)
Q Consensus 276 ------------------------------------------qhqCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL 313 (770)
.-.|+||.+.|-......+--+.|.-..|.+.||..|.
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 12788888877654444456689999999999999997
Q ss_pred cc
Q 004169 314 SK 315 (770)
Q Consensus 314 ~~ 315 (770)
..
T Consensus 155 Q~ 156 (900)
T KOG0956|consen 155 QR 156 (900)
T ss_pred hh
Confidence 53
No 17
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=96.70 E-value=0.0031 Score=63.24 Aligned_cols=26 Identities=31% Similarity=0.494 Sum_probs=22.2
Q ss_pred cCccceeeccccccccccccCCCCcc
Q 004169 356 VEDLQLAICRRCPKAYHRKCLPTEIT 381 (770)
Q Consensus 356 ~~e~qLi~C~RCP~AYH~kCLP~~~~ 381 (770)
+.+.-|++|..|-.|||...||+...
T Consensus 119 N~~nVLFRC~~C~RawH~~HLP~~~~ 144 (175)
T PF15446_consen 119 NPDNVLFRCTSCHRAWHFEHLPPPSG 144 (175)
T ss_pred ChhheEEecCCccceeehhhCCCCcC
Confidence 35668999999999999999999654
No 18
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=96.60 E-value=0.00079 Score=79.95 Aligned_cols=51 Identities=35% Similarity=0.813 Sum_probs=39.7
Q ss_pred cCCCcccccccCCCCceeecCCccccccccccccCccccccccCCcccccCCCCcccCccccc
Q 004169 212 DENYFAVCAICDDGGDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVY 274 (770)
Q Consensus 212 dd~~d~VC~IC~~gGeLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~ 274 (770)
++.....|.||.++|++|+|+ .|+.+||+.|+ |....++ +.+.|+|+.|..
T Consensus 43 ~~~~~e~c~ic~~~g~~l~c~-tC~~s~h~~cl----------~~pl~~~-p~~~~~c~Rc~~ 93 (696)
T KOG0383|consen 43 DDAEQEACRICADGGELLWCD-TCPASFHASCL----------GPPLTPQ-PNGEFICPRCFC 93 (696)
T ss_pred chhhhhhhhhhcCCCcEEEec-cccHHHHHHcc----------CCCCCcC-Cccceeeeeecc
Confidence 455568899999999999999 79999999974 3333333 445599999953
No 19
>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 KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=95.73 E-value=0.0059 Score=74.74 Aligned_cols=50 Identities=24% Similarity=0.500 Sum_probs=37.7
Q ss_pred cCCCcccccccCCCCceeecCCccccccccccccCccccccccCCcccccCCCCcccCcccc
Q 004169 212 DENYFAVCAICDDGGDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCV 273 (770)
Q Consensus 212 dd~~d~VC~IC~~gGeLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~ 273 (770)
....+++|.+|.+.|+++||+ .|+|.+|.+|..... ...+...|.|.=|.
T Consensus 340 ~~~~ddhcrf~~d~~~~lc~E-t~prvvhlEcv~hP~-----------~~~~s~~~e~evc~ 389 (1414)
T KOG1473|consen 340 EIEYDDHCRFCHDLGDLLCCE-TCPRVVHLECVFHPR-----------FAVPSAFWECEVCN 389 (1414)
T ss_pred ceeecccccccCcccceeecc-cCCceEEeeecCCcc-----------ccCCCccchhhhhh
Confidence 566789999999999999999 799999999854211 11145678777544
No 21
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.35 E-value=0.0096 Score=70.69 Aligned_cols=47 Identities=23% Similarity=0.564 Sum_probs=35.3
Q ss_pred cccccccCCCC---ceeecCCccccc-cccccccCccccccccCCcccccCCCCcccCccccc
Q 004169 216 FAVCAICDDGG---DVTFCDGRCLRS-FHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVY 274 (770)
Q Consensus 216 d~VC~IC~~gG---eLL~CdG~C~Rs-FH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~ 274 (770)
..-|.||+... -||.|++ |... ||..|++ ++.-++ +.+.|+|.+|.-
T Consensus 215 ~~~C~IC~~~DpEdVLLLCDs-CN~~~YH~YCLD----------Pdl~ei-P~~eWYC~NC~d 265 (1134)
T KOG0825|consen 215 EVKCDICTVHDPEDVLLLCDS-CNKVYYHVYCLD----------PDLSES-PVNEWYCTNCSL 265 (1134)
T ss_pred cccceeeccCChHHhheeecc-cccceeeccccC----------cccccc-cccceecCcchh
Confidence 45699999775 2999995 9999 9999854 222233 468999999973
No 22
>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=95.23 E-value=0.015 Score=46.38 Aligned_cols=34 Identities=35% Similarity=0.774 Sum_probs=27.9
Q ss_pred ccccCcCCccCccCccceeeccccccccccccCCCCcc
Q 004169 344 KCFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPTEIT 381 (770)
Q Consensus 344 ~C~~C~~~edk~~~e~qLi~C~RCP~AYH~kCLP~~~~ 381 (770)
+|.+|++.++ +..++.|..|..+||..|+.+...
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 4888988443 458999999999999999988654
No 23
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=94.26 E-value=0.026 Score=60.71 Aligned_cols=69 Identities=22% Similarity=0.490 Sum_probs=47.8
Q ss_pred CceeeccCCCcCCcCcchhhcccCCCCchhHHHHHHHHHhcCCceecCC-cccccCcCCccCccCccceeeccccccccc
Q 004169 294 QEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCPV-HKCFVCQQSEDMNVEDLQLAICRRCPKAYH 372 (770)
Q Consensus 294 ~eV~kCsv~~CGrfYH~~CL~~~~~p~~~~~~~el~krV~~g~~F~CPl-H~C~~C~~~edk~~~e~qLi~C~RCP~AYH 372 (770)
..++.| +.|-..|||.|+.-.+ +|...+ ..-.|.|-- ..|..|.+... +..++-|++|.+.||
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 356778 8999999999997543 221111 123466642 46777777653 346899999999999
Q ss_pred cccCCC
Q 004169 373 RKCLPT 378 (770)
Q Consensus 373 ~kCLP~ 378 (770)
+.|+--
T Consensus 341 T~CVGL 346 (381)
T KOG1512|consen 341 TLCVGL 346 (381)
T ss_pred cccccc
Confidence 999744
No 24
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=94.12 E-value=0.007 Score=67.97 Aligned_cols=87 Identities=20% Similarity=0.481 Sum_probs=55.7
Q ss_pred cCCCcccccccCCC--CceeecCCccccccccccccCccccccccCCccccc-CCCCcccCcccccc-CcccccccccCC
Q 004169 212 DENYFAVCAICDDG--GDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQI-DAVPNFLCQNCVYQ-EHQCFACGMLGS 287 (770)
Q Consensus 212 dd~~d~VC~IC~~g--GeLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev-~~~~~W~C~eC~~~-qhqCfvCgklGs 287 (770)
++.+. +|..|.++ |+-.-|. -=.+.||..|..=. .|. -.|....+ .-.+.-+|..|-.. ...|.+|++.-.
T Consensus 271 ~~~~~-iC~~C~K~V~g~~~ac~-Am~~~fHv~CFtC~--~C~-r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~ 345 (468)
T KOG1701|consen 271 EDYFG-ICAFCHKTVSGQGLAVE-AMDQLFHVQCFTCR--TCR-RQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPIM 345 (468)
T ss_pred hhhhh-hhhhcCCcccCcchHHH-HhhhhhcccceehH--hhh-hhhccccccccCCcccchHHHHHHHHHHhhhhhHHH
Confidence 33333 99999986 7777786 46799999985410 020 00111110 11467889999653 478999998653
Q ss_pred CCCCCCCceeeccCCCcCCcCcchhh
Q 004169 288 SDKSSSQEVFPCVSATCGQFYHPECV 313 (770)
Q Consensus 288 sd~ss~~eV~kCsv~~CGrfYH~~CL 313 (770)
..++ ..||+.||+.|.
T Consensus 346 ------d~iL----rA~GkayHp~CF 361 (468)
T KOG1701|consen 346 ------DRIL----RALGKAYHPGCF 361 (468)
T ss_pred ------HHHH----HhcccccCCCce
Confidence 2444 469999999993
No 25
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=94.11 E-value=0.022 Score=65.07 Aligned_cols=57 Identities=21% Similarity=0.486 Sum_probs=39.8
Q ss_pred cccCCCcccccccCCCC-----ceeecCCccccccccccccCccccccccCCccccc-CCCCcccCcccccc
Q 004169 210 DKDENYFAVCAICDDGG-----DVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQI-DAVPNFLCQNCVYQ 275 (770)
Q Consensus 210 d~dd~~d~VC~IC~~gG-----eLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev-~~~~~W~C~eC~~~ 275 (770)
|.....+..|.+|..|| .||.|++ |..+||..|.... ++.+.. ++...|+|.-|.++
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-CRQWYHQACHQPL--------IKDELAGDPFYEWFCDVCNRG 224 (464)
T ss_pred CccccccceeeeeecCCcCccceeeeecc-cccHHHHHhccCC--------CCHhhccCccceEeehhhccc
Confidence 44444455699998764 5999995 9999999996532 222221 24578999999875
No 26
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=93.38 E-value=0.045 Score=65.53 Aligned_cols=81 Identities=27% Similarity=0.673 Sum_probs=57.4
Q ss_pred ccccccccccccCccccccccCCcccccCCCCcccCcccccc---------------CcccccccccCCCCCCCCCceee
Q 004169 234 RCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQ---------------EHQCFACGMLGSSDKSSSQEVFP 298 (770)
Q Consensus 234 ~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~~---------------qhqCfvCgklGssd~ss~~eV~k 298 (770)
.|.|.+|..|..+ .+. .++...|.|+.|... +..|.+|+.. ++++.
T Consensus 1 ~~~r~~~~~~~~p--------~~~---~~~~~~~k~~~~e~~~~~~~~~~~~~~~~~~e~c~ic~~~--------g~~l~ 61 (696)
T KOG0383|consen 1 TCPRAYHRVCLDP--------KLK---EEPEMDPKCPGCESSSAQVEAKDDDWDDAEQEACRICADG--------GELLW 61 (696)
T ss_pred CCCcccCcCCCCc--------ccc---cCCcCCccCcchhhcccccccccCCcchhhhhhhhhhcCC--------CcEEE
Confidence 3899999998542 122 223678999998732 3589999864 47888
Q ss_pred ccCCCcCCcCcchhhcccCCCCchhHHHHHHHHHhcCCceecCCcccccCcCC
Q 004169 299 CVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCPVHKCFVCQQS 351 (770)
Q Consensus 299 Csv~~CGrfYH~~CL~~~~~p~~~~~~~el~krV~~g~~F~CPlH~C~~C~~~ 351 (770)
| ..|...||..|+.....+ +..+. |.|| .| .|-..
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 899999999999765432 22345 9998 56 66554
No 27
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=92.47 E-value=0.071 Score=63.72 Aligned_cols=33 Identities=33% Similarity=0.837 Sum_probs=27.9
Q ss_pred ccccCcCCccCccCccceeeccccccc-cccccCCCCc
Q 004169 344 KCFVCQQSEDMNVEDLQLAICRRCPKA-YHRKCLPTEI 380 (770)
Q Consensus 344 ~C~~C~~~edk~~~e~qLi~C~RCP~A-YH~kCLP~~~ 380 (770)
.|..|...+. +.-|+.|+-|..+ ||.+||.++.
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 6888888654 4479999999999 9999999965
No 28
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=92.22 E-value=0.16 Score=46.74 Aligned_cols=84 Identities=19% Similarity=0.430 Sum_probs=48.8
Q ss_pred cccccCCC-CceeecCCccccccccccccCccc-cccccCCcccccCCCCcccCccccccCcccccccccCCCCCCCCCc
Q 004169 218 VCAICDDG-GDVTFCDGRCLRSFHATITAGKNA-LCQSLGYTQAQIDAVPNFLCQNCVYQEHQCFACGMLGSSDKSSSQE 295 (770)
Q Consensus 218 VC~IC~~g-GeLL~CdG~C~RsFH~~Cl~g~~s-~C~sLGlt~~ev~~~~~W~C~eC~~~qhqCfvCgklGssd~ss~~e 295 (770)
.|.+|... |.|..-. -.++.|..|..-... .... +.+..++. .... =++ .....|.+|++. .+-
T Consensus 2 ~C~lC~~~~Galk~t~--~~~WvHv~Cal~~~~~~~~~-~~~~~~v~-~~~i-~~~--~~~~~C~iC~~~-------~G~ 67 (110)
T PF13832_consen 2 SCVLCPKRGGALKRTS--DGQWVHVLCALWIPEVIFNN-GESMEPVD-ISNI-PPS--RFKLKCSICGKS-------GGA 67 (110)
T ss_pred ccEeCCCCCCcccCcc--CCcEEEeEccceeCccEEee-chhcCccc-ceee-cch--hcCCcCcCCCCC-------Cce
Confidence 58999876 4454444 489999999532110 0000 00001110 0000 010 135679999874 356
Q ss_pred eeeccCCCcCCcCcchhhcc
Q 004169 296 VFPCVSATCGQFYHPECVSK 315 (770)
Q Consensus 296 V~kCsv~~CGrfYH~~CL~~ 315 (770)
.++|...+|.+.||+.|...
T Consensus 68 ~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 68 CIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred eEEcCCCCCCcCCCHHHHHH
Confidence 89999999999999999754
No 29
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=92.09 E-value=0.088 Score=48.52 Aligned_cols=102 Identities=23% Similarity=0.437 Sum_probs=58.4
Q ss_pred ccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcccCCCCchhHHHHHH----HHHhcCCceecCCcccccCcCCcc
Q 004169 278 QCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELR----ERIAAGESFTCPVHKCFVCQQSED 353 (770)
Q Consensus 278 qCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~~p~~~~~~~el~----krV~~g~~F~CPlH~C~~C~~~ed 353 (770)
.|.+|...| ..++- ..-+.+.|..|..-.+.....+.. .+. .++.. .. -...|..|+...
T Consensus 2 ~C~lC~~~~--------Galk~--t~~~~WvHv~Cal~~~~~~~~~~~-~~~~v~~~~i~~-~~---~~~~C~iC~~~~- 65 (110)
T PF13832_consen 2 SCVLCPKRG--------GALKR--TSDGQWVHVLCALWIPEVIFNNGE-SMEPVDISNIPP-SR---FKLKCSICGKSG- 65 (110)
T ss_pred ccEeCCCCC--------CcccC--ccCCcEEEeEccceeCccEEeech-hcCcccceeecc-hh---cCCcCcCCCCCC-
Confidence 588998754 23333 235899999998654432211110 000 00100 11 135789999863
Q ss_pred CccCccceeeccc--cccccccccCCC-CccccccchhhhhhhhhcccCCCceEEEccCC
Q 004169 354 MNVEDLQLAICRR--CPKAYHRKCLPT-EITFSDADENNFQRAWVDLLPNNRILIYCLEH 410 (770)
Q Consensus 354 k~~~e~qLi~C~R--CP~AYH~kCLP~-~~~f~~~~~e~~~raW~~lL~~~~~LI~C~~H 410 (770)
+..++|.. |..+||..|.-. +..+..... . .+....+||.+|
T Consensus 66 -----G~~i~C~~~~C~~~fH~~CA~~~g~~~~~~~~-------~---~~~~~~~~C~~H 110 (110)
T PF13832_consen 66 -----GACIKCSHPGCSTAFHPTCARKAGLYFEIENE-------E---DNVQFIAYCPKH 110 (110)
T ss_pred -----ceeEEcCCCCCCcCCCHHHHHHCCCeEEeeec-------C---CCceEEEECCCC
Confidence 36899999 999999999743 333322110 0 023678999988
No 30
>PRK05785 hypothetical protein; Provisional
Probab=90.33 E-value=0.56 Score=48.75 Aligned_cols=47 Identities=21% Similarity=0.380 Sum_probs=36.3
Q ss_pred cccccCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 674 RYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 674 rytsfgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
|..|||++-- --+++++.+..|..+|.+|+|++||..+++..+.++.
T Consensus 27 ~~~s~g~~~~---wr~~~~~~l~~~~~~~~~VLDlGcGtG~~~~~l~~~~ 73 (226)
T PRK05785 27 RFISFNQDVR---WRAELVKTILKYCGRPKKVLDVAAGKGELSYHFKKVF 73 (226)
T ss_pred hhccCCCcHH---HHHHHHHHHHHhcCCCCeEEEEcCCCCHHHHHHHHhc
Confidence 5678888832 2235667777777789999999999999999987763
No 31
>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]
Probab=89.85 E-value=0.27 Score=52.20 Aligned_cols=59 Identities=19% Similarity=0.381 Sum_probs=44.9
Q ss_pred hhhhhHHHHhhccccccccccccccccccCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 650 EILCQIFQWKRKLDVYLAPFLHGMRYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 650 ~~l~q~~~w~~kl~~~lapfl~g~rytsfgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
.+-.+|..+-+... +-=|||.|.+--.+|.+....- +|+.|+|.|||+.|+..++.+.-
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 45566666666655 3348999999998877665433 99999999999999998877653
No 32
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=87.53 E-value=0.62 Score=49.23 Aligned_cols=44 Identities=18% Similarity=0.375 Sum_probs=39.1
Q ss_pred ccCccc-chhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 677 SFGRHF-TKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 677 sfgrhf-tk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
+||.|| +...-+..|++.+. +++|++|+|+.||...++..|.++
T Consensus 6 ~~GQnfl~d~~~~~~iv~~~~--~~~~~~VLEIG~G~G~lt~~L~~~ 50 (258)
T PRK14896 6 KLGQHFLIDDRVVDRIVEYAE--DTDGDPVLEIGPGKGALTDELAKR 50 (258)
T ss_pred cCCccccCCHHHHHHHHHhcC--CCCcCeEEEEeCccCHHHHHHHHh
Confidence 799999 78889999999886 779999999999999998887764
No 33
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=86.92 E-value=0.84 Score=48.70 Aligned_cols=49 Identities=24% Similarity=0.407 Sum_probs=38.3
Q ss_pred ccc-ccccCcccc-hhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 672 GMR-YTSFGRHFT-KVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 672 g~r-ytsfgrhft-k~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
|+| -.+||+||. ..+-+..|++.+. +.+|++|+|+.||...++..+.++
T Consensus 13 ~~~~~k~~gq~fl~~~~i~~~i~~~l~--~~~~~~VLEiG~G~G~lt~~L~~~ 63 (272)
T PRK00274 13 GHRAKKSLGQNFLIDENILDKIVDAAG--PQPGDNVLEIGPGLGALTEPLLER 63 (272)
T ss_pred CCCCCcccCcCcCCCHHHHHHHHHhcC--CCCcCeEEEeCCCccHHHHHHHHh
Confidence 444 367999995 5555677888885 479999999999999999877654
No 34
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=84.61 E-value=0.53 Score=41.70 Aligned_cols=33 Identities=30% Similarity=0.595 Sum_probs=27.7
Q ss_pred CCCcccccccCCC-Cceeec-CCcccccccccccc
Q 004169 213 ENYFAVCAICDDG-GDVTFC-DGRCLRSFHATITA 245 (770)
Q Consensus 213 d~~d~VC~IC~~g-GeLL~C-dG~C~RsFH~~Cl~ 245 (770)
..+...|.+|... |..+.| .+.|.++||+.|..
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 4556899999999 998888 45799999999953
No 35
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=83.89 E-value=0.53 Score=54.32 Aligned_cols=52 Identities=29% Similarity=0.539 Sum_probs=39.5
Q ss_pred cccccCcCCccCccCccceeeccccccccccccCCCCccccccchhhhhhhhhcccCCCceEEEccCCc
Q 004169 343 HKCFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPTEITFSDADENNFQRAWVDLLPNNRILIYCLEHK 411 (770)
Q Consensus 343 H~C~~C~~~edk~~~e~qLi~C~RCP~AYH~kCLP~~~~f~~~~~e~~~raW~~lL~~~~~LI~C~~H~ 411 (770)
-.|-+|+.+-+.- .+++|+.|...||..||.+++..+++. +....|.|..|.
T Consensus 545 ysCgiCkks~dQH----ll~~CDtC~lhYHlGCL~PPLTR~Pkk-------------~kn~gWqCsECd 596 (707)
T KOG0957|consen 545 YSCGICKKSTDQH----LLTQCDTCHLHYHLGCLSPPLTRLPKK-------------NKNFGWQCSECD 596 (707)
T ss_pred eeeeeeccchhhH----HHhhcchhhceeeccccCCccccCccc-------------ccCcceeecccc
Confidence 4699999876542 678999999999999999988655422 124568888884
No 36
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=82.77 E-value=1.5 Score=47.83 Aligned_cols=49 Identities=22% Similarity=0.485 Sum_probs=41.2
Q ss_pred ccccc-cccCccc-chhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHH
Q 004169 671 HGMRY-TSFGRHF-TKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 671 ~g~ry-tsfgrhf-tk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~ 721 (770)
||+|. -+||.|| +...-+..||+.+. +.+||+|+|+-||...++..+-+
T Consensus 6 ~~~~~kk~~GQnFL~d~~i~~~Iv~~~~--~~~~~~VLEIG~G~G~LT~~Ll~ 56 (294)
T PTZ00338 6 SGMVFNKKFGQHILKNPLVLDKIVEKAA--IKPTDTVLEIGPGTGNLTEKLLQ 56 (294)
T ss_pred CCcCcCCCCCccccCCHHHHHHHHHhcC--CCCcCEEEEecCchHHHHHHHHH
Confidence 56653 4899999 78889999999885 78999999999999999876654
No 37
>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional
Probab=82.29 E-value=1.3 Score=45.62 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=32.1
Q ss_pred hhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 685 VEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 685 ~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
.-||.||-+++. |+.+|++|||++||...|+..+-+..
T Consensus 36 ~~kl~~~~~~~~-~~~~~~~VLDlG~GtG~~t~~l~~~~ 73 (209)
T PRK11188 36 WFKLDEIQQSDK-LFKPGMTVVDLGAAPGGWSQYAVTQI 73 (209)
T ss_pred HHhhHHHHHHhc-cCCCCCEEEEEcccCCHHHHHHHHHc
Confidence 347888888876 67999999999999999999777654
No 38
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=81.98 E-value=0.64 Score=53.67 Aligned_cols=50 Identities=24% Similarity=0.486 Sum_probs=36.9
Q ss_pred CcccccccCCCCc---eeecCCccccccccccccCccccccccCCcccccCC-CCcccCcccc
Q 004169 215 YFAVCAICDDGGD---VTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDA-VPNFLCQNCV 273 (770)
Q Consensus 215 ~d~VC~IC~~gGe---LL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~-~~~W~C~eC~ 273 (770)
....|.||....+ |+.|| .|...||+.|+. ..||..+-.. .-.|.|.+|.
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 3466999998765 89999 799999999764 4566554322 4579888874
No 39
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=81.44 E-value=0.79 Score=52.88 Aligned_cols=53 Identities=21% Similarity=0.396 Sum_probs=37.9
Q ss_pred cccCcCCccCccCccceeeccccccccccccCCCCccccccchhhhhhhhhcccCCCceEEEccCCcc
Q 004169 345 CFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPTEITFSDADENNFQRAWVDLLPNNRILIYCLEHKI 412 (770)
Q Consensus 345 C~~C~~~edk~~~e~qLi~C~RCP~AYH~kCLP~~~~f~~~~~e~~~raW~~lL~~~~~LI~C~~H~i 412 (770)
|.+|..+.... .+ +|+.|.+|-.+||..|..+.+.-+ +..+....|+|..|--
T Consensus 171 c~vC~~g~~~~-~N-rmlqC~~C~~~fHq~Chqp~i~~~-------------l~~D~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 171 CSVCYCGGPGA-GN-RMLQCDKCRQWYHQACHQPLIKDE-------------LAGDPFYEWFCDVCNR 223 (464)
T ss_pred eeeeecCCcCc-cc-eeeeecccccHHHHHhccCCCCHh-------------hccCccceEeehhhcc
Confidence 88888765431 23 899999999999999998876422 1233356788888774
No 40
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=80.13 E-value=1 Score=48.62 Aligned_cols=27 Identities=22% Similarity=0.598 Sum_probs=23.3
Q ss_pred CCceeeccCCCcC-CcCcchhhcccCCC
Q 004169 293 SQEVFPCVSATCG-QFYHPECVSKLLHP 319 (770)
Q Consensus 293 ~~eV~kCsv~~CG-rfYH~~CL~~~~~p 319 (770)
.++++.|...+|. ..||..||+.-..|
T Consensus 229 yg~Mi~CDn~~C~~eWFH~~CVGL~~~P 256 (274)
T KOG1973|consen 229 YGKMIGCDNPGCPIEWFHFTCVGLKTKP 256 (274)
T ss_pred cccccccCCCCCCcceEEEeccccccCC
Confidence 4699999999999 99999999976544
No 41
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=78.37 E-value=2.7 Score=44.23 Aligned_cols=45 Identities=18% Similarity=0.354 Sum_probs=38.4
Q ss_pred cccCccc-chhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 676 TSFGRHF-TKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 676 tsfgrhf-tk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
.+||-|| +..+-+.+|++.+.+ .+|++|+|+.||...++..|.++
T Consensus 5 k~~gq~fl~d~~i~~~i~~~~~~--~~~~~VLEiG~G~G~lt~~L~~~ 50 (253)
T TIGR00755 5 KSLGQNFLIDESVIQKIVEAANV--LEGDVVLEIGPGLGALTEPLLKR 50 (253)
T ss_pred CCCCCccCCCHHHHHHHHHhcCC--CCcCEEEEeCCCCCHHHHHHHHh
Confidence 4689999 677778889998864 68999999999999999998754
No 42
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=77.43 E-value=1 Score=53.84 Aligned_cols=58 Identities=26% Similarity=0.649 Sum_probs=36.9
Q ss_pred cCCCcccccccCCCC--------ceeec-CCccccccccccccCccccccccCCcccccCCCCcccCccccc
Q 004169 212 DENYFAVCAICDDGG--------DVTFC-DGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVY 274 (770)
Q Consensus 212 dd~~d~VC~IC~~gG--------eLL~C-dG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~ 274 (770)
.|.+...|+||+..| ....| .-.|.++||.+|.....-.|..-|.-.+ .--||-.|.|
T Consensus 113 ~dRfnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~d-----NVKYCGYCk~ 179 (900)
T KOG0956|consen 113 HDRFNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISD-----NVKYCGYCKY 179 (900)
T ss_pred hhhhcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccc-----cceechhHHH
Confidence 356778899998754 35566 4469999999996544444533222112 2346777775
No 43
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=76.38 E-value=0.73 Score=59.62 Aligned_cols=61 Identities=20% Similarity=0.438 Sum_probs=42.8
Q ss_pred cCCCcccccccCCCC---ceeecCCccccccccccccCccccccccCCcccccCCCCcccCccccccC---cccccccc
Q 004169 212 DENYFAVCAICDDGG---DVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQE---HQCFACGM 284 (770)
Q Consensus 212 dd~~d~VC~IC~~gG---eLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~~q---hqCfvCgk 284 (770)
.......|.+|...+ +++.|++ |.+.||..|+. ..++.. +.+.|+|+.|...+ .+++.++.
T Consensus 1104 ~s~~~~~c~~cr~k~~~~~m~lc~~-c~~~~h~~C~r--------p~~~~~---~~~dW~C~~c~~e~~~rr~~~~~~~ 1170 (1404)
T KOG1245|consen 1104 RSAVNALCKVCRRKKQDEKMLLCDE-CLSGFHLFCLR--------PALSSV---PPGDWMCPSCRKEHRARRQKRFRKE 1170 (1404)
T ss_pred cccchhhhhhhhhcccchhhhhhHh-hhhhHHHHhhh--------hhhccC---CcCCccCCccchhhhhhhhhhhhcc
Confidence 345567899998765 4999995 99999999743 223332 46889999998643 34555544
No 44
>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=76.24 E-value=2.3 Score=43.64 Aligned_cols=51 Identities=12% Similarity=0.036 Sum_probs=44.8
Q ss_pred cccccccCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 672 GMRYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 672 g~rytsfgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
|.+|+.-.|+..-+.+.-+.+.++-+++.++++|+|+-||...+...|.+.
T Consensus 14 g~~~~~rn~~~~~~~~~~~~~~~~l~~~~~~~~VLDiGCG~G~~~~~L~~~ 64 (204)
T TIGR03587 14 GKEYIDRNSRQSLVAAKLAMFARALNRLPKIASILELGANIGMNLAALKRL 64 (204)
T ss_pred cchhhhccccHHHHHHHHHHHHHHHHhcCCCCcEEEEecCCCHHHHHHHHh
Confidence 779999999888888888888888889999999999999999998877665
No 45
>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=73.82 E-value=1.4 Score=46.30 Aligned_cols=43 Identities=28% Similarity=0.499 Sum_probs=19.2
Q ss_pred cccccCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHH
Q 004169 674 RYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 674 rytsfgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~ 721 (770)
+--|||.|--=-.++.+++ -.++|++|+|.|||..|++..+-+
T Consensus 25 ~~ls~g~~~~wr~~~~~~~-----~~~~g~~vLDv~~GtG~~~~~l~~ 67 (233)
T PF01209_consen 25 DLLSFGQDRRWRRKLIKLL-----GLRPGDRVLDVACGTGDVTRELAR 67 (233)
T ss_dssp ------------SHHHHHH-----T--S--EEEEET-TTSHHHHHHGG
T ss_pred cccCCcHHHHHHHHHHhcc-----CCCCCCEEEEeCCChHHHHHHHHH
Confidence 4468887754444555544 368999999999999999876643
No 46
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=73.79 E-value=2 Score=38.07 Aligned_cols=33 Identities=21% Similarity=0.585 Sum_probs=27.2
Q ss_pred CcccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcc
Q 004169 276 EHQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSK 315 (770)
Q Consensus 276 qhqCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~ 315 (770)
...|.+|++. .+-.+.|....|.+.||+.|...
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 4579999875 13678999999999999999764
No 47
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=73.58 E-value=0.96 Score=34.74 Aligned_cols=35 Identities=26% Similarity=0.705 Sum_probs=17.1
Q ss_pred CceeecCCccccccccccccCccccccccCCcccccCCCCcccCcccc
Q 004169 226 GDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCV 273 (770)
Q Consensus 226 GeLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~ 273 (770)
..||.|+ .|.-++|..| -|+...+ ....|+|.-|+
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 5999999997 5665443 23469998774
No 48
>PHA03412 putative methyltransferase; Provisional
Probab=71.31 E-value=2.9 Score=44.77 Aligned_cols=42 Identities=21% Similarity=0.396 Sum_probs=30.7
Q ss_pred ccCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 677 SFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 677 sfgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
..|..||...=-+.++ -|.. .|..|||+|||+..|+..|-.+
T Consensus 29 ~~GqFfTP~~iAr~~~---i~~~-~~grVLDlG~GSG~Lalala~~ 70 (241)
T PHA03412 29 ELGAFFTPIGLARDFT---IDAC-TSGSVVDLCAGIGGLSFAMVHM 70 (241)
T ss_pred cCCccCCCHHHHHHHH---Hhcc-CCCEEEEccChHHHHHHHHHHh
Confidence 4588888887434443 1222 4789999999999999988665
No 49
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=71.16 E-value=3.2 Score=42.94 Aligned_cols=46 Identities=20% Similarity=0.460 Sum_probs=35.6
Q ss_pred cCccccccCcccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcc
Q 004169 268 LCQNCVYQEHQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSK 315 (770)
Q Consensus 268 ~C~eC~~~qhqCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~ 315 (770)
-|.-|..+...|-+|...+..-......+.+| ..|+..||..|...
T Consensus 144 ~C~lC~~kGfiCe~C~~~~~IfPF~~~~~~~C--~~C~~v~H~~C~~~ 189 (202)
T PF13901_consen 144 SCELCQQKGFICEICNSDDIIFPFQIDTTVRC--PKCKSVFHKSCFRK 189 (202)
T ss_pred HhHHHHhCCCCCccCCCCCCCCCCCCCCeeeC--CcCccccchhhcCC
Confidence 68888888888999976544333334588999 89999999999763
No 50
>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=69.68 E-value=5.7 Score=46.29 Aligned_cols=49 Identities=27% Similarity=0.466 Sum_probs=39.2
Q ss_pred ccCcccchhhHHHHHHhhhceeee-----cCCeEEeeccCCChhhhHHHHHHHH
Q 004169 677 SFGRHFTKVEKLKEIVDRLHWYVR-----SGDTIVDFCCGANDFSCMMKVKLEQ 725 (770)
Q Consensus 677 sfgrhftk~ekl~~iv~~lhwyv~-----~gd~ivdfccg~n~f~~~~~~~l~~ 725 (770)
+.|.+||...=-+.||+.+-=+.. .+.+|+|.|||+.-|..-+-+++.+
T Consensus 2 ~~GqfyTP~~ia~~mv~~~~~~~~~~~~~~~~~ilDP~cGsG~fl~~~~~~~~~ 55 (524)
T TIGR02987 2 AYGTFFTPPDIAKAMVANLVNEIGKNDKSTKTKIIDPCCGDGRLIAALLKKNEE 55 (524)
T ss_pred CCcccCCcHHHHHHHHHHHhhhcchhhcccceEEEeCCCCccHHHHHHHHHHHh
Confidence 579999999988888888743333 3458999999999999888777754
No 51
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=68.24 E-value=4 Score=51.55 Aligned_cols=67 Identities=24% Similarity=0.433 Sum_probs=47.3
Q ss_pred cccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcccCCCCchhHHHHHHHHHhcCCceecCCcccccCcCCccCcc
Q 004169 277 HQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCPVHKCFVCQQSEDMNV 356 (770)
Q Consensus 277 hqCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~~p~~~~~~~el~krV~~g~~F~CPlH~C~~C~~~edk~~ 356 (770)
..|.+|..-... ....++.| ..|+..+|..|.+..+-|+ ..| .|..|-++..
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 358888764332 23567889 8999999999999544342 345 6788988765
Q ss_pred Cccceeeccccccccccc
Q 004169 357 EDLQLAICRRCPKAYHRK 374 (770)
Q Consensus 357 ~e~qLi~C~RCP~AYH~k 374 (770)
..+.|.-||.+=|..
T Consensus 272 ---~~v~c~~cp~~~gAF 286 (1051)
T KOG0955|consen 272 ---RPVRCLLCPSKGGAF 286 (1051)
T ss_pred ---cccceEeccCCCCcc
Confidence 348999999876653
No 52
>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=68.08 E-value=5 Score=43.06 Aligned_cols=46 Identities=24% Similarity=0.463 Sum_probs=30.2
Q ss_pred cccCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 676 TSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 676 tsfgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
-+.|-+||+.+=-+-+|+.+ =.++|++|+|.|||+..|---+.+.+
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 36788999887666666666 45778999999999999965544443
No 53
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=67.15 E-value=3.1 Score=42.33 Aligned_cols=37 Identities=27% Similarity=0.622 Sum_probs=28.7
Q ss_pred ccccCcCCccCccCccceeeccccccccccccCCCCcc
Q 004169 344 KCFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPTEIT 381 (770)
Q Consensus 344 ~C~~C~~~edk~~~e~qLi~C~RCP~AYH~kCLP~~~~ 381 (770)
.|.+|...+++ ...++|+-|--|..|||..||-.-+.
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 48899764432 23569999999999999999976554
No 54
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=66.32 E-value=3.8 Score=35.64 Aligned_cols=39 Identities=23% Similarity=0.512 Sum_probs=16.1
Q ss_pred cccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcccC
Q 004169 277 HQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLL 317 (770)
Q Consensus 277 hqCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~ 317 (770)
..|.+|...-..+ .......|....|++.||..||..|+
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 3588887543211 12356899999999999999999886
No 55
>PRK00312 pcm protein-L-isoaspartate O-methyltransferase; Reviewed
Probab=65.40 E-value=18 Score=36.63 Aligned_cols=72 Identities=14% Similarity=0.212 Sum_probs=46.9
Q ss_pred CchhhhhHHHHhhccccc--c--ccccccccccccCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHH
Q 004169 648 PPEILCQIFQWKRKLDVY--L--APFLHGMRYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 648 ~p~~l~q~~~w~~kl~~~--l--apfl~g~rytsfgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~ 721 (770)
+|.++.-+..+-+..-|. . ..+..+.-...+|++.+.++=...+.+.|+ +++|++|+|++||+.-++.+|..
T Consensus 23 ~~~~~~a~~~~~r~~f~p~~~~~~ay~d~~~~~~~~~~~~~p~~~~~l~~~l~--~~~~~~VLeiG~GsG~~t~~la~ 98 (212)
T PRK00312 23 DERVLEAIEATPRELFVPEAFKHKAYENRALPIGCGQTISQPYMVARMTELLE--LKPGDRVLEIGTGSGYQAAVLAH 98 (212)
T ss_pred CHHHHHHHHcCCHhHcCCchHHhcCccCCCccCCCCCeeCcHHHHHHHHHhcC--CCCCCEEEEECCCccHHHHHHHH
Confidence 467777777665543222 0 112222223345666778877667777665 68999999999999999887754
No 56
>TIGR00080 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt.
Probab=65.15 E-value=7.5 Score=39.77 Aligned_cols=52 Identities=8% Similarity=0.143 Sum_probs=38.2
Q ss_pred cccccccc--CcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHHH
Q 004169 671 HGMRYTSF--GRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLE 724 (770)
Q Consensus 671 ~g~rytsf--grhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l~ 724 (770)
|..+-.+| |++++.+--...+++.|. +++|+.|+|+.||+.-++.+|.+...
T Consensus 47 y~d~~~~~~~~~~~~~p~~~~~~~~~l~--~~~~~~VLDiG~GsG~~a~~la~~~~ 100 (215)
T TIGR00080 47 YVDTPLEIGYGQTISAPHMVAMMTELLE--LKPGMKVLEIGTGSGYQAAVLAEIVG 100 (215)
T ss_pred cCCCCcccCCCCEechHHHHHHHHHHhC--CCCcCEEEEECCCccHHHHHHHHHhC
Confidence 33333444 677777666666777764 78999999999999999988876653
No 57
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.65 E-value=3.5 Score=46.30 Aligned_cols=92 Identities=14% Similarity=0.024 Sum_probs=46.9
Q ss_pred eEeecCCCCceEeeeeeeeccccccCCCCcceEEEeecccCCccceeeeEEEeeeeccCCcceEEEEecCCceeEcCCCc
Q 004169 18 YEFLDQNEESISFSVLPLQWDGCDIVGSSEMQVFLHGNIGDGPWNFNEQVIAWKFELSYAQPEIWVLSKQNNWIMLQSPK 97 (770)
Q Consensus 18 y~f~d~~~~~v~fs~lp~~~~~~~~~~~~~~~v~l~g~~d~gl~~v~~~v~aW~~~l~~~~p~i~vls~~~~Wi~L~kPr 97 (770)
+--+-++..--+|.-+|-.|+.+=...+.. ++.+.--..|+=.+|+.--.+ - +....|+-|..=-
T Consensus 24 ~v~~~~~n~S~sf~d~~a~f~~s~~~e~~~-G~l~~~ep~~aC~~i~~~p~~----~----------~~~~~~laLI~Rg 88 (348)
T KOG4628|consen 24 AVALVDRNTSLSFADLPALFGPSLPSEGNL-GVLVVAEPLNACNPITNFPEH----S----------TRSTSFLALIRRG 88 (348)
T ss_pred EEEEccccccccccCCccccCCccccccce-eeeecCCCccccCccccCccC----C----------CCCcceEEEEEcc
Confidence 333344455558888898888863322222 333333334454555442111 1 2223555554333
Q ss_pred -hhHHHHHHHHHHHhhhhhhhccCCccc
Q 004169 98 -KSFKNIVRTILITVHWLYCVKQNPEAS 124 (770)
Q Consensus 98 -~~ye~~ir~vlitv~~LhfvkknPe~s 124 (770)
-+|++.|+.+==+.|--+-|--|+..+
T Consensus 89 ~CsFe~Kv~~AQ~aGfkaaIVynn~~~~ 116 (348)
T KOG4628|consen 89 GCSFEDKVLNAQRAGFKAAIVYNNVGSE 116 (348)
T ss_pred CCchHHHHhhcccccCceEEEecCCCCc
Confidence 349999988655555555555544443
No 58
>PF13679 Methyltransf_32: Methyltransferase domain
Probab=64.06 E-value=8.6 Score=36.96 Aligned_cols=43 Identities=23% Similarity=0.273 Sum_probs=33.3
Q ss_pred hhhHHHHHHhhhce---eeecCCeEEeeccCCChhhhHHHHHHHHh
Q 004169 684 KVEKLKEIVDRLHW---YVRSGDTIVDFCCGANDFSCMMKVKLEQM 726 (770)
Q Consensus 684 k~ekl~~iv~~lhw---yv~~gd~ivdfccg~n~f~~~~~~~l~~~ 726 (770)
.++.+.++++.+-= -.+++.+|||||||-.-.|+++...|.+.
T Consensus 5 Ei~~~~~~i~~~~~~~~~~~~~~~vvD~GsG~GyLs~~La~~l~~~ 50 (141)
T PF13679_consen 5 EIERMAELIDSLCDSVGESKRCITVVDLGSGKGYLSRALAHLLCNS 50 (141)
T ss_pred HHHHHHHHHHHHHHHhhccCCCCEEEEeCCChhHHHHHHHHHHHhc
Confidence 35566666666533 34778999999999999999999987766
No 59
>TIGR00438 rrmJ cell division protein FtsJ.
Probab=63.78 E-value=8.3 Score=38.47 Aligned_cols=37 Identities=19% Similarity=0.435 Sum_probs=30.8
Q ss_pred HHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHHH
Q 004169 687 KLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLE 724 (770)
Q Consensus 687 kl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l~ 724 (770)
||.++.+++. .+++|++|+|++||..-++..+..+..
T Consensus 19 ~~~~~~~~~~-~i~~g~~VLDiG~GtG~~~~~l~~~~~ 55 (188)
T TIGR00438 19 KLLQLNQKFK-LIKPGDTVLDLGAAPGGWSQVAVEQVG 55 (188)
T ss_pred HHHHHHHHhc-ccCCCCEEEEecCCCCHHHHHHHHHhC
Confidence 6777777776 457999999999999999998877763
No 60
>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=63.38 E-value=6.5 Score=40.09 Aligned_cols=45 Identities=29% Similarity=0.595 Sum_probs=31.9
Q ss_pred cccccCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 674 RYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 674 rytsfgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
++.|||+|..-.+ +++.+| .+++|++|+|+.||...+++.|.+..
T Consensus 23 ~~~~~~~~~~~~~---~~l~~l--~~~~~~~vLDiGcG~G~~~~~la~~~ 67 (231)
T TIGR02752 23 SVISFQRHKKWRK---DTMKRM--NVQAGTSALDVCCGTADWSIALAEAV 67 (231)
T ss_pred HHhcCCchHHHHH---HHHHhc--CCCCCCEEEEeCCCcCHHHHHHHHHh
Confidence 3456666654443 344444 47899999999999999998877654
No 61
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=63.23 E-value=5.2 Score=33.74 Aligned_cols=33 Identities=30% Similarity=0.779 Sum_probs=25.8
Q ss_pred cccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcc
Q 004169 277 HQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSK 315 (770)
Q Consensus 277 hqCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~ 315 (770)
..|.+||+.-. .+..++.| +.||.-||..|..+
T Consensus 6 ~~C~~Cg~~~~----~~dDiVvC--p~CgapyHR~C~~~ 38 (54)
T PF14446_consen 6 CKCPVCGKKFK----DGDDIVVC--PECGAPYHRDCWEK 38 (54)
T ss_pred ccChhhCCccc----CCCCEEEC--CCCCCcccHHHHhh
Confidence 35888987542 24689999 89999999999754
No 62
>PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=62.85 E-value=7.6 Score=39.93 Aligned_cols=46 Identities=9% Similarity=0.327 Sum_probs=39.1
Q ss_pred cccCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 676 TSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 676 tsfgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
+.+|++-+.+.-...+++.|. +++|++|+|+.||+.-++.+|.+.+
T Consensus 53 ~~~g~~~~~p~~~~~~~~~l~--~~~g~~VLdIG~GsG~~t~~la~~~ 98 (212)
T PRK13942 53 IGYGQTISAIHMVAIMCELLD--LKEGMKVLEIGTGSGYHAAVVAEIV 98 (212)
T ss_pred CCCCCEeCcHHHHHHHHHHcC--CCCcCEEEEECCcccHHHHHHHHhc
Confidence 346888899998889999886 6899999999999999998876554
No 63
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=61.73 E-value=9.7 Score=40.50 Aligned_cols=51 Identities=16% Similarity=0.377 Sum_probs=37.4
Q ss_pred ccccccccc---------cCcccchh---hHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHH
Q 004169 669 FLHGMRYTS---------FGRHFTKV---EKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 669 fl~g~ryts---------fgrhftk~---ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~ 721 (770)
||.-.+||+ ||-.|--+ |-..+++++| .+.+|.+|+|+.||...++..|..
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 555556664 56555555 5667777776 678999999999999988877643
No 64
>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=61.71 E-value=5 Score=40.09 Aligned_cols=26 Identities=15% Similarity=0.434 Sum_probs=18.6
Q ss_pred cccccccCccccccccCCcccccCCCCcccCcccccc
Q 004169 239 FHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQ 275 (770)
Q Consensus 239 FH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~~ 275 (770)
||+.|+.+ .++. + |.+.|+|+.|..+
T Consensus 2 ~H~~CL~P--------pl~~--~-P~g~W~Cp~C~~~ 27 (148)
T cd04718 2 FHLCCLRP--------PLKE--V-PEGDWICPFCEVE 27 (148)
T ss_pred cccccCCC--------CCCC--C-CCCCcCCCCCcCC
Confidence 89998643 3433 3 5799999999853
No 65
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=59.97 E-value=6.1 Score=46.83 Aligned_cols=51 Identities=24% Similarity=0.195 Sum_probs=35.0
Q ss_pred chHhhhccCCCCccccc--CCccccceeeecccchhhHH--------HHH--HHHHHhhcCCC
Q 004169 589 NEEEFMKSHIVPITHAH--HSKHLLEKSITLGLVEGSVK--------AVR--AALEMLDGGCD 639 (770)
Q Consensus 589 ~~~~~~~~~~~~~t~~~--~~~~~~~k~i~~g~~e~sv~--------a~~--~al~~le~g~~ 639 (770)
+.||+.++-++|-++.. .+..-+++.+-.|+--+.|. +-| --|+||-.|..
T Consensus 447 s~eDi~k~sk~p~~~~pdpas~~~~e~~~w~~~ps~~V~~~~~~~R~~~R~~eql~Kl~sgig 509 (670)
T KOG1044|consen 447 SSEDIIKFSKFPAAQAPDPASTPEIETDHWPGKPSFAVPGPEMKRRSLGRQEEQLMKLNSGLG 509 (670)
T ss_pred cccchhhhhcCCcccCCCCCCCCcccccCCCCCCcccccCchhhhhhccchhhhhhhccchhh
Confidence 38999999999988653 23333567777777666665 333 35778888865
No 66
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=59.96 E-value=5.4 Score=42.46 Aligned_cols=25 Identities=4% Similarity=0.100 Sum_probs=20.5
Q ss_pred eeecCCeEEeeccCCChhhhHHHHH
Q 004169 698 YVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 698 yv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
.+++|++|+|+|||...++..|-+.
T Consensus 68 ~~~~g~~VLDl~ag~G~kt~~la~~ 92 (264)
T TIGR00446 68 EPDPPERVLDMAAAPGGKTTQISAL 92 (264)
T ss_pred CCCCcCEEEEECCCchHHHHHHHHH
Confidence 4689999999999999888766443
No 67
>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=59.83 E-value=5.2 Score=39.52 Aligned_cols=38 Identities=21% Similarity=0.293 Sum_probs=31.5
Q ss_pred hHHHHHHhhhceeee-cCCeEEeeccCCChhhhHHHHHH
Q 004169 686 EKLKEIVDRLHWYVR-SGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 686 ekl~~iv~~lhwyv~-~gd~ivdfccg~n~f~~~~~~~l 723 (770)
-||.||-++..+.-. ++.+|||+||+-.-||..+-++.
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 499999999996533 45999999999999999988877
No 68
>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]
Probab=56.83 E-value=11 Score=41.46 Aligned_cols=37 Identities=24% Similarity=0.474 Sum_probs=33.0
Q ss_pred hhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 684 KVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 684 k~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
+.-||+.|+++|| +++|+||+||=||...++..|-++
T Consensus 57 Q~~k~~~~~~kl~--L~~G~~lLDiGCGWG~l~~~aA~~ 93 (283)
T COG2230 57 QRAKLDLILEKLG--LKPGMTLLDIGCGWGGLAIYAAEE 93 (283)
T ss_pred HHHHHHHHHHhcC--CCCCCEEEEeCCChhHHHHHHHHH
Confidence 3558999999999 899999999999999999888665
No 69
>PRK08287 cobalt-precorrin-6Y C(15)-methyltransferase; Validated
Probab=56.40 E-value=17 Score=36.17 Aligned_cols=41 Identities=17% Similarity=0.217 Sum_probs=32.9
Q ss_pred CcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHH
Q 004169 679 GRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 679 grhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~ 721 (770)
.+..|+.+--.-+++.|. +.+|++|+|+.||+.-++..+..
T Consensus 11 ~~~~~~~~~r~~~~~~l~--~~~~~~vLDiG~G~G~~~~~la~ 51 (187)
T PRK08287 11 KVPMTKEEVRALALSKLE--LHRAKHLIDVGAGTGSVSIEAAL 51 (187)
T ss_pred CCCCchHHHHHHHHHhcC--CCCCCEEEEECCcCCHHHHHHHH
Confidence 567888887777778886 46899999999999988876643
No 70
>PRK13944 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=56.31 E-value=14 Score=37.76 Aligned_cols=44 Identities=11% Similarity=0.203 Sum_probs=33.9
Q ss_pred cCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 678 FGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 678 fgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
+|++++.+.-+..+.+.|. +++|+.|+|+.||+.-++.+|.+.+
T Consensus 51 ~~~~~~~p~~~~~~~~~l~--~~~~~~VLDiG~GsG~~~~~la~~~ 94 (205)
T PRK13944 51 AGATISAPHMVAMMCELIE--PRPGMKILEVGTGSGYQAAVCAEAI 94 (205)
T ss_pred CCCEechHHHHHHHHHhcC--CCCCCEEEEECcCccHHHHHHHHhc
Confidence 4677777776666777664 6899999999999998887765543
No 71
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=56.02 E-value=6.4 Score=33.22 Aligned_cols=32 Identities=31% Similarity=0.822 Sum_probs=24.2
Q ss_pred ccccCcCCccCccCccceeeccccccccccccCCC
Q 004169 344 KCFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPT 378 (770)
Q Consensus 344 ~C~~C~~~edk~~~e~qLi~C~RCP~AYH~kCLP~ 378 (770)
.|..|+..-. .+..+++|..|.+-||+.|-..
T Consensus 7 ~C~~Cg~~~~---~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 7 KCPVCGKKFK---DGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cChhhCCccc---CCCCEEECCCCCCcccHHHHhh
Confidence 5778887542 2347999999999999999533
No 72
>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=55.14 E-value=9.1 Score=37.97 Aligned_cols=48 Identities=27% Similarity=0.331 Sum_probs=26.1
Q ss_pred cccccccccccccccC----cccc-hhhHHHHHHhhhceeeecCCeEEeeccCCC
Q 004169 664 VYLAPFLHGMRYTSFG----RHFT-KVEKLKEIVDRLHWYVRSGDTIVDFCCGAN 713 (770)
Q Consensus 664 ~~lapfl~g~rytsfg----rhft-k~ekl~~iv~~lhwyv~~gd~ivdfccg~n 713 (770)
|+..+.+...++.+-| .|-| |+.+|.|-+ +..|-.+||+|+|+++||.
T Consensus 151 ~w~~~~~~~~~~~~~~~~~~~h~~~kP~~l~~~l--I~~~t~~gdiVlDpF~GSG 203 (231)
T PF01555_consen 151 VWPFSIIPPSRKNSKGNTKGKHPTQKPVELIERL--IKASTNPGDIVLDPFAGSG 203 (231)
T ss_dssp EEE-SEEETTSTT--CHH----TT-S-HHHHHHH--HHHHS-TT-EEEETT-TTT
T ss_pred ccccccccccccccccccccceeecCCHHHHHHH--HHhhhccceeeehhhhccC
Confidence 3345566777776653 4554 566654433 3457899999999999996
No 73
>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=54.69 E-value=4.6 Score=33.99 Aligned_cols=9 Identities=67% Similarity=1.789 Sum_probs=8.1
Q ss_pred EeeccCCCh
Q 004169 706 VDFCCGAND 714 (770)
Q Consensus 706 vdfccg~n~ 714 (770)
+|||||.|.
T Consensus 24 IDfCCgG~~ 32 (56)
T PF04405_consen 24 IDFCCGGNR 32 (56)
T ss_pred CcccCCCCc
Confidence 799999985
No 74
>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=51.84 E-value=20 Score=32.06 Aligned_cols=36 Identities=19% Similarity=0.247 Sum_probs=26.3
Q ss_pred hhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 685 VEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 685 ~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
.+....+++.| ++++|++|+|+.||..-++..+-++
T Consensus 5 ~~~~~~~~~~~--~~~~~~~vldlG~G~G~~~~~l~~~ 40 (124)
T TIGR02469 5 REVRALTLSKL--RLRPGDVLWDIGAGSGSITIEAARL 40 (124)
T ss_pred HHHHHHHHHHc--CCCCCCEEEEeCCCCCHHHHHHHHH
Confidence 34444455555 6778999999999999988766544
No 75
>PLN02233 ubiquinone biosynthesis methyltransferase
Probab=49.12 E-value=19 Score=38.22 Aligned_cols=25 Identities=32% Similarity=0.869 Sum_probs=21.7
Q ss_pred eeecCCeEEeeccCCChhhhHHHHH
Q 004169 698 YVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 698 yv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
.+++|++|+|+.||..+|+..+.++
T Consensus 70 ~~~~~~~VLDlGcGtG~~~~~la~~ 94 (261)
T PLN02233 70 GAKMGDRVLDLCCGSGDLAFLLSEK 94 (261)
T ss_pred CCCCCCEEEEECCcCCHHHHHHHHH
Confidence 3689999999999999999887665
No 76
>PTZ00146 fibrillarin; Provisional
Probab=48.94 E-value=11 Score=41.56 Aligned_cols=26 Identities=4% Similarity=0.117 Sum_probs=23.5
Q ss_pred eeecCCeEEeeccCCChhhhHHHHHH
Q 004169 698 YVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 698 yv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
++++|++|+|+|||+.-|+..|-+.+
T Consensus 129 ~IkpG~~VLDLGaG~G~~t~~lAdiV 154 (293)
T PTZ00146 129 PIKPGSKVLYLGAASGTTVSHVSDLV 154 (293)
T ss_pred ccCCCCEEEEeCCcCCHHHHHHHHHh
Confidence 68999999999999999998888765
No 77
>PHA03411 putative methyltransferase; Provisional
Probab=48.44 E-value=22 Score=39.02 Aligned_cols=40 Identities=20% Similarity=0.282 Sum_probs=31.2
Q ss_pred cCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHH
Q 004169 678 FGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 678 fgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~ 721 (770)
.|-.||...=+..++ +...++++|+|++||+..|+..+-.
T Consensus 45 ~G~FfTP~~i~~~f~----~~~~~~grVLDLGcGsGilsl~la~ 84 (279)
T PHA03411 45 SGAFFTPEGLAWDFT----IDAHCTGKVLDLCAGIGRLSFCMLH 84 (279)
T ss_pred ceeEcCCHHHHHHHH----hccccCCeEEEcCCCCCHHHHHHHH
Confidence 499999887765554 3345678999999999999887744
No 78
>smart00650 rADc Ribosomal RNA adenine dimethylases.
Probab=48.37 E-value=17 Score=35.73 Aligned_cols=33 Identities=21% Similarity=0.395 Sum_probs=26.3
Q ss_pred HHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 688 LKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 688 l~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
++.|++.+.+ ++|++|+|+.||...++..|-++
T Consensus 2 ~~~i~~~~~~--~~~~~vLEiG~G~G~lt~~l~~~ 34 (169)
T smart00650 2 IDKIVRAANL--RPGDTVLEIGPGKGALTEELLER 34 (169)
T ss_pred HHHHHHhcCC--CCcCEEEEECCCccHHHHHHHhc
Confidence 3567777775 68999999999999998876543
No 79
>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=48.27 E-value=19 Score=36.13 Aligned_cols=31 Identities=19% Similarity=0.623 Sum_probs=24.4
Q ss_pred HHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 688 LKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 688 l~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
|.+|.+.+ .+|++|+|+.||...|...+.+.
T Consensus 4 ~~~i~~~i----~~~~~iLDiGcG~G~~~~~l~~~ 34 (194)
T TIGR02081 4 LESILNLI----PPGSRVLDLGCGDGELLALLRDE 34 (194)
T ss_pred HHHHHHhc----CCCCEEEEeCCCCCHHHHHHHhc
Confidence 45565544 58999999999999999887543
No 80
>PRK08317 hypothetical protein; Provisional
Probab=47.47 E-value=22 Score=35.45 Aligned_cols=31 Identities=23% Similarity=0.491 Sum_probs=24.2
Q ss_pred HHhhhceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 691 IVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 691 iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
+.++++ +.+|++|||++||...++..|.+.+
T Consensus 11 ~~~~~~--~~~~~~vLdiG~G~G~~~~~~a~~~ 41 (241)
T PRK08317 11 TFELLA--VQPGDRVLDVGCGPGNDARELARRV 41 (241)
T ss_pred HHHHcC--CCCCCEEEEeCCCCCHHHHHHHHhc
Confidence 444444 4678999999999999998887654
No 81
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=47.15 E-value=18 Score=41.35 Aligned_cols=23 Identities=26% Similarity=0.674 Sum_probs=20.0
Q ss_pred eecCCeEEeeccCCChhhhHHHH
Q 004169 699 VRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 699 v~~gd~ivdfccg~n~f~~~~~~ 721 (770)
+++|++|+|++||+..|+..|..
T Consensus 295 ~~~~~~VLDlgcGtG~~sl~la~ 317 (443)
T PRK13168 295 PQPGDRVLDLFCGLGNFTLPLAR 317 (443)
T ss_pred CCCCCEEEEEeccCCHHHHHHHH
Confidence 46899999999999999988754
No 82
>PRK07402 precorrin-6B methylase; Provisional
Probab=47.06 E-value=27 Score=35.04 Aligned_cols=40 Identities=18% Similarity=0.243 Sum_probs=32.3
Q ss_pred CcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHH
Q 004169 679 GRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMK 720 (770)
Q Consensus 679 grhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~ 720 (770)
|.-.|+.|--.-++..|. +++|++|+|++||+.-|+..+.
T Consensus 20 ~~p~t~~~v~~~l~~~l~--~~~~~~VLDiG~G~G~~~~~la 59 (196)
T PRK07402 20 GIPLTKREVRLLLISQLR--LEPDSVLWDIGAGTGTIPVEAG 59 (196)
T ss_pred CCCCCHHHHHHHHHHhcC--CCCCCEEEEeCCCCCHHHHHHH
Confidence 444788887777888885 5799999999999999877663
No 83
>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=46.69 E-value=19 Score=40.95 Aligned_cols=38 Identities=21% Similarity=0.374 Sum_probs=28.8
Q ss_pred hhhHHHHHHhhhceee--ecCCeEEeeccCCChhhhHHHH
Q 004169 684 KVEKLKEIVDRLHWYV--RSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 684 k~ekl~~iv~~lhwyv--~~gd~ivdfccg~n~f~~~~~~ 721 (770)
+.+-.+.+++++.-++ ++|++|+|++||+.-|+..|..
T Consensus 273 N~~~~~~l~~~~~~~l~~~~~~~vLDl~cG~G~~sl~la~ 312 (431)
T TIGR00479 273 NSGQNEKLVDRALEALELQGEELVVDAYCGVGTFTLPLAK 312 (431)
T ss_pred CHHHHHHHHHHHHHHhccCCCCEEEEcCCCcCHHHHHHHH
Confidence 4555666666666665 4779999999999999987753
No 84
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=46.38 E-value=8.2 Score=38.49 Aligned_cols=32 Identities=28% Similarity=0.587 Sum_probs=23.7
Q ss_pred eecCCcccccCcCCccCccCccceeecccccccccc-ccCC
Q 004169 338 FTCPVHKCFVCQQSEDMNVEDLQLAICRRCPKAYHR-KCLP 377 (770)
Q Consensus 338 F~CPlH~C~~C~~~edk~~~e~qLi~C~RCP~AYH~-kCLP 377 (770)
|.=++++|.+|+-.+ .-.|..|...|.. .|+.
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 333478999999543 4579999999997 5754
No 85
>PRK14967 putative methyltransferase; Provisional
Probab=44.12 E-value=21 Score=36.79 Aligned_cols=34 Identities=15% Similarity=0.401 Sum_probs=26.2
Q ss_pred hhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHH
Q 004169 685 VEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMK 720 (770)
Q Consensus 685 ~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~ 720 (770)
.+.|.+++.++. +.+|++|+|++||..-++..+.
T Consensus 22 s~~l~~~l~~~~--~~~~~~vLDlGcG~G~~~~~la 55 (223)
T PRK14967 22 TQLLADALAAEG--LGPGRRVLDLCTGSGALAVAAA 55 (223)
T ss_pred HHHHHHHHHhcc--cCCCCeEEEecCCHHHHHHHHH
Confidence 356777776654 7899999999999987776654
No 86
>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=44.01 E-value=6.9 Score=30.36 Aligned_cols=33 Identities=24% Similarity=0.609 Sum_probs=22.0
Q ss_pred ccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcccC
Q 004169 278 QCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLL 317 (770)
Q Consensus 278 qCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~ 317 (770)
.|.+|...-. .+..++.. .||+.||..|+..|+
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 4677754332 13455544 499999999998874
No 87
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=43.32 E-value=15 Score=42.01 Aligned_cols=23 Identities=26% Similarity=0.531 Sum_probs=18.7
Q ss_pred eecCCeEEeeccCCChhhhHHHH
Q 004169 699 VRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 699 v~~gd~ivdfccg~n~f~~~~~~ 721 (770)
.++|++|+|+|||...++..|-+
T Consensus 248 ~~~g~~VLDlgaG~G~kt~~la~ 270 (445)
T PRK14904 248 PQPGSTVLDLCAAPGGKSTFMAE 270 (445)
T ss_pred CCCCCEEEEECCCCCHHHHHHHH
Confidence 46899999999999988765544
No 88
>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=43.20 E-value=11 Score=39.04 Aligned_cols=43 Identities=28% Similarity=0.491 Sum_probs=26.4
Q ss_pred ccccccccccccccccccCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHH
Q 004169 661 KLDVYLAPFLHGMRYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 661 kl~~~lapfl~g~rytsfgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~ 721 (770)
--+||.+|-|.+-|- .|++ .|++|++|+|++||-.-|+-.+-.
T Consensus 79 ~~kvyfs~rl~~Er~--------------Ri~~----~v~~~e~VlD~faGIG~f~l~~ak 121 (200)
T PF02475_consen 79 LSKVYFSPRLSTERR--------------RIAN----LVKPGEVVLDMFAGIGPFSLPIAK 121 (200)
T ss_dssp TTTS---GGGHHHHH--------------HHHT----C--TT-EEEETT-TTTTTHHHHHH
T ss_pred cceEEEccccHHHHH--------------HHHh----cCCcceEEEEccCCccHHHHHHhh
Confidence 347888887766542 2333 399999999999999999988764
No 89
>TIGR02021 BchM-ChlM magnesium protoporphyrin O-methyltransferase. This model represents the S-adenosylmethionine-dependent O-methyltransferase responsible for methylation of magnesium protoporphyrin IX. This step is essentiasl for the biosynthesis of both chlorophyll and bacteriochlorophyll. This model encompasses two closely related clades, from cyanobacteria (and plants) where it is called ChlM and other photosynthetic bacteria where it is known as BchM.
Probab=42.55 E-value=18 Score=36.76 Aligned_cols=33 Identities=18% Similarity=0.341 Sum_probs=24.8
Q ss_pred HHHHhhhceeee----cCCeEEeeccCCChhhhHHHH
Q 004169 689 KEIVDRLHWYVR----SGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 689 ~~iv~~lhwyv~----~gd~ivdfccg~n~f~~~~~~ 721 (770)
..+++++-+|++ ++++|+|+.||...|+..|..
T Consensus 39 ~~~~~~~~~~l~~~~~~~~~vLDiGcG~G~~~~~la~ 75 (219)
T TIGR02021 39 AAMRRKLLDWLPKDPLKGKRVLDAGCGTGLLSIELAK 75 (219)
T ss_pred HHHHHHHHHHHhcCCCCCCEEEEEeCCCCHHHHHHHH
Confidence 345556666665 589999999999999877753
No 90
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=42.05 E-value=16 Score=41.83 Aligned_cols=23 Identities=17% Similarity=0.400 Sum_probs=18.7
Q ss_pred eecCCeEEeeccCCChhhhHHHH
Q 004169 699 VRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 699 v~~gd~ivdfccg~n~f~~~~~~ 721 (770)
+++|++|+|+|||..-++..|-+
T Consensus 250 ~~~g~~VLDl~ag~G~kt~~la~ 272 (434)
T PRK14901 250 PQPGEVILDACAAPGGKTTHIAE 272 (434)
T ss_pred CCCcCEEEEeCCCCchhHHHHHH
Confidence 57899999999999877765543
No 91
>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=41.95 E-value=28 Score=37.70 Aligned_cols=35 Identities=23% Similarity=0.545 Sum_probs=26.8
Q ss_pred hHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 686 EKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 686 ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
-||.-|++||. +++|++|+|+=||-.-|+..|-++
T Consensus 49 ~k~~~~~~~~~--l~~G~~vLDiGcGwG~~~~~~a~~ 83 (273)
T PF02353_consen 49 RKLDLLCEKLG--LKPGDRVLDIGCGWGGLAIYAAER 83 (273)
T ss_dssp HHHHHHHTTTT----TT-EEEEES-TTSHHHHHHHHH
T ss_pred HHHHHHHHHhC--CCCCCEEEEeCCCccHHHHHHHHH
Confidence 46777888885 999999999999999999988777
No 92
>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=41.35 E-value=24 Score=33.09 Aligned_cols=35 Identities=20% Similarity=0.525 Sum_probs=27.1
Q ss_pred HHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 688 LKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 688 l~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
+.+++.+|--+..++..|+||=||..-|++.|.+.
T Consensus 9 ~~~~~~~~~~~~~~~~~vLDiGcG~G~~~~~l~~~ 43 (161)
T PF13489_consen 9 YADLLERLLPRLKPGKRVLDIGCGTGSFLRALAKR 43 (161)
T ss_dssp HHHHHHHHHTCTTTTSEEEEESSTTSHHHHHHHHT
T ss_pred HHHHHHHHhcccCCCCEEEEEcCCCCHHHHHHHHh
Confidence 34555555545789999999999999999999553
No 93
>COG4798 Predicted methyltransferase [General function prediction only]
Probab=41.01 E-value=13 Score=39.19 Aligned_cols=49 Identities=16% Similarity=0.242 Sum_probs=43.2
Q ss_pred ceeeecCCeEEeeccCCChhhhHHHHHHHHhCCccCCCcccccCCCCCc
Q 004169 696 HWYVRSGDTIVDFCCGANDFSCMMKVKLEQMGKSCSFRNYDLIQPKVVG 744 (770)
Q Consensus 696 hwyv~~gd~ivdfccg~n~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 744 (770)
-|=|.+|+||||..-|..+|.|++..-+-..|+.-.|---+++-|++++
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 4779999999999999999999999999999988888777777777764
No 94
>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=41.00 E-value=6.8 Score=34.21 Aligned_cols=16 Identities=38% Similarity=1.045 Sum_probs=14.4
Q ss_pred CCcCCcCcchhhcccC
Q 004169 302 ATCGQFYHPECVSKLL 317 (770)
Q Consensus 302 ~~CGrfYH~~CL~~~~ 317 (770)
..||+.||..|+..|+
T Consensus 48 ~~C~H~FH~~Ci~~Wl 63 (73)
T PF12678_consen 48 GPCGHIFHFHCISQWL 63 (73)
T ss_dssp ETTSEEEEHHHHHHHH
T ss_pred cccCCCEEHHHHHHHH
Confidence 5799999999999886
No 95
>PRK06202 hypothetical protein; Provisional
Probab=40.74 E-value=24 Score=36.37 Aligned_cols=25 Identities=20% Similarity=0.315 Sum_probs=20.8
Q ss_pred ecCCeEEeeccCCChhhhHHHHHHH
Q 004169 700 RSGDTIVDFCCGANDFSCMMKVKLE 724 (770)
Q Consensus 700 ~~gd~ivdfccg~n~f~~~~~~~l~ 724 (770)
.++.+|+|+.||..+++..|.+.+.
T Consensus 59 ~~~~~iLDlGcG~G~~~~~L~~~~~ 83 (232)
T PRK06202 59 DRPLTLLDIGCGGGDLAIDLARWAR 83 (232)
T ss_pred CCCcEEEEeccCCCHHHHHHHHHHH
Confidence 6789999999999999888765443
No 96
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=40.67 E-value=19 Score=42.53 Aligned_cols=33 Identities=33% Similarity=0.522 Sum_probs=29.4
Q ss_pred ccCCCcccccccCCCCceeecCCccccccccccc
Q 004169 211 KDENYFAVCAICDDGGDVTFCDGRCLRSFHATIT 244 (770)
Q Consensus 211 ~dd~~d~VC~IC~~gGeLL~CdG~C~RsFH~~Cl 244 (770)
...+.+..|.-|.-+|..+.|+ .|.|+||-.|+
T Consensus 55 ~~~N~d~~cfechlpg~vl~c~-vc~Rs~h~~c~ 87 (588)
T KOG3612|consen 55 PSSNIDPFCFECHLPGAVLKCI-VCHRSFHENCQ 87 (588)
T ss_pred cccCCCcccccccCCcceeeee-hhhcccccccc
Confidence 3467789999999999999999 79999999974
No 97
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=40.47 E-value=37 Score=34.30 Aligned_cols=37 Identities=30% Similarity=0.503 Sum_probs=28.1
Q ss_pred cchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHH
Q 004169 682 FTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMK 720 (770)
Q Consensus 682 ftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~ 720 (770)
+|+.|-=.-++.+|. +++|++|+|++||+..|+..+-
T Consensus 23 ~t~~~~r~~~l~~l~--~~~~~~vlDlG~GtG~~s~~~a 59 (198)
T PRK00377 23 MTKEEIRALALSKLR--LRKGDMILDIGCGTGSVTVEAS 59 (198)
T ss_pred CCHHHHHHHHHHHcC--CCCcCEEEEeCCcCCHHHHHHH
Confidence 777766433456765 6799999999999999987553
No 98
>COG0293 FtsJ 23S rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=39.84 E-value=30 Score=36.40 Aligned_cols=53 Identities=25% Similarity=0.334 Sum_probs=44.4
Q ss_pred hhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHHHHhCCccCCCcccccCCC
Q 004169 685 VEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQMGKSCSFRNYDLIQPK 741 (770)
Q Consensus 685 ~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l~~~~~~~~~~~~~~~~~~ 741 (770)
.=||.||-+|- -.+.+|+.|||+|+--.-+|+...+++...++.. -||+-|=+
T Consensus 30 a~KL~el~~k~-~i~~~~~~ViDLGAAPGgWsQva~~~~~~~~~iv---avDi~p~~ 82 (205)
T COG0293 30 AYKLLELNEKF-KLFKPGMVVVDLGAAPGGWSQVAAKKLGAGGKIV---AVDILPMK 82 (205)
T ss_pred HHHHHHHHHhc-CeecCCCEEEEcCCCCCcHHHHHHHHhCCCCcEE---EEECcccc
Confidence 45999999998 7899999999999999999999999998877633 45655433
No 99
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=39.77 E-value=26 Score=38.64 Aligned_cols=34 Identities=29% Similarity=0.399 Sum_probs=29.7
Q ss_pred HHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 688 LKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 688 l~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
|.|+++-|- +++|+++||..||..-+|..|-+++
T Consensus 8 l~Evl~~L~--~~pg~~vlD~TlG~GGhS~~il~~~ 41 (296)
T PRK00050 8 LDEVVDALA--IKPDGIYVDGTFGGGGHSRAILERL 41 (296)
T ss_pred HHHHHHhhC--CCCCCEEEEeCcCChHHHHHHHHhC
Confidence 678888886 5899999999999999999887665
No 100
>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=39.31 E-value=37 Score=36.05 Aligned_cols=46 Identities=24% Similarity=0.376 Sum_probs=39.2
Q ss_pred cccCcccc-hhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 676 TSFGRHFT-KVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 676 tsfgrhft-k~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
.+||-||- ...-...||+.+..- +||+|||.-.|..-|++.|.++.
T Consensus 6 k~~gQnFL~~~~~~~~Iv~~~~~~--~~~~VlEiGpG~G~lT~~L~~~~ 52 (262)
T PF00398_consen 6 KSLGQNFLVDPNIADKIVDALDLS--EGDTVLEIGPGPGALTRELLKRG 52 (262)
T ss_dssp CGCTSSEEEHHHHHHHHHHHHTCG--TTSEEEEESSTTSCCHHHHHHHS
T ss_pred CCCCcCeeCCHHHHHHHHHhcCCC--CCCEEEEeCCCCccchhhHhccc
Confidence 58999997 667778899999665 99999999999999999886553
No 101
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=39.22 E-value=21 Score=30.76 Aligned_cols=32 Identities=31% Similarity=0.783 Sum_probs=24.3
Q ss_pred CCcccCcccccc-CcccccccccCCCCCCCCCceeeccCCCcC
Q 004169 264 VPNFLCQNCVYQ-EHQCFACGMLGSSDKSSSQEVFPCVSATCG 305 (770)
Q Consensus 264 ~~~W~C~eC~~~-qhqCfvCgklGssd~ss~~eV~kCsv~~CG 305 (770)
...|.|++|-.. ...|..|.+++ ..+.| +.||
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 457999999654 67899998765 56788 6776
No 102
>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=38.94 E-value=24 Score=31.71 Aligned_cols=22 Identities=27% Similarity=0.466 Sum_probs=19.6
Q ss_pred CCeEEeeccCCChhhhHHHHHH
Q 004169 702 GDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 702 gd~ivdfccg~n~f~~~~~~~l 723 (770)
|++|+|.|||+.-|...+.+..
T Consensus 1 g~~vlD~~~G~G~~~~~~~~~~ 22 (117)
T PF13659_consen 1 GDRVLDPGCGSGTFLLAALRRG 22 (117)
T ss_dssp TEEEEEETSTTCHHHHHHHHHC
T ss_pred CCEEEEcCcchHHHHHHHHHHC
Confidence 7899999999999998887664
No 103
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=38.63 E-value=25 Score=38.18 Aligned_cols=27 Identities=30% Similarity=0.693 Sum_probs=22.4
Q ss_pred CCceeeccCCCcC-CcCcchhhcccCCC
Q 004169 293 SQEVFPCVSATCG-QFYHPECVSKLLHP 319 (770)
Q Consensus 293 ~~eV~kCsv~~CG-rfYH~~CL~~~~~p 319 (770)
-++++.|..++|. -.||..||+.--.|
T Consensus 231 yGqMVaCDn~nCkrEWFH~~CVGLk~pP 258 (271)
T COG5034 231 YGQMVACDNANCKREWFHLECVGLKEPP 258 (271)
T ss_pred cccceecCCCCCchhheeccccccCCCC
Confidence 4799999999996 58999999875544
No 104
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=38.50 E-value=17 Score=42.14 Aligned_cols=29 Identities=21% Similarity=0.462 Sum_probs=18.8
Q ss_pred cccccccCCC----CceeecCCcccccccccccc
Q 004169 216 FAVCAICDDG----GDVTFCDGRCLRSFHATITA 245 (770)
Q Consensus 216 d~VC~IC~~g----GeLL~CdG~C~RsFH~~Cl~ 245 (770)
-+.|.+|-.- -..|.=- .|.-+||..|+.
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 4779999531 1122222 689999999864
No 105
>PRK00216 ubiE ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed
Probab=37.17 E-value=32 Score=34.61 Aligned_cols=45 Identities=27% Similarity=0.507 Sum_probs=31.4
Q ss_pred cccccCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 674 RYTSFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 674 rytsfgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
+|.++|.|- .-+.++++.|.. .+|.+|+|+.||...++..+...+
T Consensus 29 ~~~~~~~~~---~~~~~~~~~~~~--~~~~~vldiG~G~G~~~~~l~~~~ 73 (239)
T PRK00216 29 DLLSFGLHR---VWRRKTIKWLGV--RPGDKVLDLACGTGDLAIALAKAV 73 (239)
T ss_pred HHHhcCCcH---HHHHHHHHHhCC--CCCCeEEEeCCCCCHHHHHHHHHc
Confidence 344455432 444566666663 478999999999999998876655
No 106
>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB. The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles.
Probab=36.25 E-value=24 Score=40.20 Aligned_cols=23 Identities=17% Similarity=0.312 Sum_probs=18.3
Q ss_pred eecCCeEEeeccCCChhhhHHHH
Q 004169 699 VRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 699 v~~gd~ivdfccg~n~f~~~~~~ 721 (770)
+++|++|+|+|||...++..|-+
T Consensus 236 ~~~g~~VLDlcag~G~kt~~la~ 258 (426)
T TIGR00563 236 PQNEETILDACAAPGGKTTHILE 258 (426)
T ss_pred CCCCCeEEEeCCCccHHHHHHHH
Confidence 46799999999998877765543
No 107
>PLN02336 phosphoethanolamine N-methyltransferase
Probab=35.39 E-value=42 Score=38.47 Aligned_cols=34 Identities=29% Similarity=0.559 Sum_probs=26.2
Q ss_pred HHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 687 KLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 687 kl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
-.+.+++.+- +.+|++|+|+.||+..+...|.+.
T Consensus 254 ~te~l~~~~~--~~~~~~vLDiGcG~G~~~~~la~~ 287 (475)
T PLN02336 254 TTKEFVDKLD--LKPGQKVLDVGCGIGGGDFYMAEN 287 (475)
T ss_pred HHHHHHHhcC--CCCCCEEEEEeccCCHHHHHHHHh
Confidence 4456666665 488999999999999888777654
No 108
>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=35.30 E-value=30 Score=35.38 Aligned_cols=28 Identities=11% Similarity=0.206 Sum_probs=21.1
Q ss_pred hceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 695 LHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 695 lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
|.+.-..+.+|+|++||+.-|...|...
T Consensus 81 l~~~~~~~~~ilDig~G~G~~~~~l~~~ 108 (251)
T TIGR03534 81 LERLKKGPLRVLDLGTGSGAIALALAKE 108 (251)
T ss_pred HHhcccCCCeEEEEeCcHhHHHHHHHHH
Confidence 3444456679999999999998777654
No 109
>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=34.97 E-value=43 Score=36.13 Aligned_cols=38 Identities=24% Similarity=0.223 Sum_probs=27.5
Q ss_pred CcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHH
Q 004169 679 GRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMK 720 (770)
Q Consensus 679 grhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~ 720 (770)
|.|-|..-.|+- |.-|+.+|++|+|+.||+.-++..+.
T Consensus 141 G~h~tt~l~l~~----l~~~~~~g~~VLDvGcGsG~lai~aa 178 (288)
T TIGR00406 141 GTHPTTSLCLEW----LEDLDLKDKNVIDVGCGSGILSIAAL 178 (288)
T ss_pred CCCHHHHHHHHH----HHhhcCCCCEEEEeCCChhHHHHHHH
Confidence 477776554443 33367899999999999987776554
No 110
>PRK04266 fibrillarin; Provisional
Probab=34.97 E-value=30 Score=36.43 Aligned_cols=34 Identities=9% Similarity=0.225 Sum_probs=26.0
Q ss_pred HHHhhh-ceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 690 EIVDRL-HWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 690 ~iv~~l-hwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
.|..++ .--+++|++|+|++||+.-++..|.+..
T Consensus 60 ~ll~~~~~l~i~~g~~VlD~G~G~G~~~~~la~~v 94 (226)
T PRK04266 60 AILKGLKNFPIKKGSKVLYLGAASGTTVSHVSDIV 94 (226)
T ss_pred HHHhhHhhCCCCCCCEEEEEccCCCHHHHHHHHhc
Confidence 344544 3468899999999999998888876654
No 111
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.64 E-value=24 Score=39.91 Aligned_cols=29 Identities=31% Similarity=0.542 Sum_probs=22.4
Q ss_pred ccccccCCC---CceeecCCccccccccccccC
Q 004169 217 AVCAICDDG---GDVTFCDGRCLRSFHATITAG 246 (770)
Q Consensus 217 ~VC~IC~~g---GeLL~CdG~C~RsFH~~Cl~g 246 (770)
+.|+||-+. |+.|.== +|.-.||..|++.
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 799999763 7755544 8999999998654
No 112
>PF12847 Methyltransf_18: Methyltransferase domain; PDB: 3G2Q_A 3G2O_A 3G2M_B 3G2P_B 3D2L_B 1IM8_B 3NJR_A 3E05_H 3EVZ_A 3HM2_A ....
Probab=34.21 E-value=37 Score=30.16 Aligned_cols=21 Identities=24% Similarity=0.605 Sum_probs=18.2
Q ss_pred cCCeEEeeccCCChhhhHHHH
Q 004169 701 SGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 701 ~gd~ivdfccg~n~f~~~~~~ 721 (770)
||.+|+|+.||...++..+.+
T Consensus 1 p~~~vLDlGcG~G~~~~~l~~ 21 (112)
T PF12847_consen 1 PGGRVLDLGCGTGRLSIALAR 21 (112)
T ss_dssp TTCEEEEETTTTSHHHHHHHH
T ss_pred CCCEEEEEcCcCCHHHHHHHh
Confidence 689999999999999876655
No 113
>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed
Probab=33.95 E-value=31 Score=37.63 Aligned_cols=33 Identities=18% Similarity=0.395 Sum_probs=23.1
Q ss_pred hHHHHHHhhhceee-ecCCeEEeeccCCChhhhHHH
Q 004169 686 EKLKEIVDRLHWYV-RSGDTIVDFCCGANDFSCMMK 720 (770)
Q Consensus 686 ekl~~iv~~lhwyv-~~gd~ivdfccg~n~f~~~~~ 720 (770)
|+|.+.+.+ |.- .+|++|+|+|||+..|+..+-
T Consensus 159 ~~l~~~v~~--~l~~~~~~~VLDl~cG~G~~sl~la 192 (315)
T PRK03522 159 AQLYATARD--WVRELPPRSMWDLFCGVGGFGLHCA 192 (315)
T ss_pred HHHHHHHHH--HHHhcCCCEEEEccCCCCHHHHHHH
Confidence 555554432 332 268999999999999987654
No 114
>PRK11705 cyclopropane fatty acyl phospholipid synthase; Provisional
Probab=33.31 E-value=47 Score=37.62 Aligned_cols=35 Identities=23% Similarity=0.446 Sum_probs=28.1
Q ss_pred hHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 686 EKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 686 ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
.|+..|+++|. +++|++|+|+.||...+...+.+.
T Consensus 154 ~k~~~l~~~l~--l~~g~rVLDIGcG~G~~a~~la~~ 188 (383)
T PRK11705 154 AKLDLICRKLQ--LKPGMRVLDIGCGWGGLARYAAEH 188 (383)
T ss_pred HHHHHHHHHhC--CCCCCEEEEeCCCccHHHHHHHHH
Confidence 46666777763 789999999999999998877653
No 115
>PHA02929 N1R/p28-like protein; Provisional
Probab=32.85 E-value=33 Score=36.80 Aligned_cols=16 Identities=19% Similarity=0.621 Sum_probs=14.2
Q ss_pred CCcCCcCcchhhcccC
Q 004169 302 ATCGQFYHPECVSKLL 317 (770)
Q Consensus 302 ~~CGrfYH~~CL~~~~ 317 (770)
..||+.||..|+..|.
T Consensus 198 ~~C~H~FC~~CI~~Wl 213 (238)
T PHA02929 198 SNCNHVFCIECIDIWK 213 (238)
T ss_pred CCCCCcccHHHHHHHH
Confidence 6899999999998775
No 116
>KOG3285 consensus Spindle assembly checkpoint protein [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=30.87 E-value=43 Score=34.75 Aligned_cols=47 Identities=30% Similarity=0.367 Sum_probs=34.7
Q ss_pred eecCCCCceEeeee---------eeeccccc-cCCCCcceEEEeecccCCccceeeeE
Q 004169 20 FLDQNEESISFSVL---------PLQWDGCD-IVGSSEMQVFLHGNIGDGPWNFNEQV 67 (770)
Q Consensus 20 f~d~~~~~v~fs~l---------p~~~~~~~-~~~~~~~~v~l~g~~d~gl~~v~~~v 67 (770)
|.--=+++.+|.+| |..|.+|. .+-.....|.||++. .++.+|--+|
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 44445666777764 99999987 446677789999998 7777776554
No 117
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=30.51 E-value=25 Score=32.32 Aligned_cols=17 Identities=29% Similarity=0.755 Sum_probs=14.8
Q ss_pred CCcCCcCcchhhcccCC
Q 004169 302 ATCGQFYHPECVSKLLH 318 (770)
Q Consensus 302 ~~CGrfYH~~CL~~~~~ 318 (770)
..|++.||..|+.+++.
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 118
>cd04813 PA_1 PA_1: Protease-associated (PA) domain subgroup 1. A subgroup of PA-domain containing proteins. Proteins in this subgroup contain a RING-finger (Really Interesting New Gene) domain C-terminal to this PA domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins in this group contain a C-terminal RING-finger domain. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases: such as hSPPL2a and 2b, ii) various E3 ubiquitin ligases similar to human GRAIL (gene related to anergy in lymphocytes) protein, iii) various proteins containing a RING finger motif such as Arabid
Probab=30.34 E-value=22 Score=33.81 Aligned_cols=16 Identities=38% Similarity=0.509 Sum_probs=13.9
Q ss_pred cccccccccCcccchh
Q 004169 670 LHGMRYTSFGRHFTKV 685 (770)
Q Consensus 670 l~g~rytsfgrhftk~ 685 (770)
|-|.||-|||-+||..
T Consensus 2 ~~~~~~~~~~~~~~~~ 17 (117)
T cd04813 2 LIGGRYASFSPILNPH 17 (117)
T ss_pred cccccccccCCccCcc
Confidence 4689999999999875
No 119
>PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed
Probab=30.31 E-value=40 Score=34.48 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=19.5
Q ss_pred eeecCCeEEeeccCCChhhhHHHH
Q 004169 698 YVRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 698 yv~~gd~ivdfccg~n~f~~~~~~ 721 (770)
|+++|.+|+|+.||...++..|..
T Consensus 42 ~l~~g~~VLDiGcGtG~~al~la~ 65 (187)
T PRK00107 42 YLPGGERVLDVGSGAGFPGIPLAI 65 (187)
T ss_pred hcCCCCeEEEEcCCCCHHHHHHHH
Confidence 345699999999999998886643
No 120
>KOG4217 consensus Nuclear receptors of the nerve growth factor-induced protein B type [Transcription]
Probab=29.96 E-value=17 Score=42.34 Aligned_cols=60 Identities=27% Similarity=0.621 Sum_probs=38.6
Q ss_pred cCCCcccccccCCCC-----ceeecCCccccccccccccCccccccccCCcccccCCCCcccCccccc
Q 004169 212 DENYFAVCAICDDGG-----DVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVY 274 (770)
Q Consensus 212 dd~~d~VC~IC~~gG-----eLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~ 274 (770)
+...+..|++|++.- -.-.|+| |...|..+-..+....| |+-+.=+++...+-.|..|++
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 445588999999852 1567997 99999988654444444 444333444444566777765
No 121
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=29.77 E-value=31 Score=39.63 Aligned_cols=23 Identities=13% Similarity=0.333 Sum_probs=18.5
Q ss_pred eecCCeEEeeccCCChhhhHHHH
Q 004169 699 VRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 699 v~~gd~ivdfccg~n~f~~~~~~ 721 (770)
+++|++|+|+|||..-.+..|-+
T Consensus 235 ~~~g~~VLD~cagpGgkt~~la~ 257 (431)
T PRK14903 235 LEPGLRVLDTCAAPGGKTTAIAE 257 (431)
T ss_pred CCCCCEEEEeCCCccHHHHHHHH
Confidence 46899999999999988765443
No 122
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=29.76 E-value=40 Score=38.64 Aligned_cols=25 Identities=24% Similarity=0.457 Sum_probs=20.9
Q ss_pred eecCCeEEeeccCCChhhhHHHHHH
Q 004169 699 VRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 699 v~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
+++|++|+|+|||...++..|-+.+
T Consensus 248 ~~~g~~VLDlgaG~G~~t~~la~~~ 272 (444)
T PRK14902 248 PKGGDTVLDACAAPGGKTTHIAELL 272 (444)
T ss_pred CCCCCEEEEeCCCCCHHHHHHHHHh
Confidence 4789999999999999987766554
No 123
>COG0286 HsdM Type I restriction-modification system methyltransferase subunit [Defense mechanisms]
Probab=29.45 E-value=59 Score=38.10 Aligned_cols=49 Identities=22% Similarity=0.269 Sum_probs=43.4
Q ss_pred ccCcccchhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHHHHHhC
Q 004169 677 SFGRHFTKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKLEQMG 727 (770)
Q Consensus 677 sfgrhftk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l~~~~ 727 (770)
+.|-+||..+=-+=||..|-- +++++|.|=|||+.-|-....+-|.+-.
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 679999999999999999988 9999999999999999888888776544
No 124
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=29.43 E-value=32 Score=40.00 Aligned_cols=34 Identities=21% Similarity=0.470 Sum_probs=23.0
Q ss_pred ccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcccC
Q 004169 278 QCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLL 317 (770)
Q Consensus 278 qCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~ 317 (770)
.|.+|-+.-.++ .+ .++. ..|.+.||-.|+..|.
T Consensus 177 TCpVCLERMD~s--~~-gi~t---~~c~Hsfh~~cl~~w~ 210 (493)
T KOG0804|consen 177 TCPVCLERMDSS--TT-GILT---ILCNHSFHCSCLMKWW 210 (493)
T ss_pred CcchhHhhcCcc--cc-ceee---eecccccchHHHhhcc
Confidence 577886655432 22 3332 5799999999999885
No 125
>PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed
Probab=29.35 E-value=43 Score=34.16 Aligned_cols=28 Identities=11% Similarity=0.178 Sum_probs=22.5
Q ss_pred hceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 695 LHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 695 lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
+-++.++++.|||+.||...++..|.++
T Consensus 34 ~~~~~~~~~~VLDiGcGtG~~~~~la~~ 61 (202)
T PRK00121 34 AELFGNDAPIHLEIGFGKGEFLVEMAKA 61 (202)
T ss_pred HHHcCCCCCeEEEEccCCCHHHHHHHHH
Confidence 3446668999999999999998887654
No 126
>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=29.13 E-value=15 Score=33.48 Aligned_cols=15 Identities=47% Similarity=1.088 Sum_probs=13.1
Q ss_pred hcCCCcccccccCCc
Q 004169 635 DGGCDIEDAKAVCPP 649 (770)
Q Consensus 635 e~g~~i~~aka~c~p 649 (770)
..||||+||||+|+.
T Consensus 41 NkGCsidD~k~iC~~ 55 (92)
T PF05413_consen 41 NKGCSIDDLKAICEK 55 (92)
T ss_pred cCCCCHHHHHHHHhh
Confidence 368999999999975
No 127
>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=28.70 E-value=63 Score=34.98 Aligned_cols=23 Identities=17% Similarity=0.345 Sum_probs=18.6
Q ss_pred ecCCeEEeeccCCChhhhHHHHH
Q 004169 700 RSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 700 ~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
.++.+|+|++||+.-|+..+...
T Consensus 120 ~~~~~vLDlG~GsG~i~~~la~~ 142 (284)
T TIGR03533 120 EPVKRILDLCTGSGCIAIACAYA 142 (284)
T ss_pred CCCCEEEEEeCchhHHHHHHHHH
Confidence 45689999999999888776653
No 128
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=28.57 E-value=28 Score=30.32 Aligned_cols=34 Identities=24% Similarity=0.575 Sum_probs=12.7
Q ss_pred ccccCcCCccCccCccceeecc--ccccccccccCCC
Q 004169 344 KCFVCQQSEDMNVEDLQLAICR--RCPKAYHRKCLPT 378 (770)
Q Consensus 344 ~C~~C~~~edk~~~e~qLi~C~--RCP~AYH~kCLP~ 378 (770)
.|..|...... ..+...+.|. +|...||..||-.
T Consensus 4 ~C~IC~~~~~~-~~~~p~~~C~n~~C~~~fH~~CL~~ 39 (70)
T PF11793_consen 4 ECGICYSYRLD-DGEIPDVVCPNPSCGKKFHLLCLSE 39 (70)
T ss_dssp S-SSS--SS-T-T-----B--S-TT----B-SGGGHH
T ss_pred CCCcCCcEecC-CCCcCceEcCCcccCCHHHHHHHHH
Confidence 57788875431 2234568897 9999999999843
No 129
>PRK11524 putative methyltransferase; Provisional
Probab=28.49 E-value=45 Score=35.94 Aligned_cols=32 Identities=28% Similarity=0.238 Sum_probs=21.1
Q ss_pred cccc-hhhHHHHHHhhhceeeecCCeEEeeccCCC
Q 004169 680 RHFT-KVEKLKEIVDRLHWYVRSGDTIVDFCCGAN 713 (770)
Q Consensus 680 rhft-k~ekl~~iv~~lhwyv~~gd~ivdfccg~n 713 (770)
.|.| |++.|-|-.= .=|-.+||+|+|+++||.
T Consensus 188 ~HPt~kP~~L~erlI--~~~S~~GD~VLDPF~GSG 220 (284)
T PRK11524 188 NHPTQKPEALLKRII--LASSNPGDIVLDPFAGSF 220 (284)
T ss_pred cCcccChHHHHHHHH--HHhCCCCCEEEECCCCCc
Confidence 4766 3444433222 234589999999999996
No 130
>PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=28.27 E-value=63 Score=33.78 Aligned_cols=25 Identities=8% Similarity=0.207 Sum_probs=19.8
Q ss_pred eecCCeEEeeccCCChhhhHHHHHH
Q 004169 699 VRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 699 v~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
..++.+|+|++||+.-++..|...+
T Consensus 106 ~~~~~~vLDiG~GsG~~~~~la~~~ 130 (275)
T PRK09328 106 LKEPLRVLDLGTGSGAIALALAKER 130 (275)
T ss_pred ccCCCEEEEEcCcHHHHHHHHHHHC
Confidence 3578899999999998877765543
No 131
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=27.62 E-value=44 Score=38.13 Aligned_cols=23 Identities=13% Similarity=0.381 Sum_probs=18.5
Q ss_pred eecCCeEEeeccCCChhhhHHHH
Q 004169 699 VRSGDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 699 v~~gd~ivdfccg~n~f~~~~~~ 721 (770)
+++|++|+|+|||..-++..|-+
T Consensus 242 ~~~g~~VLDlgaG~G~~t~~la~ 264 (427)
T PRK10901 242 PQNGERVLDACAAPGGKTAHILE 264 (427)
T ss_pred CCCCCEEEEeCCCCChHHHHHHH
Confidence 45899999999999887766543
No 132
>TIGR01934 MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis methyltransferases. Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases.
Probab=27.44 E-value=63 Score=32.16 Aligned_cols=33 Identities=18% Similarity=0.414 Sum_probs=24.8
Q ss_pred HHHHhhhceeeecCCeEEeeccCCChhhhHHHHHH
Q 004169 689 KEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 689 ~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
..+++.++. .+|.+|+|+.||...++..+..++
T Consensus 29 ~~~~~~~~~--~~~~~vldiG~G~G~~~~~~~~~~ 61 (223)
T TIGR01934 29 RRAVKLIGV--FKGQKVLDVACGTGDLAIELAKSA 61 (223)
T ss_pred HHHHHHhcc--CCCCeEEEeCCCCChhHHHHHHhc
Confidence 344555543 289999999999999998886655
No 133
>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=27.22 E-value=33 Score=37.42 Aligned_cols=59 Identities=31% Similarity=0.623 Sum_probs=35.0
Q ss_pred CCCcccccccCC-----CCceeecCCccccccccccccC---ccccccccCCcccccCCCCcccCccccc-cCccccccc
Q 004169 213 ENYFAVCAICDD-----GGDVTFCDGRCLRSFHATITAG---KNALCQSLGYTQAQIDAVPNFLCQNCVY-QEHQCFACG 283 (770)
Q Consensus 213 d~~d~VC~IC~~-----gGeLL~CdG~C~RsFH~~Cl~g---~~s~C~sLGlt~~ev~~~~~W~C~eC~~-~qhqCfvCg 283 (770)
.+.+.+|.-|+. ||.+..|. -|..+. |.+- -+..|+-| ..++|.|..|.. ||+.|.-|+
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 566788888865 57888887 566543 2211 01234322 245787887753 677776664
No 134
>PF14881 Tubulin_3: Tubulin domain
Probab=26.75 E-value=38 Score=34.64 Aligned_cols=52 Identities=19% Similarity=0.357 Sum_probs=40.6
Q ss_pred cccchhhHHHHHHhh-hceeeecCCe------EEeeccCCChhhhHHHHHH-HHhCCccC
Q 004169 680 RHFTKVEKLKEIVDR-LHWYVRSGDT------IVDFCCGANDFSCMMKVKL-EQMGKSCS 731 (770)
Q Consensus 680 rhftk~ekl~~iv~~-lhwyv~~gd~------ivdfccg~n~f~~~~~~~l-~~~~~~~~ 731 (770)
-.|...++..++.|| ||+|||.=|+ ++|..-|-.-|+.=|-+-| ++.+|+..
T Consensus 48 ~~f~~~~~~~d~~D~~lR~f~EECD~lQGfQ~~~d~d~gwgGfas~~Le~L~DEy~k~~i 107 (180)
T PF14881_consen 48 ELFKSLDYEEDFFDRDLRFFLEECDSLQGFQVLTDVDDGWGGFASSLLEHLRDEYPKKPI 107 (180)
T ss_pred HHHhhhhhhhHHHHHHHHHHHHHcccccceEEEecCCCchHhHHHHHHHHHHHHcCCCce
Confidence 468888999999998 9999999998 5888888888876555555 45666653
No 135
>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=26.59 E-value=59 Score=23.82 Aligned_cols=29 Identities=28% Similarity=0.567 Sum_probs=22.7
Q ss_pred cccccCcCCccCccCccc-eeeccccccccccccC
Q 004169 343 HKCFVCQQSEDMNVEDLQ-LAICRRCPKAYHRKCL 376 (770)
Q Consensus 343 H~C~~C~~~edk~~~e~q-Li~C~RCP~AYH~kCL 376 (770)
++|.+|.+.-+. . +-.|..|....|..|.
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 8899999999999883
No 136
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=26.53 E-value=38 Score=29.34 Aligned_cols=32 Identities=34% Similarity=0.896 Sum_probs=24.7
Q ss_pred CCcccCcccc-ccCcccccccccCCCCCCCCCceeeccCCCcC
Q 004169 264 VPNFLCQNCV-YQEHQCFACGMLGSSDKSSSQEVFPCVSATCG 305 (770)
Q Consensus 264 ~~~W~C~eC~-~~qhqCfvCgklGssd~ss~~eV~kCsv~~CG 305 (770)
...|.|++|- .-...|..|.++| ..++| +.||
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 3579999997 5567899998875 57888 6777
No 137
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=26.46 E-value=23 Score=27.29 Aligned_cols=19 Identities=32% Similarity=0.751 Sum_probs=13.3
Q ss_pred ceeeccccccccccccCCC
Q 004169 360 QLAICRRCPKAYHRKCLPT 378 (770)
Q Consensus 360 qLi~C~RCP~AYH~kCLP~ 378 (770)
+|+.|.+|..+.|..|---
T Consensus 3 ~ll~C~~C~v~VH~~CYGv 21 (36)
T PF13831_consen 3 PLLFCDNCNVAVHQSCYGV 21 (36)
T ss_dssp EEEE-SSS--EEEHHHHT-
T ss_pred ceEEeCCCCCcCChhhCCc
Confidence 7999999999999999533
No 138
>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=26.24 E-value=1.8e+02 Score=31.19 Aligned_cols=95 Identities=16% Similarity=0.280 Sum_probs=61.5
Q ss_pred HHHHHHHHHHhhcCCCcccccccCCchhhhhHHHHhhcccccc---------------------------cccc--cccc
Q 004169 624 VKAVRAALEMLDGGCDIEDAKAVCPPEILCQIFQWKRKLDVYL---------------------------APFL--HGMR 674 (770)
Q Consensus 624 v~a~~~al~~le~g~~i~~aka~c~p~~l~q~~~w~~kl~~~l---------------------------apfl--~g~r 674 (770)
-..|..|.+|+++|.++++. +.+|..++++-.+|+ -|+| ..-.
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 34677788999999987653 444444554444442 3444 2346
Q ss_pred ccccCcccchhhHHHHHHhhhceeeecCC--eEEeeccCCChhhhHHHHHHHHh
Q 004169 675 YTSFGRHFTKVEKLKEIVDRLHWYVRSGD--TIVDFCCGANDFSCMMKVKLEQM 726 (770)
Q Consensus 675 ytsfgrhftk~ekl~~iv~~lhwyv~~gd--~ivdfccg~n~f~~~~~~~l~~~ 726 (770)
...+|+..+.---++++++.+.=++.+++ .|.=..+|..+=...+++.|.+.
T Consensus 194 i~~~~k~Rg~kka~~~l~~~~~~~~~~~~~~~i~i~~~~~~e~~~~l~~~l~~~ 247 (275)
T TIGR00762 194 LVPIEKVRGRKKAIKKLVELVKEDIKDGKPKRVAIIHADAEEEAEELKEKLKEK 247 (275)
T ss_pred EEEeeccccHHHHHHHHHHHHHHhhccCCCcEEEEEeCCCHHHHHHHHHHHHhH
Confidence 78889999887778888888876666543 33344566655566677777763
No 139
>PLN02244 tocopherol O-methyltransferase
Probab=25.90 E-value=70 Score=35.45 Aligned_cols=24 Identities=29% Similarity=0.415 Sum_probs=20.8
Q ss_pred ecCCeEEeeccCCChhhhHHHHHH
Q 004169 700 RSGDTIVDFCCGANDFSCMMKVKL 723 (770)
Q Consensus 700 ~~gd~ivdfccg~n~f~~~~~~~l 723 (770)
++|++|+|+.||...++..|.++.
T Consensus 117 ~~~~~VLDiGCG~G~~~~~La~~~ 140 (340)
T PLN02244 117 KRPKRIVDVGCGIGGSSRYLARKY 140 (340)
T ss_pred CCCCeEEEecCCCCHHHHHHHHhc
Confidence 689999999999999988877653
No 140
>PRK13943 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=25.53 E-value=97 Score=34.53 Aligned_cols=38 Identities=8% Similarity=0.162 Sum_probs=28.1
Q ss_pred chhhHHHHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 683 TKVEKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 683 tk~ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
+.+.-+-.+++.|. +++|++|+|++||+..++..|.+.
T Consensus 64 ~~p~l~a~ll~~L~--i~~g~~VLDIG~GtG~~a~~LA~~ 101 (322)
T PRK13943 64 SQPSLMALFMEWVG--LDKGMRVLEIGGGTGYNAAVMSRV 101 (322)
T ss_pred CcHHHHHHHHHhcC--CCCCCEEEEEeCCccHHHHHHHHh
Confidence 35555555556554 689999999999999988877653
No 141
>PRK01683 trans-aconitate 2-methyltransferase; Provisional
Probab=25.14 E-value=69 Score=33.34 Aligned_cols=32 Identities=16% Similarity=0.470 Sum_probs=25.3
Q ss_pred HHHHhhhceeeecCCeEEeeccCCChhhhHHHHH
Q 004169 689 KEIVDRLHWYVRSGDTIVDFCCGANDFSCMMKVK 722 (770)
Q Consensus 689 ~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~~~ 722 (770)
+++++++ .+.+|+.|+|+.||...|+..+.+.
T Consensus 21 ~~ll~~~--~~~~~~~vLDiGcG~G~~~~~la~~ 52 (258)
T PRK01683 21 RDLLARV--PLENPRYVVDLGCGPGNSTELLVER 52 (258)
T ss_pred HHHHhhC--CCcCCCEEEEEcccCCHHHHHHHHH
Confidence 3556655 3578999999999999999888765
No 142
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.84 E-value=29 Score=39.73 Aligned_cols=28 Identities=32% Similarity=0.942 Sum_probs=22.5
Q ss_pred CCcCCcCcchhhcccCCCCchhHHHHHHHHHhcCCceecCC-cccccCc
Q 004169 302 ATCGQFYHPECVSKLLHPDNESLAEELRERIAAGESFTCPV-HKCFVCQ 349 (770)
Q Consensus 302 ~~CGrfYH~~CL~~~~~p~~~~~~~el~krV~~g~~F~CPl-H~C~~C~ 349 (770)
..||+.||..|+..|.. .||. ..|..|.
T Consensus 24 ~~cGhifh~~cl~qwfe--------------------~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 24 GTCGHIFHTTCLTQWFE--------------------GDPSNRGCPICQ 52 (465)
T ss_pred cchhhHHHHHHHHHHHc--------------------cCCccCCCCcee
Confidence 67999999999988752 4676 4788888
No 143
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=24.48 E-value=1.3e+02 Score=25.80 Aligned_cols=49 Identities=18% Similarity=0.274 Sum_probs=37.9
Q ss_pred ChhHHHHHHHhhhccCC-CCchHhhhccCCCCcccccCCccccceeeecccchhhHHHHHHHHHHhhcCCCcc
Q 004169 570 DAEMEKELLALIKDSTS-SFNEEEFMKSHIVPITHAHHSKHLLEKSITLGLVEGSVKAVRAALEMLDGGCDIE 641 (770)
Q Consensus 570 d~~~e~r~l~~~~~~~s-~~~~~~~~~~~~~~~t~~~~~~~~~~k~i~~g~~e~sv~a~~~al~~le~g~~i~ 641 (770)
..+++++||.++++... .+|..++-+...++. .+|+.+|..|++-+-|+
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~-----------------------~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNLGLPK-----------------------KEVNRVLYSLEKKGKVC 53 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCH-----------------------HHHHHHHHHHHHCCCEE
Confidence 36788999999999866 599999998887765 35677788887766554
No 144
>PF03291 Pox_MCEL: mRNA capping enzyme; InterPro: IPR004971 This is a family of viral mRNA capping enzymes. The enzyme catalyses the first two reactions in the mRNA cap formation pathway. It is a heterodimer consisting of a large and small subunit. This entry is the large subunit. ; GO: 0006370 mRNA capping; PDB: 3EPP_A 3BGV_C 2VDW_C 1RI5_A 1RI3_A 1RI1_A 1Z3C_A 1RI2_A 2HV9_A 1RI4_A.
Probab=23.90 E-value=32 Score=38.35 Aligned_cols=19 Identities=37% Similarity=0.871 Sum_probs=13.5
Q ss_pred cCCeEEeeccC-CChhhhHH
Q 004169 701 SGDTIVDFCCG-ANDFSCMM 719 (770)
Q Consensus 701 ~gd~ivdfccg-~n~f~~~~ 719 (770)
+|++|+|+||| ..|.-...
T Consensus 62 ~~~~VLDl~CGkGGDL~Kw~ 81 (331)
T PF03291_consen 62 PGLTVLDLCCGKGGDLQKWQ 81 (331)
T ss_dssp TT-EEEEET-TTTTTHHHHH
T ss_pred CCCeEEEecCCCchhHHHHH
Confidence 99999999999 77765443
No 145
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=23.56 E-value=27 Score=38.89 Aligned_cols=63 Identities=19% Similarity=0.380 Sum_probs=36.5
Q ss_pred cccccccCCC----CceeecCCccccccccccccCccccccccCCcccccCCCCcccCccccccCcccccccccCCCCCC
Q 004169 216 FAVCAICDDG----GDVTFCDGRCLRSFHATITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQEHQCFACGMLGSSDKS 291 (770)
Q Consensus 216 d~VC~IC~~g----GeLL~CdG~C~RsFH~~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~~qhqCfvCgklGssd~s 291 (770)
-.+|--|+-+ |.+|-|+ -.|.++| .- . ...-+|+-|......=..|.
T Consensus 90 VHfCd~Cd~PI~IYGRmIPCk----HvFCl~C--------Ar--~-------~~dK~Cp~C~d~VqrIeq~~-------- 140 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPCK----HVFCLEC--------AR--S-------DSDKICPLCDDRVQRIEQIM-------- 140 (389)
T ss_pred eEeecccCCcceeeecccccc----hhhhhhh--------hh--c-------CccccCcCcccHHHHHHHhc--------
Confidence 4669999975 7888666 4444443 11 1 12457888876533222332
Q ss_pred CCCceeeccCCC-cCCcC
Q 004169 292 SSQEVFPCVSAT-CGQFY 308 (770)
Q Consensus 292 s~~eV~kCsv~~-CGrfY 308 (770)
-+.+|.|+... |-|.|
T Consensus 141 -~g~iFmC~~~~GC~RTy 157 (389)
T KOG2932|consen 141 -MGGIFMCAAPHGCLRTY 157 (389)
T ss_pred -ccceEEeecchhHHHHH
Confidence 24799996443 55555
No 146
>cd06569 GH20_Sm-chitobiase-like The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=23.53 E-value=47 Score=38.56 Aligned_cols=24 Identities=21% Similarity=0.486 Sum_probs=21.2
Q ss_pred CcccchhhHHHHHH--------hhhceeeecC
Q 004169 679 GRHFTKVEKLKEIV--------DRLHWYVRSG 702 (770)
Q Consensus 679 grhftk~ekl~~iv--------~~lhwyv~~g 702 (770)
+|||-.+|.|++++ +.|||++-+.
T Consensus 15 aR~f~~~~~ik~~Id~ma~~K~N~lHlHLtDd 46 (445)
T cd06569 15 ARNFHSKETVLKLLDQMAAYKLNKLHLHLTDD 46 (445)
T ss_pred cCCCCCHHHHHHHHHHHHHhCCceEEEEeecC
Confidence 79999999999999 4699998664
No 147
>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=23.33 E-value=48 Score=27.03 Aligned_cols=37 Identities=24% Similarity=0.566 Sum_probs=20.6
Q ss_pred ccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcccC
Q 004169 278 QCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLL 317 (770)
Q Consensus 278 qCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~ 317 (770)
+|.+|...+. + .+.-+..|.=..--+++|..|+..|.
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 12233445212223899999999885
No 148
>PF15656 Tox-HDC: Toxin with a H, D/N and C signature
Probab=23.13 E-value=61 Score=31.53 Aligned_cols=26 Identities=31% Similarity=0.784 Sum_probs=20.9
Q ss_pred hhhHHHHHHhhhceeeecCCeEEeeccCCCh
Q 004169 684 KVEKLKEIVDRLHWYVRSGDTIVDFCCGAND 714 (770)
Q Consensus 684 k~ekl~~iv~~lhwyv~~gd~ivdfccg~n~ 714 (770)
..|+|..++..- ++-.|.-||||+||
T Consensus 89 ~~~el~~~l~~~-----~~hvIlgyC~S~~D 114 (119)
T PF15656_consen 89 SMEELNNILNNI-----NGHVILGYCFSRND 114 (119)
T ss_pred CHHHHHHHhcCC-----CCeEEEEEEecCCC
Confidence 347777777766 67779999999998
No 149
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=23.11 E-value=34 Score=31.41 Aligned_cols=30 Identities=27% Similarity=0.527 Sum_probs=18.3
Q ss_pred cccccccCCCCc-eeecCCcccccccccccc
Q 004169 216 FAVCAICDDGGD-VTFCDGRCLRSFHATITA 245 (770)
Q Consensus 216 d~VC~IC~~gGe-LL~CdG~C~RsFH~~Cl~ 245 (770)
|..|..|.-+|+ --.+-|.|...||..|+.
T Consensus 32 dg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~ 62 (85)
T PF12861_consen 32 DGCCPDCKFPGDDCPLVWGKCSHNFHMHCIL 62 (85)
T ss_pred ccCCCCccCCCCCCceeeccCccHHHHHHHH
Confidence 344444445564 112346799999999864
No 150
>PF00728 Glyco_hydro_20: Glycosyl hydrolase family 20, catalytic domain; InterPro: IPR015883 Glycoside hydrolase family 20 GH20 from CAZY comprises enzymes with several known activities; beta-hexosaminidase (3.2.1.52 from EC); lacto-N-biosidase (3.2.1.140 from EC). Carbonyl oxygen of the C-2 acetamido group of the substrate acts as the catalytic nucleophile/base in this family of enzymes. In the brain and other tissues, beta-hexosaminidase A degrades GM2 gangliosides; specifically, the enzyme hydrolyses terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. There are 3 forms of beta-hexosaminidase: hexosaminidase A is a trimer, with one alpha, one beta-A and one beta-B chain; hexosaminidase B is a tetramer of two beta-A and two beta-B chains; and hexosaminidase S is a homodimer of alpha chains. The two beta chains are derived from the cleavage of a precursor. Mutations in the beta-chain lead to Sandhoff disease, a lysosomal storage disorder characterised by accumulation of GM2 ganglioside [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds; PDB: 3RPM_A 1C7T_A 1QBA_A 1QBB_A 1C7S_A 3RCN_A 2YL8_A 2YL6_A 2YLL_A 2YL5_C ....
Probab=23.03 E-value=58 Score=35.45 Aligned_cols=24 Identities=33% Similarity=0.696 Sum_probs=20.0
Q ss_pred CcccchhhHHHHHHhh--------hceeeecC
Q 004169 679 GRHFTKVEKLKEIVDR--------LHWYVRSG 702 (770)
Q Consensus 679 grhftk~ekl~~iv~~--------lhwyv~~g 702 (770)
||||=.++.|++++|. |||++.+-
T Consensus 11 aR~~~~~~~ik~~id~ma~~k~N~lhlhl~D~ 42 (351)
T PF00728_consen 11 ARHFFSVDTIKRLIDQMAYYKLNVLHLHLSDD 42 (351)
T ss_dssp SSS-B-HHHHHHHHHHHHHTT-SEEEEEEESS
T ss_pred CCCCCCHHHHHHHHHHHHHcCCcEEEEEEecC
Confidence 8999999999999997 79999865
No 151
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=22.97 E-value=31 Score=36.30 Aligned_cols=9 Identities=56% Similarity=1.675 Sum_probs=8.1
Q ss_pred EeeccCCCh
Q 004169 706 VDFCCGAND 714 (770)
Q Consensus 706 vdfccg~n~ 714 (770)
+|||||.|.
T Consensus 27 idfCcgG~~ 35 (220)
T PRK10992 27 LDFCCGGKQ 35 (220)
T ss_pred CcccCCCCc
Confidence 899999984
No 152
>PRK11036 putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=22.86 E-value=84 Score=32.95 Aligned_cols=32 Identities=13% Similarity=0.187 Sum_probs=24.4
Q ss_pred hHHHHHHhhhceeeecCCeEEeeccCCChhhhHHH
Q 004169 686 EKLKEIVDRLHWYVRSGDTIVDFCCGANDFSCMMK 720 (770)
Q Consensus 686 ekl~~iv~~lhwyv~~gd~ivdfccg~n~f~~~~~ 720 (770)
..|.++++.|- ..+.+|+|+.||...++..|.
T Consensus 32 ~~~~~~l~~l~---~~~~~vLDiGcG~G~~a~~la 63 (255)
T PRK11036 32 QDLDRLLAELP---PRPLRVLDAGGGEGQTAIKLA 63 (255)
T ss_pred HHHHHHHHhcC---CCCCEEEEeCCCchHHHHHHH
Confidence 34566666653 778999999999998876664
No 153
>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=22.58 E-value=67 Score=29.37 Aligned_cols=29 Identities=31% Similarity=0.814 Sum_probs=21.1
Q ss_pred CCcccccccCCCCc-----eeecCCcccccccccc
Q 004169 214 NYFAVCAICDDGGD-----VTFCDGRCLRSFHATI 243 (770)
Q Consensus 214 ~~d~VC~IC~~gGe-----LL~CdG~C~RsFH~~C 243 (770)
.....|.||++... .+.|.| |.-.|.-..
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 678985 888887764
No 154
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=22.50 E-value=19 Score=45.73 Aligned_cols=51 Identities=8% Similarity=0.072 Sum_probs=37.7
Q ss_pred cccccccCCCCceeecCCcccccccc-ccccCccccccccCCcccccCCCCcccCcccccc
Q 004169 216 FAVCAICDDGGDVTFCDGRCLRSFHA-TITAGKNALCQSLGYTQAQIDAVPNFLCQNCVYQ 275 (770)
Q Consensus 216 d~VC~IC~~gGeLL~CdG~C~RsFH~-~Cl~g~~s~C~sLGlt~~ev~~~~~W~C~eC~~~ 275 (770)
-.-|.||+..|.+|+|+|.|+..||+ .|++.. +=+..+ +.+.|+|++|...
T Consensus 428 ~rrl~Ie~~det~l~yysT~pqly~ll~cLd~~--------~~e~~L-~d~i~~~~ee~~r 479 (1414)
T KOG1473|consen 428 SRRLRIEGMDETLLWYYSTCPQLYHLLRCLDRT--------YVEMYL-CDGIWERREEIIR 479 (1414)
T ss_pred eeeeEEecCCCcEEEEecCcHHHHHHHHHhchH--------HHHHhh-ccchhhhHHHHHH
Confidence 45699999999999999999999999 764321 111112 4578999999754
No 155
>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=22.02 E-value=73 Score=25.47 Aligned_cols=34 Identities=29% Similarity=0.390 Sum_probs=24.3
Q ss_pred cccccCcCCccCccCccceeeccccccccccccCCC
Q 004169 343 HKCFVCQQSEDMNVEDLQLAICRRCPKAYHRKCLPT 378 (770)
Q Consensus 343 H~C~~C~~~edk~~~e~qLi~C~RCP~AYH~kCLP~ 378 (770)
-+|..|+..=-. ...+-++|..|...+|.+|++.
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 378888885411 2347789999999999999876
No 156
>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=21.91 E-value=55 Score=38.16 Aligned_cols=42 Identities=21% Similarity=0.753 Sum_probs=33.0
Q ss_pred CcccCccccccCcccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcc
Q 004169 265 PNFLCQNCVYQEHQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSK 315 (770)
Q Consensus 265 ~~W~C~eC~~~qhqCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~ 315 (770)
.+-+|..|. |.+|++... ...+--++.| ..||+.-|..|--.
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 456799998 999998643 3345688999 68999999999643
No 157
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.68 E-value=29 Score=38.00 Aligned_cols=42 Identities=14% Similarity=0.364 Sum_probs=24.5
Q ss_pred CcccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcccC
Q 004169 276 EHQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLL 317 (770)
Q Consensus 276 qhqCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~ 317 (770)
+..|-+||+.-..++...+-+-.=..-.|++.||..|+..|-
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWc 265 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWC 265 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhhe
Confidence 346889987543222111111111225799999999998774
No 158
>PTZ00487 ceramidase; Provisional
Probab=21.67 E-value=73 Score=39.33 Aligned_cols=72 Identities=18% Similarity=0.242 Sum_probs=50.3
Q ss_pred cccCCCCCChhHHHHHHHhhhccCC--CCchHhhhccCCCCcccccCCccccceee----e-cc--------cchhhHHH
Q 004169 562 VNISQPSVDAEMEKELLALIKDSTS--SFNEEEFMKSHIVPITHAHHSKHLLEKSI----T-LG--------LVEGSVKA 626 (770)
Q Consensus 562 ~~~s~~~~d~~~e~r~l~~~~~~~s--~~~~~~~~~~~~~~~t~~~~~~~~~~k~i----~-~g--------~~e~sv~a 626 (770)
++.-+..++.+.-.+|++.+++... -++.+.|. +..||||++-....... + .| .|+|.|+|
T Consensus 93 Vs~Dl~~i~~~v~~~V~~~L~~~~Gi~~y~~~NVl----lsATHTHSGPgg~~~~~l~~~ts~Gf~~qy~~~lvdgIv~A 168 (715)
T PTZ00487 93 VSTDSCMIFQEVKIGVVPKLQEIFGPDLYTLDNVL----LSGTHTHSGPAGFSFYALYGITTLGFYKKNFDTICEGIVQA 168 (715)
T ss_pred EEEcccCCCHHHHHHHHHHHHHHhCcCcCChhhEE----EEeeecCCCCcccccccccccccccccHHHHHHHHHHHHHH
Confidence 4555677778888889988877653 34655553 56778888775432221 1 11 58999999
Q ss_pred HHHHHHHhhcC
Q 004169 627 VRAALEMLDGG 637 (770)
Q Consensus 627 ~~~al~~le~g 637 (770)
|+.|.+-|+.|
T Consensus 169 I~~A~~nL~Pa 179 (715)
T PTZ00487 169 IVKAHKSVQPA 179 (715)
T ss_pred HHHHHhcCCcE
Confidence 99999999988
No 159
>TIGR00138 gidB 16S rRNA methyltransferase GidB. GidB (glucose-inhibited division protein B) appears to be present and in a single copy in nearly all complete eubacterial genomes. It is missing only from some obligate intracellular species of various lineages (Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera, etc.). GidB shows a methytransferase fold in its the crystal structure, and acts as a 7-methylguanosine (m(7)G) methyltransferase, apparently specific to 16S rRNA.
Probab=21.58 E-value=1e+02 Score=31.08 Aligned_cols=25 Identities=24% Similarity=0.331 Sum_probs=19.3
Q ss_pred hceeeecCCeEEeeccCCChhhhHHH
Q 004169 695 LHWYVRSGDTIVDFCCGANDFSCMMK 720 (770)
Q Consensus 695 lhwyv~~gd~ivdfccg~n~f~~~~~ 720 (770)
+.++++ |++|+|+.||+..++..|.
T Consensus 37 ~~~~~~-~~~vLDiGcGtG~~s~~la 61 (181)
T TIGR00138 37 LLEYLD-GKKVIDIGSGAGFPGIPLA 61 (181)
T ss_pred HHHhcC-CCeEEEecCCCCccHHHHH
Confidence 345664 9999999999998776653
No 160
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=21.40 E-value=50 Score=23.98 Aligned_cols=29 Identities=31% Similarity=0.672 Sum_probs=12.2
Q ss_pred ccccccccCCCCCCCCCceeeccCCCcCCcCcchhh
Q 004169 278 QCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECV 313 (770)
Q Consensus 278 qCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL 313 (770)
.|.+|++.+. +.-++.| ..|.-..|..|+
T Consensus 2 ~C~~C~~~~~-----~~~~Y~C--~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPID-----GGWFYRC--SECDFDLHEECA 30 (30)
T ss_dssp --TTTS---------S--EEE---TTT-----HHHH
T ss_pred cCCcCCCcCC-----CCceEEC--ccCCCccChhcC
Confidence 4778887653 2378999 899999999984
No 161
>PHA02862 5L protein; Provisional
Probab=21.09 E-value=47 Score=33.45 Aligned_cols=36 Identities=14% Similarity=0.330 Sum_probs=25.2
Q ss_pred cccccccccCCCCCCCCCceeeccCCCcCCcCcchhhcccCC
Q 004169 277 HQCFACGMLGSSDKSSSQEVFPCVSATCGQFYHPECVSKLLH 318 (770)
Q Consensus 277 hqCfvCgklGssd~ss~~eV~kCsv~~CGrfYH~~CL~~~~~ 318 (770)
+.|.+|...+. .++..|.-.+--++-|..|+..|..
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 2356774445579999999999863
No 162
>cd06568 GH20_SpHex_like A subgroup of the Glycosyl hydrolase family 20 (GH20) catalytic domain found in proteins similar to the N-acetylhexosaminidase from Streptomyces plicatus (SpHex). SpHex catalyzes the hydrolysis of N-acetyl-beta-hexosaminides. An Asp residue within the active site plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Proteins belonging to this subgroup lack the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases.
Probab=20.92 E-value=63 Score=35.91 Aligned_cols=24 Identities=33% Similarity=0.560 Sum_probs=21.7
Q ss_pred CcccchhhHHHHHHhh--------hceeeecC
Q 004169 679 GRHFTKVEKLKEIVDR--------LHWYVRSG 702 (770)
Q Consensus 679 grhftk~ekl~~iv~~--------lhwyv~~g 702 (770)
||||-.+|-|++++|. |||++.+.
T Consensus 11 aR~f~~~~~lk~~id~ma~~KlN~lhlHLtD~ 42 (329)
T cd06568 11 ARHFFTVAEVKRYIDLLALYKLNVLHLHLTDD 42 (329)
T ss_pred cCCCcCHHHHHHHHHHHHHhCCcEEEEEeecC
Confidence 8999999999999986 89999764
No 163
>cd06570 GH20_chitobiase-like_1 A functionally uncharacterized subgroup of the Glycosyl hydrolase family 20 (GH20) catalytic domain found in proteins similar to the chitobiase of Serratia marcescens, a beta-N-1,4-acetylhexosaminidase that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. This subgroup lacks the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=20.70 E-value=65 Score=35.61 Aligned_cols=24 Identities=33% Similarity=0.711 Sum_probs=21.3
Q ss_pred CcccchhhHHHHHHhh--------hceeeecC
Q 004169 679 GRHFTKVEKLKEIVDR--------LHWYVRSG 702 (770)
Q Consensus 679 grhftk~ekl~~iv~~--------lhwyv~~g 702 (770)
||||-.+|.|++++|. |||++-+.
T Consensus 11 aR~f~~~~~ik~~Id~ma~~KlN~lh~HltDd 42 (311)
T cd06570 11 SRHFIPVAVIKRQLDAMASVKLNVFHWHLTDD 42 (311)
T ss_pred CCCCcCHHHHHHHHHHHHHhCCeEEEEEEecC
Confidence 8999999999999986 79998654
No 164
>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=20.62 E-value=96 Score=33.35 Aligned_cols=19 Identities=16% Similarity=0.209 Sum_probs=15.9
Q ss_pred CeEEeeccCCChhhhHHHH
Q 004169 703 DTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 703 d~ivdfccg~n~f~~~~~~ 721 (770)
..|+|+|||+.-++..+..
T Consensus 116 ~~vLDlG~GsG~i~l~la~ 134 (284)
T TIGR00536 116 LHILDLGTGSGCIALALAY 134 (284)
T ss_pred CEEEEEeccHhHHHHHHHH
Confidence 7999999999988766654
No 165
>COG3764 SrtA Sortase (surface protein transpeptidase) [Cell envelope biogenesis, outer membrane]
Probab=20.61 E-value=57 Score=34.44 Aligned_cols=21 Identities=43% Similarity=0.616 Sum_probs=18.3
Q ss_pred ccccccccccCcccchhhHHH
Q 004169 669 FLHGMRYTSFGRHFTKVEKLK 689 (770)
Q Consensus 669 fl~g~rytsfgrhftk~ekl~ 689 (770)
.|.|-|=+.+|+.|+.+++|+
T Consensus 116 ~laGHr~~~~~~~F~~L~~lk 136 (210)
T COG3764 116 VLAGHRGTRYGSLFRPLGKLK 136 (210)
T ss_pred EEEecccccccccccchhhhc
Confidence 368999999999999999953
No 166
>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=20.22 E-value=52 Score=29.45 Aligned_cols=29 Identities=21% Similarity=0.444 Sum_probs=19.4
Q ss_pred cccccccCCC-CceeecCCccccccccccc
Q 004169 216 FAVCAICDDG-GDVTFCDGRCLRSFHATIT 244 (770)
Q Consensus 216 d~VC~IC~~g-GeLL~CdG~C~RsFH~~Cl 244 (770)
+..|++|++. |+-..---+|...||..|.
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 4779999985 3322222267799999984
No 167
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=20.16 E-value=37 Score=35.84 Aligned_cols=8 Identities=63% Similarity=1.900 Sum_probs=7.1
Q ss_pred EeeccCCC
Q 004169 706 VDFCCGAN 713 (770)
Q Consensus 706 vdfccg~n 713 (770)
+|||||.+
T Consensus 27 iDFCCGG~ 34 (221)
T COG2846 27 IDFCCGGK 34 (221)
T ss_pred CceecCCh
Confidence 79999985
No 168
>PRK05031 tRNA (uracil-5-)-methyltransferase; Validated
Probab=20.07 E-value=84 Score=35.27 Aligned_cols=41 Identities=12% Similarity=0.323 Sum_probs=27.4
Q ss_pred ccchh--hHHHHHHhhhceeeec-CCeEEeeccCCChhhhHHHH
Q 004169 681 HFTKV--EKLKEIVDRLHWYVRS-GDTIVDFCCGANDFSCMMKV 721 (770)
Q Consensus 681 hftk~--ekl~~iv~~lhwyv~~-gd~ivdfccg~n~f~~~~~~ 721 (770)
.|.++ +-.+.+++.+.-|++. +.+|+|+|||+.-|+..+..
T Consensus 183 sF~Q~N~~~~e~l~~~v~~~~~~~~~~vLDl~~G~G~~sl~la~ 226 (362)
T PRK05031 183 SFTQPNAAVNEKMLEWALDATKGSKGDLLELYCGNGNFTLALAR 226 (362)
T ss_pred CeeccCHHHHHHHHHHHHHHhhcCCCeEEEEeccccHHHHHHHh
Confidence 35443 2344555555555653 45799999999999987764
No 169
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=20.03 E-value=53 Score=25.06 Aligned_cols=13 Identities=31% Similarity=0.843 Sum_probs=7.8
Q ss_pred CCceeeccCCCcC
Q 004169 293 SQEVFPCVSATCG 305 (770)
Q Consensus 293 ~~eV~kCsv~~CG 305 (770)
.-+||+|+.+.|.
T Consensus 21 eikvfrcsnpacd 33 (36)
T PF09151_consen 21 EIKVFRCSNPACD 33 (36)
T ss_dssp -EEEEEES-TT--
T ss_pred cEEEEEcCCCccc
Confidence 3478999988886
Done!