Query 000595
Match_columns 1401
No_of_seqs 230 out of 636
Neff 3.3
Searched_HMMs 46136
Date Mon Apr 1 20:21:39 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000595.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000595hhsearch_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 2.6E-20 5.6E-25 186.2 2.5 131 7-141 1-145 (146)
2 KOG4443 Putative transcription 98.7 2.8E-09 6.1E-14 127.3 1.9 102 288-422 19-121 (694)
3 KOG1244 Predicted transcriptio 98.7 7.5E-09 1.6E-13 113.9 3.5 81 305-408 244-325 (336)
4 KOG4299 PHD Zn-finger protein 98.2 1.1E-06 2.3E-11 105.6 4.9 49 355-414 255-303 (613)
5 KOG4443 Putative transcription 97.9 3.2E-06 6.9E-11 102.0 2.1 103 225-362 16-124 (694)
6 KOG1512 PHD Zn-finger protein 97.8 9.7E-06 2.1E-10 90.5 2.0 78 306-408 278-356 (381)
7 KOG0956 PHD finger protein AF1 97.7 2.4E-05 5.2E-10 94.7 3.0 169 229-436 7-193 (900)
8 KOG4299 PHD Zn-finger protein 97.5 3.3E-05 7E-10 93.3 0.6 54 223-286 249-305 (613)
9 KOG1512 PHD Zn-finger protein 97.4 6.5E-05 1.4E-09 84.1 2.5 82 225-328 256-348 (381)
10 COG5141 PHD zinc finger-contai 97.4 4.6E-05 1E-09 89.7 1.1 89 225-327 191-336 (669)
11 KOG0954 PHD finger protein [Ge 97.4 0.00011 2.4E-09 89.9 3.5 134 226-393 270-417 (893)
12 KOG1244 Predicted transcriptio 97.3 0.00012 2.6E-09 81.7 2.6 82 225-328 222-315 (336)
13 KOG0955 PHD finger protein BR1 97.3 0.00018 3.8E-09 92.1 4.3 136 225-394 217-368 (1051)
14 PRK00274 ksgA 16S ribosomal RN 97.2 0.00026 5.5E-09 78.3 4.1 152 701-861 18-188 (272)
15 PHA03412 putative methyltransf 97.1 0.0011 2.3E-08 73.8 7.1 172 702-888 29-230 (241)
16 PF00628 PHD: PHD-finger; Int 97.0 0.00023 5E-09 60.1 1.3 47 229-285 1-50 (51)
17 KOG0383 Predicted helicase [Ge 97.0 0.00047 1E-08 85.5 3.9 92 314-439 1-114 (696)
18 KOG1473 Nucleosome remodeling 96.9 0.00046 1E-08 87.5 2.8 119 220-391 337-461 (1414)
19 PF02384 N6_Mtase: N-6 DNA Met 96.9 0.0014 3E-08 72.8 5.8 124 702-828 24-187 (311)
20 COG5034 TNG2 Chromatin remodel 96.8 0.00078 1.7E-08 75.0 2.7 45 227-285 221-269 (271)
21 TIGR02987 met_A_Alw26 type II 96.7 0.004 8.6E-08 74.8 8.0 49 702-750 2-55 (524)
22 smart00249 PHD PHD zinc finger 96.6 0.0012 2.6E-08 53.0 2.4 44 229-283 1-47 (47)
23 KOG0825 PHD Zn-finger protein 96.6 0.0017 3.6E-08 80.3 4.6 46 354-412 216-262 (1134)
24 KOG1973 Chromatin remodeling p 96.6 0.00074 1.6E-08 75.7 1.5 46 226-285 220-267 (274)
25 TIGR00755 ksgA dimethyladenosi 96.4 0.0069 1.5E-07 66.2 7.3 148 702-861 6-176 (253)
26 PRK14896 ksgA 16S ribosomal RN 96.4 0.0027 5.8E-08 69.8 3.8 149 702-861 6-172 (258)
27 PF00628 PHD: PHD-finger; Int 96.3 0.003 6.5E-08 53.5 3.0 45 355-408 1-45 (51)
28 KOG0383 Predicted helicase [Ge 96.2 0.0018 3.9E-08 80.5 1.1 50 223-284 43-92 (696)
29 PF15446 zf-PHD-like: PHD/FYVE 96.1 0.0048 1E-07 65.6 3.6 94 289-392 1-144 (175)
30 smart00249 PHD PHD zinc finger 95.9 0.0072 1.6E-07 48.5 3.1 44 355-408 1-44 (47)
31 PTZ00338 dimethyladenosine tra 95.7 0.015 3.3E-07 65.9 5.6 154 696-861 6-184 (294)
32 PF01170 UPF0020: Putative RNA 95.5 0.029 6.2E-07 59.2 6.8 107 715-826 19-152 (179)
33 PF13659 Methyltransf_26: Meth 94.0 0.033 7.1E-07 52.7 2.2 87 727-814 1-103 (117)
34 PF15446 zf-PHD-like: PHD/FYVE 93.8 0.076 1.6E-06 56.9 4.7 93 229-327 1-142 (175)
35 PF00398 RrnaAD: Ribosomal RNA 93.5 0.061 1.3E-06 59.5 3.6 155 701-861 6-181 (262)
36 PRK10909 rsmD 16S rRNA m(2)G96 93.0 0.33 7.3E-06 52.6 8.2 120 725-853 52-184 (199)
37 KOG1701 Focal adhesion adaptor 92.8 0.016 3.6E-07 68.5 -2.3 141 228-388 275-429 (468)
38 KOG1973 Chromatin remodeling p 92.3 0.066 1.4E-06 60.5 1.7 24 305-328 230-254 (274)
39 KOG0825 PHD Zn-finger protein 92.2 0.078 1.7E-06 66.4 2.3 47 227-285 215-265 (1134)
40 TIGR00479 rumA 23S rRNA (uraci 92.2 0.22 4.8E-06 58.6 5.9 129 709-841 273-416 (431)
41 KOG4323 Polycomb-like PHD Zn-f 91.0 0.086 1.9E-06 63.5 0.9 51 227-286 168-224 (464)
42 PF13832 zf-HC5HC2H_2: PHD-zin 90.9 0.22 4.8E-06 48.4 3.5 84 229-327 2-88 (110)
43 PF13771 zf-HC5HC2H: PHD-like 90.9 0.089 1.9E-06 49.2 0.8 40 220-259 29-70 (90)
44 TIGR01177 conserved hypothetic 90.7 1 2.2E-05 51.6 9.1 104 713-828 171-298 (329)
45 KOG0957 PHD finger protein [Ge 90.6 0.1 2.2E-06 63.0 1.0 47 355-408 546-592 (707)
46 smart00650 rADc Ribosomal RNA 90.3 0.27 5.8E-06 50.7 3.7 141 713-860 2-159 (169)
47 PF13832 zf-HC5HC2H_2: PHD-zin 90.3 0.21 4.6E-06 48.5 2.8 102 289-422 2-110 (110)
48 TIGR02085 meth_trns_rumB 23S r 89.6 0.34 7.3E-06 56.7 4.1 115 708-828 213-338 (374)
49 PF05175 MTS: Methyltransferas 88.3 0.44 9.6E-06 49.4 3.6 84 726-814 31-128 (170)
50 KOG4323 Polycomb-like PHD Zn-f 87.5 0.33 7.2E-06 58.7 2.4 48 356-408 171-218 (464)
51 PRK03522 rumB 23S rRNA methylu 87.2 0.62 1.3E-05 53.1 4.2 93 726-824 173-273 (315)
52 PRK13168 rumA 23S rRNA m(5)U19 86.7 0.87 1.9E-05 54.3 5.2 124 713-841 282-420 (443)
53 COG2263 Predicted RNA methylas 86.2 2.3 5E-05 46.9 7.6 99 716-828 30-148 (198)
54 TIGR03533 L3_gln_methyl protei 85.2 1.4 3E-05 49.9 5.6 72 725-801 120-202 (284)
55 KOG0955 PHD finger protein BR1 84.4 0.69 1.5E-05 60.7 3.1 58 355-423 221-283 (1051)
56 PF07669 Eco57I: Eco57I restri 84.3 0.84 1.8E-05 44.7 3.0 39 790-829 5-56 (106)
57 PHA03411 putative methyltransf 84.0 0.73 1.6E-05 52.9 2.7 40 703-746 45-84 (279)
58 TIGR03534 RF_mod_PrmC protein- 83.7 2.1 4.5E-05 45.9 5.9 70 724-802 85-168 (251)
59 COG2265 TrmA SAM-dependent met 83.4 1.9 4.1E-05 52.1 6.0 116 697-824 260-395 (432)
60 COG2226 UbiE Methylase involve 83.3 1.3 2.9E-05 49.7 4.4 58 675-747 15-72 (238)
61 KOG0957 PHD finger protein [Ge 82.7 0.49 1.1E-05 57.4 0.8 49 226-283 543-595 (707)
62 PRK11805 N5-glutamine S-adenos 82.6 2.2 4.7E-05 49.1 5.8 69 728-801 135-214 (307)
63 PRK11188 rrmJ 23S rRNA methylt 82.2 7.6 0.00016 42.2 9.4 65 710-778 36-102 (209)
64 PRK14967 putative methyltransf 81.1 5.3 0.00011 43.2 7.8 34 711-746 23-56 (223)
65 PF13771 zf-HC5HC2H: PHD-like 80.9 0.83 1.8E-05 42.8 1.5 34 287-328 36-70 (90)
66 PF02475 Met_10: Met-10+ like- 78.6 0.71 1.5E-05 50.4 0.2 101 685-816 78-192 (200)
67 COG5034 TNG2 Chromatin remodel 76.7 1.5 3.3E-05 49.8 2.2 35 305-354 232-267 (271)
68 COG0030 KsgA Dimethyladenosine 76.7 5.4 0.00012 45.7 6.4 116 701-833 6-139 (259)
69 TIGR00095 RNA methyltransferas 75.8 8.8 0.00019 41.2 7.5 107 713-823 37-157 (189)
70 TIGR03704 PrmC_rel_meth putati 75.1 1.9 4.1E-05 48.1 2.3 68 727-799 87-164 (251)
71 KOG0956 PHD finger protein AF1 75.1 1.1 2.4E-05 56.2 0.7 41 222-262 112-161 (900)
72 PRK05785 hypothetical protein; 74.8 3.7 8.1E-05 45.0 4.5 59 676-747 14-72 (226)
73 PRK05031 tRNA (uracil-5-)-meth 73.4 4.5 9.8E-05 47.4 5.0 115 709-828 188-324 (362)
74 COG2520 Predicted methyltransf 72.5 1.6 3.5E-05 51.4 1.1 102 688-815 168-278 (341)
75 PLN02672 methionine S-methyltr 71.8 10 0.00022 50.8 8.0 165 618-802 6-217 (1082)
76 TIGR02143 trmA_only tRNA (urac 71.6 3.9 8.4E-05 47.9 3.9 115 714-833 184-320 (353)
77 PRK09328 N5-glutamine S-adenos 70.9 5.7 0.00012 43.5 4.7 74 724-803 106-190 (275)
78 cd04718 BAH_plant_2 BAH, or Br 67.5 4.7 0.0001 42.9 3.1 21 381-408 1-21 (148)
79 TIGR03587 Pse_Me-ase pseudamin 66.6 6.3 0.00014 42.8 3.9 51 697-747 14-64 (204)
80 KOG1245 Chromatin remodeling c 64.0 1.8 3.9E-05 58.8 -0.9 60 224-295 1105-1170(1404)
81 TIGR00536 hemK_fam HemK family 61.0 6.6 0.00014 44.3 3.0 68 728-800 116-194 (284)
82 KOG1473 Nucleosome remodeling 58.3 5.8 0.00013 52.5 2.1 42 355-410 346-387 (1414)
83 TIGR00762 DegV EDD domain prot 58.3 48 0.001 37.5 9.0 94 648-750 122-246 (275)
84 PF13679 Methyltransf_32: Meth 57.8 54 0.0012 33.5 8.5 108 710-825 6-132 (141)
85 PF13901 DUF4206: Domain of un 56.5 7.3 0.00016 42.7 2.2 46 279-326 144-189 (202)
86 KOG0954 PHD finger protein [Ge 56.0 6.5 0.00014 50.2 2.0 43 355-408 273-315 (893)
87 PF11793 FANCL_C: FANCL C-term 55.9 7.2 0.00016 36.3 1.8 39 289-329 4-42 (70)
88 PF13489 Methyltransf_23: Meth 55.4 15 0.00032 36.2 4.0 36 711-746 7-42 (161)
89 smart00550 Zalpha Z-DNA-bindin 55.1 22 0.00049 32.7 4.8 46 601-663 5-51 (68)
90 KOG4628 Predicted E3 ubiquitin 54.1 6.9 0.00015 46.5 1.7 69 28-111 30-99 (348)
91 KOG1245 Chromatin remodeling c 54.1 3.6 7.8E-05 56.1 -0.6 43 355-408 1110-1152(1404)
92 COG5141 PHD zinc finger-contai 53.2 11 0.00024 46.5 3.1 72 355-437 195-272 (669)
93 COG0286 HsdM Type I restrictio 53.1 15 0.00032 45.2 4.3 49 702-752 164-212 (489)
94 PF01209 Ubie_methyltran: ubiE 52.5 8.2 0.00018 42.9 1.9 56 676-746 12-67 (233)
95 KOG1044 Actin-binding LIM Zn-f 51.4 9.3 0.0002 47.9 2.2 27 227-256 16-44 (670)
96 PF13831 PHD_2: PHD-finger; PD 51.1 3.3 7.1E-05 34.5 -1.1 35 237-284 2-36 (36)
97 KOG3612 PHD Zn-finger protein 50.7 12 0.00026 46.6 3.0 38 217-255 50-87 (588)
98 TIGR00080 pimt protein-L-isoas 50.3 21 0.00047 38.4 4.6 45 703-749 56-100 (215)
99 PRK15001 SAM-dependent 23S rib 50.1 22 0.00048 42.6 5.0 123 697-824 198-339 (378)
100 TIGR02021 BchM-ChlM magnesium 48.9 14 0.00031 39.6 2.9 35 713-747 38-76 (219)
101 KOG3420 Predicted RNA methylas 48.8 4.8 0.0001 43.4 -0.6 105 708-816 28-143 (185)
102 COG3802 GguC Uncharacterized p 48.4 9.1 0.0002 44.1 1.4 66 797-863 186-285 (333)
103 PRK13942 protein-L-isoaspartat 48.0 21 0.00046 38.8 4.1 45 702-748 54-98 (212)
104 cd04718 BAH_plant_2 BAH, or Br 47.3 10 0.00022 40.5 1.5 26 250-286 2-27 (148)
105 PF13412 HTH_24: Winged helix- 46.9 33 0.00071 28.9 4.2 43 602-662 3-45 (48)
106 PRK14968 putative methyltransf 46.4 51 0.0011 33.8 6.3 23 725-747 22-44 (188)
107 PRK14966 unknown domain/N5-glu 46.1 17 0.00036 44.5 3.2 82 715-801 240-332 (423)
108 PTZ00098 phosphoethanolamine N 46.1 24 0.00051 39.7 4.2 50 694-745 10-71 (263)
109 TIGR02081 metW methionine bios 45.7 24 0.00051 37.4 4.0 30 713-746 4-33 (194)
110 COG0293 FtsJ 23S rRNA methylas 45.7 24 0.00051 39.5 4.1 43 710-753 30-72 (205)
111 TIGR02752 MenG_heptapren 2-hep 44.5 22 0.00048 38.1 3.5 43 700-747 24-66 (231)
112 PRK09489 rsmC 16S ribosomal RN 44.0 63 0.0014 38.2 7.3 21 727-747 197-217 (342)
113 PRK00312 pcm protein-L-isoaspa 43.4 78 0.0017 34.0 7.4 44 702-747 56-99 (212)
114 PRK13944 protein-L-isoaspartat 43.2 30 0.00065 37.3 4.3 45 703-749 51-95 (205)
115 COG2230 Cfa Cyclopropane fatty 42.5 25 0.00055 41.0 3.8 35 711-747 59-93 (283)
116 TIGR02469 CbiT precorrin-6Y C5 42.4 35 0.00075 32.3 4.2 35 710-746 5-39 (124)
117 PRK01544 bifunctional N5-gluta 41.7 17 0.00036 44.9 2.4 72 726-801 138-219 (506)
118 PF14446 Prok-RING_1: Prokaryo 41.3 14 0.00031 33.7 1.3 32 355-389 7-38 (54)
119 PF04405 ScdA_N: Domain of Unk 40.4 17 0.00038 33.0 1.7 19 731-752 24-42 (56)
120 TIGR00438 rrmJ cell division p 40.3 34 0.00074 36.0 4.1 36 712-748 19-54 (188)
121 KOG2824 Glutaredoxin-related p 39.7 28 0.0006 40.6 3.5 26 140-165 157-185 (281)
122 KOG4628 Predicted E3 ubiquitin 39.6 16 0.00034 43.7 1.7 28 228-256 230-260 (348)
123 PF01728 FtsJ: FtsJ-like methy 38.0 23 0.0005 36.9 2.5 38 711-748 7-45 (181)
124 TIGR00406 prmA ribosomal prote 37.6 38 0.00081 38.6 4.2 38 704-745 141-178 (288)
125 PLN02585 magnesium protoporphy 37.5 26 0.00056 41.0 2.9 22 726-747 144-165 (315)
126 KOG1701 Focal adhesion adaptor 37.0 33 0.00072 42.0 3.7 75 245-327 351-431 (468)
127 KOG1081 Transcription factor N 36.4 26 0.00056 43.2 2.8 36 219-255 81-116 (463)
128 KOG2932 E3 ubiquitin ligase in 36.1 13 0.00027 43.9 0.2 64 227-320 90-158 (389)
129 PRK00050 16S rRNA m(4)C1402 me 35.2 43 0.00092 39.2 4.2 34 712-747 7-40 (296)
130 KOG0804 Cytoplasmic Zn-finger 35.0 20 0.00044 44.0 1.6 35 288-328 176-210 (493)
131 PF14446 Prok-RING_1: Prokaryo 34.9 25 0.00055 32.2 1.8 34 288-327 6-39 (54)
132 PRK11783 rlmL 23S rRNA m(2)G24 34.8 74 0.0016 40.9 6.5 66 673-741 134-205 (702)
133 PF13639 zf-RING_2: Ring finge 34.1 6.5 0.00014 32.8 -1.9 33 289-328 2-34 (44)
134 cd00315 Cyt_C5_DNA_methylase C 34.1 1E+02 0.0022 35.1 6.9 89 729-829 2-116 (275)
135 KOG4218 Nuclear hormone recept 33.3 15 0.00034 43.7 0.3 26 227-253 15-45 (475)
136 KOG1169 Diacylglycerol kinase 32.3 19 0.00041 45.9 0.8 141 229-389 46-211 (634)
137 PF01555 N6_N4_Mtase: DNA meth 32.2 28 0.00061 36.2 2.0 50 690-741 152-206 (231)
138 PLN03208 E3 ubiquitin-protein 31.9 23 0.0005 39.4 1.3 41 215-256 6-46 (193)
139 PRK08287 cobalt-precorrin-6Y C 31.8 67 0.0014 33.8 4.6 41 704-746 11-51 (187)
140 TIGR00446 nop2p NOL1/NOP2/sun 31.8 34 0.00073 38.5 2.6 41 707-748 53-93 (264)
141 PRK07402 precorrin-6B methylas 30.7 71 0.0015 33.9 4.7 41 704-746 20-60 (196)
142 KOG1829 Uncharacterized conser 30.4 17 0.00036 46.0 -0.1 48 278-327 502-549 (580)
143 TIGR01712 phage_N6A_met phage 29.3 43 0.00094 36.5 2.8 35 791-829 64-101 (166)
144 PF02353 CMAS: Mycolic acid cy 29.2 55 0.0012 37.6 3.7 34 712-747 50-83 (273)
145 PTZ00146 fibrillarin; Provisio 29.1 41 0.0009 39.4 2.8 28 723-750 129-156 (293)
146 PRK00121 trmB tRNA (guanine-N( 28.7 31 0.00067 37.2 1.6 29 720-748 34-62 (202)
147 PF05869 Dam: DNA N-6-adenine- 28.5 56 0.0012 35.8 3.5 131 707-882 15-152 (181)
148 TIGR00675 dcm DNA-methyltransf 28.3 64 0.0014 37.5 4.1 91 730-826 1-110 (315)
149 KOG0828 Predicted E3 ubiquitin 28.3 12 0.00026 46.2 -1.6 29 314-358 605-633 (636)
150 COG1307 DegV Uncharacterized p 27.2 2.4E+02 0.0052 32.8 8.4 98 646-752 123-251 (282)
151 PF12678 zf-rbx1: RING-H2 zinc 25.6 17 0.00037 34.0 -0.8 15 314-328 49-63 (73)
152 PRK14902 16S rRNA methyltransf 25.6 87 0.0019 37.9 4.7 25 724-748 248-272 (444)
153 cd02440 AdoMet_MTases S-adenos 25.6 75 0.0016 27.6 3.2 89 729-824 1-103 (107)
154 PF07227 DUF1423: Protein of u 25.3 45 0.00097 41.1 2.3 43 276-327 122-164 (446)
155 PRK04266 fibrillarin; Provisio 25.1 81 0.0018 35.2 4.1 36 713-748 58-94 (226)
156 PRK00377 cbiT cobalt-precorrin 24.9 96 0.0021 33.2 4.4 39 707-747 23-61 (198)
157 KOG1952 Transcription factor N 24.5 31 0.00068 45.2 0.8 93 221-324 185-287 (950)
158 KOG2272 Focal adhesion protein 24.5 34 0.00073 39.6 1.0 138 225-382 71-231 (332)
159 COG2890 HemK Methylase of poly 24.1 66 0.0014 37.0 3.2 65 729-799 113-187 (280)
160 PRK06202 hypothetical protein; 23.6 75 0.0016 34.6 3.4 38 725-762 59-96 (232)
161 KOG4217 Nuclear receptors of t 23.5 22 0.00048 43.9 -0.6 26 227-253 269-299 (605)
162 PF05413 Peptidase_C34: Putati 23.4 36 0.00079 33.5 0.9 14 661-674 42-55 (92)
163 PLN02271 serine hydroxymethylt 23.1 49 0.0011 42.1 2.0 17 782-799 233-249 (586)
164 PF13901 DUF4206: Domain of un 22.9 46 0.00099 36.7 1.6 40 350-389 144-189 (202)
165 COG0461 PyrE Orotate phosphori 22.6 24 0.00051 39.4 -0.6 35 640-674 117-151 (201)
166 PF12861 zf-Apc11: Anaphase-pr 22.5 47 0.001 32.9 1.4 33 289-329 34-66 (85)
167 PRK10458 DNA cytosine methylas 22.4 3.4E+02 0.0074 33.9 8.9 121 729-858 90-277 (467)
168 KOG0990 Replication factor C, 22.2 60 0.0013 39.0 2.5 40 1275-1325 33-75 (360)
169 PF10367 Vps39_2: Vacuolar sor 21.9 53 0.0012 31.2 1.7 28 227-255 78-107 (109)
170 KOG2187 tRNA uracil-5-methyltr 21.9 1.9E+02 0.0042 36.7 6.6 126 688-824 341-489 (534)
171 TIGR01091 upp uracil phosphori 21.8 44 0.00096 36.7 1.2 52 641-692 128-180 (207)
172 KOG3092 Casein kinase II, beta 21.6 84 0.0018 35.5 3.2 31 377-422 108-140 (216)
173 COG0203 RplQ Ribosomal protein 20.9 87 0.0019 32.7 2.9 38 633-683 40-82 (116)
174 PRK14904 16S rRNA methyltransf 20.8 97 0.0021 37.6 3.9 26 724-749 248-273 (445)
175 PRK14901 16S rRNA methyltransf 20.5 71 0.0015 38.6 2.7 25 724-748 250-274 (434)
176 PF10237 N6-adenineMlase: Prob 20.4 1E+02 0.0022 33.4 3.5 47 781-829 80-128 (162)
177 COG2264 PrmA Ribosomal protein 20.3 1.3E+02 0.0027 35.7 4.5 61 682-746 97-182 (300)
178 PF02645 DegV: Uncharacterised 20.2 2.7E+02 0.0058 31.8 6.9 95 648-751 124-249 (280)
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=99.79 E-value=2.6e-20 Score=186.25 Aligned_cols=131 Identities=31% Similarity=0.541 Sum_probs=101.4
Q ss_pred ccccccccccceEEeeccccccCCceeeeecceeecccccCCCCcceeEE----------EeecCCCCcEEEEEEEEEEe
Q 000595 7 EVEVGQKLVSDYYFEHEGERKQKEIISFSALPIQWNENERTGGCKELIYL----------RGAADSGLQKIFKPVIAWKF 76 (1401)
Q Consensus 7 e~E~~~~~V~~Y~f~d~~~~~~~~pVsFs~LPi~w~~~e~~~~~k~~vfL----------rG~~dnGlq~i~k~V~AWr~ 76 (1401)
|+|.++..|++|+|.|+ +++||+|+.||++|+++....|..+.+++ +|..++|++.++++|++|.+
T Consensus 1 ~~~~p~r~L~~f~~~d~----~~~~~~le~l~~~~~~~~~~sG~v~~~~~~~~~~~~~~~~g~~~~g~~~~l~~I~~W~i 76 (146)
T PF12047_consen 1 EDDLPMRSLDDFSFYDS----DGEPVSLELLPIEWNVDLFASGVVKPIGLWGDDEPSPKEKGVRDEGVRIRLGPIKEWWI 76 (146)
T ss_dssp -SSS-EEEEEEEEEEET----TSBB--STTSTTTTT--EEEEEEEEETT-------SSTS-SEEEEC----ES-ECEEEE
T ss_pred CCCCcceEEEEEEEEeC----CCCEEeeeeccccCCCcccceEEecccCcccccCccccccCccCCCcccceeceeEEEE
Confidence 56788899999999999 99999999999999998877887889998 89999999999999999999
Q ss_pred ecCCCcceEEEEecCCceEEeCCccch----HHHHHHHHHHhhhhhhhhccCchhhhhhHHHHhhhhcc
Q 000595 77 DLTNVIPEIFVLSKENSWIKLQKPRKC----YEEIYRTILIMVHCLSYAKRNPEATAKSIWDFLSRFFC 141 (1401)
Q Consensus 77 ~L~~~~PeIsVLs~e~~WI~L~KPrks----Yee~iRtvLITv~~LhfvKKnPe~s~kslwdhL~kvFs 141 (1401)
++....|.+.+++.+.+|++|+||+++ |+.++|++.||++++|||+++|+.+..++|++|.++++
T Consensus 77 ~~~~~~~~~i~i~T~~awY~L~kPs~~Y~~~y~~~~~~~~l~~~v~~~l~~~~~~~~~s~~d~l~~v~~ 145 (146)
T PF12047_consen 77 DGGDDGPPIIWISTDYAWYRLMKPSKSYAPWYEPFLRKARLTVRVIHFLKKNPRASDLSYEDLLARVFR 145 (146)
T ss_dssp E-SSSSS-EEEEEESS-EEEE-SB-TTTHHHHCCHHHHHHHHHHHHHHHHHHT---T--HHHHHHHHHH
T ss_pred EecCCCccEEEEEECCcEEEECCccHHHHHHHHHHHHHHHHHHHHHHHHhhCcccccCCHHHHHHHHhc
Confidence 999999999999999999999999999 55688999999999999999999999999999999875
No 2
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=98.74 E-value=2.8e-09 Score=127.29 Aligned_cols=102 Identities=25% Similarity=0.673 Sum_probs=81.0
Q ss_pred ccccccCCCCCCCCCCCCeeeecCCCCCCCCCcccccccccccchHHHHHHHhHhhccCCceeCCCCc-ccccCCCCCCC
Q 000595 288 HQCFACGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAGESFTCPLHK-CCICKQGENKA 366 (1401)
Q Consensus 288 HqCFVCGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLekkIaaGksFrCPlH~-C~vCkqseDkn 366 (1401)
+.|++|+..|.. ..+.++-|. .|+.+||+.|+..+... .+. ...|+||.|+ |+.|+..+|-.
T Consensus 19 ~mc~l~~s~G~~---~ag~m~ac~--~c~~~yH~~cvt~~~~~-----------~~l-~~gWrC~~crvCe~c~~~gD~~ 81 (694)
T KOG4443|consen 19 LMCPLCGSSGKG---RAGRLLACS--DCGQKYHPYCVTSWAQH-----------AVL-SGGWRCPSCRVCEACGTTGDPK 81 (694)
T ss_pred hhhhhhcccccc---ccCcchhhh--hhcccCCcchhhHHHhH-----------HHh-cCCcccCCceeeeeccccCCcc
Confidence 379999988863 234588898 99999999999976521 111 3469999997 99999887743
Q ss_pred CCCCceeecccCCccccccCCCCCccccccccccccccccccccCCCceeEeccCC
Q 000595 367 DSDLQFAVCRRCPKAYHRKCLPRKIAFEDKLEEGIITRAWEGLLPNHRILIYCLKH 422 (1401)
Q Consensus 367 ~segKLI~CdRCPkAYH~kCLPPpIsfe~~~~EgIp~RAW~cLLpncRiLIyCpkH 422 (1401)
+++.|.+|+.+||.+|+.|+.. .++...|.| +.+.-|-.|
T Consensus 82 ----kf~~Ck~cDvsyh~yc~~P~~~-------~v~sg~~~c-----kk~~~c~qc 121 (694)
T KOG4443|consen 82 ----KFLLCKRCDVSYHCYCQKPPND-------KVPSGPWLC-----KKCTRCRQC 121 (694)
T ss_pred ----cccccccccccccccccCCccc-------cccCccccc-----HHHHhhhhc
Confidence 7999999999999999999875 688899997 445666666
No 3
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=98.70 E-value=7.5e-09 Score=113.89 Aligned_cols=81 Identities=27% Similarity=0.639 Sum_probs=67.8
Q ss_pred CeeeecCCCCCCCCCcccccccccccchHHHHHHHhHhhccCCceeCCCCc-ccccCCCCCCCCCCCceeecccCCcccc
Q 000595 305 AEVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAGESFTCPLHK-CCICKQGENKADSDLQFAVCRRCPKAYH 383 (1401)
Q Consensus 305 aEVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLekkIaaGksFrCPlH~-C~vCkqseDkn~segKLI~CdRCPkAYH 383 (1401)
.+++-|+ .||+.=||.||+-.. +|...| ....|+|-.|. |..|+.++++ .||+.|+-|++.||
T Consensus 244 eelvscs--dcgrsghpsclqft~---------nm~~av-k~yrwqcieck~csicgtsend----dqllfcddcdrgyh 307 (336)
T KOG1244|consen 244 EELVSCS--DCGRSGHPSCLQFTA---------NMIAAV-KTYRWQCIECKYCSICGTSEND----DQLLFCDDCDRGYH 307 (336)
T ss_pred hhhcchh--hcCCCCCcchhhhhH---------HHHHHH-HhheeeeeecceeccccCcCCC----ceeEeecccCCcee
Confidence 4889998 999999999998653 222222 34789999887 9999999875 48999999999999
Q ss_pred ccCCCCCcccccccccccccccccc
Q 000595 384 RKCLPRKIAFEDKLEEGIITRAWEG 408 (1401)
Q Consensus 384 ~kCLPPpIsfe~~~~EgIp~RAW~c 408 (1401)
.+||-|+++ ..|.+.|.|
T Consensus 308 myclsppm~-------eppegswsc 325 (336)
T KOG1244|consen 308 MYCLSPPMV-------EPPEGSWSC 325 (336)
T ss_pred eEecCCCcC-------CCCCCchhH
Confidence 999999986 678899998
No 4
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.21 E-value=1.1e-06 Score=105.62 Aligned_cols=49 Identities=24% Similarity=0.628 Sum_probs=40.9
Q ss_pred cccccCCCCCCCCCCCceeecccCCccccccCCCCCccccccccccccccccccccCCCc
Q 000595 355 KCCICKQGENKADSDLQFAVCRRCPKAYHRKCLPRKIAFEDKLEEGIITRAWEGLLPNHR 414 (1401)
Q Consensus 355 ~C~vCkqseDkn~segKLI~CdRCPkAYH~kCLPPpIsfe~~~~EgIp~RAW~cLLpncR 414 (1401)
+|..|++.+.- ..+++|+.||++||.+||.||+.- +.+|.++|.| +.|.
T Consensus 255 fCsaCn~~~~F----~~~i~CD~Cp~sFH~~CLePPl~~-----eniP~g~W~C--~ec~ 303 (613)
T KOG4299|consen 255 FCSACNGSGLF----NDIICCDGCPRSFHQTCLEPPLEP-----ENIPPGSWFC--PECK 303 (613)
T ss_pred HHHHhCCcccc----ccceeecCCchHHHHhhcCCCCCc-----ccCCCCcccc--CCCe
Confidence 79999998853 357999999999999999999753 4789999997 6543
No 5
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=97.95 E-value=3.2e-06 Score=101.97 Aligned_cols=103 Identities=23% Similarity=0.594 Sum_probs=76.6
Q ss_pred cCCccccccCCCC-----ceeeccccccccccCccccCcccccccCCCChhhhhccCcccccccccccccccccCCCCCC
Q 000595 225 LFDSVCSFCDNGG-----DLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYKQHQCFACGKLGSS 299 (1401)
Q Consensus 225 l~DdVCaIC~dGG-----eLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~gQHqCFVCGklGSS 299 (1401)
.....|.+|+..| .|+-|. .|...||.. |+++-++.+.+ ..-|.|+.|. .|..|+..|..
T Consensus 16 ~~~~mc~l~~s~G~~~ag~m~ac~-~c~~~yH~~--------cvt~~~~~~~l--~~gWrC~~cr----vCe~c~~~gD~ 80 (694)
T KOG4443|consen 16 IVCLMCPLCGSSGKGRAGRLLACS-DCGQKYHPY--------CVTSWAQHAVL--SGGWRCPSCR----VCEACGTTGDP 80 (694)
T ss_pred hhhhhhhhhccccccccCcchhhh-hhcccCCcc--------hhhHHHhHHHh--cCCcccCCce----eeeeccccCCc
Confidence 3457788888754 699999 799999998 54454444432 4569999998 59999987754
Q ss_pred CCCCCCeeeecCCCCCCCCCcccccccccccchHHHHHHHhHhhccCCceeCCCCc-ccccCCC
Q 000595 300 DKETGAEVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAGESFTCPLHK-CCICKQG 362 (1401)
Q Consensus 300 Dk~SGaEVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLekkIaaGksFrCPlH~-C~vCkqs 362 (1401)
.+++.|. .|.-.||..|+.+... +|.. ..|.|+.|+ |+.|...
T Consensus 81 -----~kf~~Ck--~cDvsyh~yc~~P~~~------------~v~s-g~~~ckk~~~c~qc~~~ 124 (694)
T KOG4443|consen 81 -----KKFLLCK--RCDVSYHCYCQKPPND------------KVPS-GPWLCKKCTRCRQCDST 124 (694)
T ss_pred -----ccccccc--cccccccccccCCccc------------cccC-cccccHHHHhhhhcccc
Confidence 4788998 9999999999987652 2333 468888775 6666653
No 6
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.77 E-value=9.7e-06 Score=90.45 Aligned_cols=78 Identities=21% Similarity=0.439 Sum_probs=62.3
Q ss_pred eeeecCCCCCCCCCcccccccccccchHHHHHHHhHhhccCCceeCCCCc-ccccCCCCCCCCCCCceeecccCCccccc
Q 000595 306 EVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAGESFTCPLHK-CCICKQGENKADSDLQFAVCRRCPKAYHR 384 (1401)
Q Consensus 306 EVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLekkIaaGksFrCPlH~-C~vCkqseDkn~segKLI~CdRCPkAYH~ 384 (1401)
.++.|. .|...|||.||..... |.. +.+...|.|-.|. |..|.++.- +..++.|++|++.||+
T Consensus 278 S~I~C~--~C~~~~HP~Ci~M~~e---------lv~-~~KTY~W~C~~C~lC~IC~~P~~----E~E~~FCD~CDRG~HT 341 (381)
T KOG1512|consen 278 SWIVCK--PCATRPHPYCVAMIPE---------LVG-QYKTYFWKCSSCELCRICLGPVI----ESEHLFCDVCDRGPHT 341 (381)
T ss_pred cceeec--ccccCCCCcchhcCHH---------HHh-HHhhcchhhcccHhhhccCCccc----chheeccccccCCCCc
Confidence 578887 9999999999997642 211 2335789999987 999999864 3369999999999999
Q ss_pred cCCCCCcccccccccccccccccc
Q 000595 385 KCLPRKIAFEDKLEEGIITRAWEG 408 (1401)
Q Consensus 385 kCLPPpIsfe~~~~EgIp~RAW~c 408 (1401)
.|+--. .+|.+.|-|
T Consensus 342 ~CVGL~---------~lP~G~WIC 356 (381)
T KOG1512|consen 342 LCVGLQ---------DLPRGEWIC 356 (381)
T ss_pred cccccc---------cccCccchh
Confidence 997553 578899997
No 7
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.65 E-value=2.4e-05 Score=94.72 Aligned_cols=169 Identities=25% Similarity=0.524 Sum_probs=101.3
Q ss_pred cccccCCC-C----ceeecccc-ccccccCccccCcccccccCCCChhhhhccCccccccccccc----ccccccCC-CC
Q 000595 229 VCSFCDNG-G----DLLCCEGR-CLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYKQ----HQCFACGK-LG 297 (1401)
Q Consensus 229 VCaIC~dG-G----eLLCCDG~-C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~gQ----HqCFVCGk-lG 297 (1401)
-|.+|.+- | -||-|||. |.-+.|.. | +|+- +| +.+.|||..|+..+ ..|.+|-. .|
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCsVAVHQa--------C--YGIv--qV-PtGpWfCrKCesqeraarvrCeLCP~kdG 73 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCSVAVHQA--------C--YGIV--QV-PTGPWFCRKCESQERAARVRCELCPHKDG 73 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCceeeeehh--------c--ceeE--ec-CCCchhhhhhhhhhhhccceeecccCccc
Confidence 39999872 2 49999974 99999998 6 7874 34 68999999998763 57888843 33
Q ss_pred CCCCCCCCeeeecCCCCCCCCCcccccccccccchHHHHHHHhHhhccCCceeCCC----CcccccCCCCCC-CCCCCce
Q 000595 298 SSDKETGAEVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAGESFTCPL----HKCCICKQGENK-ADSDLQF 372 (1401)
Q Consensus 298 SSDk~SGaEVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLekkIaaGksFrCPl----H~C~vCkqseDk-n~segKL 372 (1401)
. |-+- .-+-|-|.-|.-+.++... ..+.-||.-|.. .-|. -.|.+|.+.+.. +...+..
T Consensus 74 A--------LKkT---Dn~GWAHVVCALYIPEVrF-gNV~TMEPIiLq----~VP~dRfnKtCYIC~E~GrpnkA~~GAC 137 (900)
T KOG0956|consen 74 A--------LKKT---DNGGWAHVVCALYIPEVRF-GNVHTMEPIILQ----DVPHDRFNKTCYICNEEGRPNKAAKGAC 137 (900)
T ss_pred c--------eecc---cCCCceEEEEEeeccceee-cccccccceeec----cCchhhhcceeeeecccCCccccccccc
Confidence 2 2222 3455678778766553210 000111110100 0121 249999987533 3456778
Q ss_pred eecc--cCCccccccCCCCCccccccccccccccccccccCCCceeEeccCCccccccCCCCCCcc
Q 000595 373 AVCR--RCPKAYHRKCLPRKIAFEDKLEEGIITRAWEGLLPNHRILIYCLKHEIDDEIGTPIRDHI 436 (1401)
Q Consensus 373 I~Cd--RCPkAYH~kCLPPpIsfe~~~~EgIp~RAW~cLLpncRiLIyCpkHeID~lLgTP~RdHI 436 (1401)
+.|- -|-.+||..|.-.. -..| ++++.. +.|-+.|-||-.| +.+++..|+-.-|
T Consensus 138 MtCNKs~CkqaFHVTCAQ~~-GLLC-EE~gn~-------~dNVKYCGYCk~H-fsKlkk~~~~k~i 193 (900)
T KOG0956|consen 138 MTCNKSGCKQAFHVTCAQRA-GLLC-EEEGNI-------SDNVKYCGYCKYH-FSKLKKSPAIKVI 193 (900)
T ss_pred eecccccchhhhhhhHhhhh-ccce-eccccc-------cccceechhHHHH-HHHhhcCCCcccC
Confidence 8884 58999999997542 1122 112222 2344667899888 6666666555544
No 8
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.46 E-value=3.3e-05 Score=93.33 Aligned_cols=54 Identities=35% Similarity=0.808 Sum_probs=41.3
Q ss_pred cccCCccccccCCCCce---eeccccccccccCccccCcccccccCCCChhhhhccCcccccccccc
Q 000595 223 DELFDSVCSFCDNGGDL---LCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYK 286 (1401)
Q Consensus 223 dDl~DdVCaIC~dGGeL---LCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~g 286 (1401)
.....++|+.|.+.|.. +|||| |+++||+.|++ +.+....+ +.+.|+|++|..+
T Consensus 249 ~~~~~~fCsaCn~~~~F~~~i~CD~-Cp~sFH~~CLe--------PPl~~eni-P~g~W~C~ec~~k 305 (613)
T KOG4299|consen 249 VEDIEDFCSACNGSGLFNDIICCDG-CPRSFHQTCLE--------PPLEPENI-PPGSWFCPECKIK 305 (613)
T ss_pred cCCHHHHHHHhCCccccccceeecC-CchHHHHhhcC--------CCCCcccC-CCCccccCCCeee
Confidence 33446799999998866 99996 99999999765 34433333 5689999999754
No 9
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.43 E-value=6.5e-05 Score=84.13 Aligned_cols=82 Identities=18% Similarity=0.254 Sum_probs=63.9
Q ss_pred cCCccccccCCC---------CceeeccccccccccCccccCcccccccCCCChhhhh--ccCccccccccccccccccc
Q 000595 225 LFDSVCSFCDNG---------GDLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVE--AMLNFFCKNCEYKQHQCFAC 293 (1401)
Q Consensus 225 l~DdVCaIC~dG---------GeLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq--~~~sW~C~nCe~gQHqCFVC 293 (1401)
.....|.+|-++ ..++||. .|.-++|+.|+ .++...+. ..-.|.|.+|. .|.+|
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-PCATRPHPYCV----------AMIPELVGQYKTYFWKCSSCE----LCRIC 320 (381)
T ss_pred cchhhhhhhhcchhhhhhhhhccceeec-ccccCCCCcch----------hcCHHHHhHHhhcchhhcccH----hhhcc
Confidence 456779999875 2699999 79999999964 34433221 24579999998 69999
Q ss_pred CCCCCCCCCCCCeeeecCCCCCCCCCccccccccc
Q 000595 294 GKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKLL 328 (1401)
Q Consensus 294 GklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~ 328 (1401)
+++.. ..+++.|+ .|.+-||..||....
T Consensus 321 ~~P~~-----E~E~~FCD--~CDRG~HT~CVGL~~ 348 (381)
T KOG1512|consen 321 LGPVI-----ESEHLFCD--VCDRGPHTLCVGLQD 348 (381)
T ss_pred CCccc-----chheeccc--cccCCCCcccccccc
Confidence 99865 35789999 999999999998653
No 10
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=97.41 E-value=4.6e-05 Score=89.72 Aligned_cols=89 Identities=29% Similarity=0.720 Sum_probs=65.3
Q ss_pred cCCccccccCCC-----CceeeccccccccccCccccCcccccccCCCChhhhhccCccccccccccccc---ccccCCC
Q 000595 225 LFDSVCSFCDNG-----GDLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYKQHQ---CFACGKL 296 (1401)
Q Consensus 225 l~DdVCaIC~dG-----GeLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~gQHq---CFVCGkl 296 (1401)
.+|++|.+|... ..++.|+| |.-+.|.. | +|+.- -+.+.|+|..|.++.++ |.-|-..
T Consensus 191 ~~d~~C~~c~~t~~eN~naiVfCdg-C~i~VHq~--------C--YGI~f---~peG~WlCrkCi~~~~~i~~C~fCps~ 256 (669)
T COG5141 191 EFDDICTKCTSTHNENSNAIVFCDG-CEICVHQS--------C--YGIQF---LPEGFWLCRKCIYGEYQIRCCSFCPSS 256 (669)
T ss_pred hhhhhhHhccccccCCcceEEEecC-cchhhhhh--------c--cccee---cCcchhhhhhhcccccceeEEEeccCC
Confidence 467899999863 46999996 99999998 5 77643 26789999999888653 6666332
Q ss_pred -CCC----C--------------------------------------------CCCCCeeeecCCCCCCCCCcccccccc
Q 000595 297 -GSS----D--------------------------------------------KETGAEVFPCVSATCGHFYHPHCVSKL 327 (1401)
Q Consensus 297 -GSS----D--------------------------------------------k~SGaEVfrCsvasCGRFYHpkCLa~l 327 (1401)
|.. | +..++--++|...+|.+.||..|....
T Consensus 257 dGaFkqT~dgrW~H~iCA~~~pelsF~~l~~~dpI~~i~sVs~srwkl~C~iCk~~~GtcIqCs~~nC~~aYHVtCArra 336 (669)
T COG5141 257 DGAFKQTSDGRWGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFNCTRAYHVTCARRA 336 (669)
T ss_pred CCceeeccCCchHhHhHHHhcchhccccccccchhhhhcccchhhHhheeeEEcccCcceeeecccchhhhhhhhhhhhc
Confidence 110 0 012345689999999999999998754
No 11
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=97.37 E-value=0.00011 Score=89.88 Aligned_cols=134 Identities=21% Similarity=0.498 Sum_probs=88.9
Q ss_pred CCccccccCCC-----CceeeccccccccccCccccCcccccccCCCChhhhhccCccccccccccc-ccccccCCCCCC
Q 000595 226 FDSVCSFCDNG-----GDLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYKQ-HQCFACGKLGSS 299 (1401)
Q Consensus 226 ~DdVCaIC~dG-----GeLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~gQ-HqCFVCGklGSS 299 (1401)
.+.+|.+|..+ .+|++|+ .|.-..|.. | +|+.+. +.+.|.|.-|..+. ..|.+|-+.|..
T Consensus 270 edviCDvCrspD~e~~neMVfCd-~Cn~cVHqa--------C--yGIle~---p~gpWlCr~Calg~~ppCvLCPkkGGa 335 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCD-KCNICVHQA--------C--YGILEV---PEGPWLCRTCALGIEPPCVLCPKKGGA 335 (893)
T ss_pred ccceeceecCCCccccceeEEec-cchhHHHHh--------h--hceeec---CCCCeeehhccccCCCCeeeccccCCc
Confidence 57889999875 4899999 799999999 5 787653 56899999998874 589999887754
Q ss_pred CCCCCCeeeecCCCCCCCCCcccccccccccchHHHHHHHhHhhccC-----CceeCCCCcccccCCCCCCCCCCCceee
Q 000595 300 DKETGAEVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAG-----ESFTCPLHKCCICKQGENKADSDLQFAV 374 (1401)
Q Consensus 300 Dk~SGaEVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLekkIaaG-----ksFrCPlH~C~vCkqseDkn~segKLI~ 374 (1401)
.+.+ +.=.+|-|..|.-..++-.++. .++.+-|.+- ..|. -.|..|+... +..|+
T Consensus 336 mK~~---------~sgT~wAHvsCALwIPEVsie~--~ekmePItkfs~IpesRws---lvC~LCk~k~------GACIq 395 (893)
T KOG0954|consen 336 MKPT---------KSGTKWAHVSCALWIPEVSIEC--PEKMEPITKFSHIPESRWS---LVCNLCKVKS------GACIQ 395 (893)
T ss_pred cccc---------CCCCeeeEeeeeeccceeeccC--HhhcCcccccCCCcHHHHH---HHHHHhcccC------cceEE
Confidence 3211 1334888999987655432211 1111112111 1121 1389997653 35777
Q ss_pred c--ccCCccccccCCC-CCccc
Q 000595 375 C--RRCPKAYHRKCLP-RKIAF 393 (1401)
Q Consensus 375 C--dRCPkAYH~kCLP-PpIsf 393 (1401)
| ..|-.+||..|.. +++.+
T Consensus 396 Cs~k~C~t~fHv~CA~~aG~~~ 417 (893)
T KOG0954|consen 396 CSNKTCRTAFHVTCAFEAGLEM 417 (893)
T ss_pred ecccchhhhccchhhhhcCCee
Confidence 7 4799999999975 44443
No 12
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.30 E-value=0.00012 Score=81.68 Aligned_cols=82 Identities=28% Similarity=0.661 Sum_probs=62.6
Q ss_pred cCCccccccCCC-------C---ceeeccccccccccCccccCcccccccCCCChhhh--hccCcccccccccccccccc
Q 000595 225 LFDSVCSFCDNG-------G---DLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEV--EAMLNFFCKNCEYKQHQCFA 292 (1401)
Q Consensus 225 l~DdVCaIC~dG-------G---eLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEv--q~~~sW~C~nCe~gQHqCFV 292 (1401)
+...+|.+|-.+ | +|+.|. -|.|+=|+.|+ -+|..-+ -..-+|.|.+|.+ |.+
T Consensus 222 ~Pn~YCDFclgdsr~nkkt~~peelvscs-dcgrsghpscl----------qft~nm~~avk~yrwqcieck~----csi 286 (336)
T KOG1244|consen 222 QPNPYCDFCLGDSRENKKTGMPEELVSCS-DCGRSGHPSCL----------QFTANMIAAVKTYRWQCIECKY----CSI 286 (336)
T ss_pred cCCcccceeccccccccccCCchhhcchh-hcCCCCCcchh----------hhhHHHHHHHHhheeeeeecce----ecc
Confidence 446789999643 2 799999 69999999964 3333111 1245899999984 999
Q ss_pred cCCCCCCCCCCCCeeeecCCCCCCCCCccccccccc
Q 000595 293 CGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKLL 328 (1401)
Q Consensus 293 CGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~ 328 (1401)
||-... ..+++.|. .|.+-||-.||.+..
T Consensus 287 cgtsen-----ddqllfcd--dcdrgyhmyclsppm 315 (336)
T KOG1244|consen 287 CGTSEN-----DDQLLFCD--DCDRGYHMYCLSPPM 315 (336)
T ss_pred ccCcCC-----CceeEeec--ccCCceeeEecCCCc
Confidence 987653 35899999 999999999999765
No 13
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=97.29 E-value=0.00018 Score=92.06 Aligned_cols=136 Identities=24% Similarity=0.512 Sum_probs=86.4
Q ss_pred cCCccccccCCC-----CceeeccccccccccCccccCcccccccCCCChhhhhccCcccccccccccc---cccccCCC
Q 000595 225 LFDSVCSFCDNG-----GDLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYKQH---QCFACGKL 296 (1401)
Q Consensus 225 l~DdVCaIC~dG-----GeLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~gQH---qCFVCGkl 296 (1401)
..|.+|.+|.++ ..+|.||+ |.-++|.. | +|.+. .+.+.|.|..|...++ .|..|-..
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD~-Cnl~VHq~--------C--ygi~~---ipeg~WlCr~Cl~s~~~~v~c~~cp~~ 282 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCDG-CNLAVHQE--------C--YGIPF---IPEGQWLCRRCLQSPQRPVRCLLCPSK 282 (1051)
T ss_pred CCCccceeecccccCCCceEEEcCC-Ccchhhhh--------c--cCCCC---CCCCcEeehhhccCcCcccceEeccCC
Confidence 457999999986 36999995 99999999 5 56432 2678999999987654 68888665
Q ss_pred CCCCCCCCCeeeecCCCCCCCCCcccccccccccchHHHHHHHh-----HhhccCCceeCCCCcccccCCCCCCCCCCCc
Q 000595 297 GSSDKETGAEVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLA-----KSIIAGESFTCPLHKCCICKQGENKADSDLQ 371 (1401)
Q Consensus 297 GSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLe-----kkIaaGksFrCPlH~C~vCkqseDkn~segK 371 (1401)
|.. |+=. .=|++-|..|....++...... ..++ ..+.. ..|. -.|..|+..+- +.
T Consensus 283 ~gA--------Fkqt--~dgrw~Hv~caiwipev~F~nt-~~~E~I~~i~~i~~-aRwk---L~cy~cK~~~~-----ga 342 (1051)
T KOG0955|consen 283 GGA--------FKQT--DDGRWAHVVCAIWIPEVSFANT-VFLEPIDSIENIPP-ARWK---LTCYICKQKGL-----GA 342 (1051)
T ss_pred CCc--------ceec--cCCceeeeehhhcccccccccc-hhhccccchhcCcH-hhhh---ceeeeeccCCC-----Cc
Confidence 431 1111 3567778777765443210000 0000 00110 0122 24999998762 35
Q ss_pred eeec--ccCCccccccCCC-CCcccc
Q 000595 372 FAVC--RRCPKAYHRKCLP-RKIAFE 394 (1401)
Q Consensus 372 LI~C--dRCPkAYH~kCLP-PpIsfe 394 (1401)
.++| .+|-.|||..|-- +++.|.
T Consensus 343 ciqcs~~~c~~a~hvtca~~agl~m~ 368 (1051)
T KOG0955|consen 343 CIQCSKANCYTAFHVTCARRAGLYMK 368 (1051)
T ss_pred ceecchhhhhhhhhhhhHhhcCceEe
Confidence 8999 4899999999964 555443
No 14
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=97.22 E-value=0.00026 Score=78.33 Aligned_cols=152 Identities=22% Similarity=0.302 Sum_probs=92.4
Q ss_pred cccCcccc-hhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhh-hCCccccccccccCC---CCCccccccc
Q 000595 701 TSFGRHFT-KVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDE-TGKNCLYKNYDILPA---KNDFNFEKRD 775 (1401)
Q Consensus 701 ts~grhft-k~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~-~gk~c~~kn~dl~~~---kn~f~Fe~~d 775 (1401)
.+||.||. ...-+..|++.+. +.+|++|+|+.||.-.++..+-++... ++.+..-.-.+.... ...+++...|
T Consensus 18 k~~gq~fl~~~~i~~~i~~~l~--~~~~~~VLEiG~G~G~lt~~L~~~~~~v~avE~d~~~~~~~~~~~~~~~v~~i~~D 95 (272)
T PRK00274 18 KSLGQNFLIDENILDKIVDAAG--PQPGDNVLEIGPGLGALTEPLLERAAKVTAVEIDRDLAPILAETFAEDNLTIIEGD 95 (272)
T ss_pred cccCcCcCCCHHHHHHHHHhcC--CCCcCeEEEeCCCccHHHHHHHHhCCcEEEEECCHHHHHHHHHhhccCceEEEECh
Confidence 37999995 4556677888774 478999999999999999888664210 011111111111110 1457788888
Q ss_pred cccccCCCCCCCCeeeeeeCCCccchhhhHHHHHHhhhcc--CCcEEEEecCCcc-ccccccCC--Cc---ee------e
Q 000595 776 WMTVEPKELAPGSRLIMGLNPPFGVKAGLANKFINKALEF--NPKLLILIVPPET-ERLDRKES--AY---EL------V 841 (1401)
Q Consensus 776 w~~v~~~elp~G~~LimgLnPPfg~~a~lAnkFi~kal~f--~Pkliili~P~~t-~rld~k~~--~Y---~l------i 841 (1401)
+.++...++. ..+|+| ||||.+- ..+|.+.|.. ...-++|++..|. +||=.++. -| .+ -
T Consensus 96 ~~~~~~~~~~--~~~vv~-NlPY~is----s~ii~~~l~~~~~~~~~~l~~QkE~A~Rl~a~pg~~~y~~lSv~~~~~~~ 168 (272)
T PRK00274 96 ALKVDLSELQ--PLKVVA-NLPYNIT----TPLLFHLLEERDPIRDMVVMVQKEVAERIVAKPGSKAYGRLSVLVQYYCD 168 (272)
T ss_pred hhcCCHHHcC--cceEEE-eCCccch----HHHHHHHHhcCCCCCeeEEEeHHHHHHHHcCCCCCccccHHHHHHHHHcc
Confidence 8887665543 457888 9999954 4555555543 3456889999887 67743321 12 11 1
Q ss_pred eccccccCCcceecCCCccc
Q 000595 842 WEDDQFLSGKSFYLPGSVDE 861 (1401)
Q Consensus 842 wed~~~l~gksFylPGsvd~ 861 (1401)
++--.-+..++||=|--||.
T Consensus 169 ~~~~~~v~~~~F~P~PkV~s 188 (272)
T PRK00274 169 VEKVFDVPPSAFVPPPKVDS 188 (272)
T ss_pred eEEEEEeChhhCCCCCCceE
Confidence 22223445677777666663
No 15
>PHA03412 putative methyltransferase; Provisional
Probab=97.09 E-value=0.0011 Score=73.79 Aligned_cols=172 Identities=17% Similarity=0.295 Sum_probs=92.1
Q ss_pred ccCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhhh------CCccccccccccCCCC--Cccccc
Q 000595 702 SFGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDET------GKNCLYKNYDILPAKN--DFNFEK 773 (1401)
Q Consensus 702 s~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~~------gk~c~~kn~dl~~~kn--~f~Fe~ 773 (1401)
..|.+||-..-.+.++ .|.. .+..|||+|||+-.|+.+|.++..+. +.+..-....+.. +| ...|..
T Consensus 29 ~~GqFfTP~~iAr~~~---i~~~-~~grVLDlG~GSG~Lalala~~~~~~~~~~V~aVEID~~Al~~Ar-~n~~~~~~~~ 103 (241)
T PHA03412 29 ELGAFFTPIGLARDFT---IDAC-TSGSVVDLCAGIGGLSFAMVHMMMYAKPREIVCVELNHTYYKLGK-RIVPEATWIN 103 (241)
T ss_pred cCCccCCCHHHHHHHH---Hhcc-CCCEEEEccChHHHHHHHHHHhcccCCCcEEEEEECCHHHHHHHH-hhccCCEEEE
Confidence 5688999887555554 2333 47899999999999999887653211 1111111111111 11 123333
Q ss_pred cccccccCCCCCCCCeeeeeeCCCccchh-----------hhHHHHHHhhhccCCcEEEEecCCccccccccCCCceeee
Q 000595 774 RDWMTVEPKELAPGSRLIMGLNPPFGVKA-----------GLANKFINKALEFNPKLLILIVPPETERLDRKESAYELVW 842 (1401)
Q Consensus 774 ~dw~~v~~~elp~G~~LimgLnPPfg~~a-----------~lAnkFi~kal~f~Pkliili~P~~t~rld~k~~~Y~liw 842 (1401)
.|.+... +..-=-|||+ ||||+.-+ .+.++||.+|+..-|.=. ||+|.-.--.+---.+| +
T Consensus 104 ~D~~~~~---~~~~FDlIIs-NPPY~~~~~~d~~ar~~g~~~~~~li~~A~~Ll~~G~-~ILP~~~~~~~y~~~~~---~ 175 (241)
T PHA03412 104 ADALTTE---FDTLFDMAIS-NPPFGKIKTSDFKGKYTGAEFEYKVIERASQIARQGT-FIIPQMSANFRYSGTHY---F 175 (241)
T ss_pred cchhccc---ccCCccEEEE-CCCCCCccccccCCcccccHHHHHHHHHHHHHcCCCE-EEeCcccccCcccCccc---e
Confidence 3433322 1111238888 99999322 457889999998765554 49998765333222222 2
Q ss_pred ccccccCCcce----------ecCCC-cccchhhhcccccCCCCeeeeecchhHHHH
Q 000595 843 EDDQFLSGKSF----------YLPGS-VDENDKQMDQWNMTAPPLYLWSRHDYAAHH 888 (1401)
Q Consensus 843 ed~~~l~gksF----------ylPGs-vd~ndk~~eqwn~~pP~l~lWsr~d~~~~h 888 (1401)
+...-..|+-+ ..||- || -.--+++|.-+-|..- -+.-|+++..
T Consensus 176 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~~~ 230 (241)
T PHA03412 176 RQDESTTSSKCKKFLDETGLEMNPGCGID-TGYYLEDWKGVKPLCE-VVCMEFNEPE 230 (241)
T ss_pred eeccCcccHHHHHHHHhcCeeecCCCCcc-ceeehhhccCCCccce-EEEEeecCcC
Confidence 22222233322 23553 33 2234578887766433 3555665544
No 16
>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=97.05 E-value=0.00023 Score=60.10 Aligned_cols=47 Identities=26% Similarity=0.711 Sum_probs=33.7
Q ss_pred cccccCC---CCceeeccccccccccCccccCcccccccCCCChhhhhccCccccccccc
Q 000595 229 VCSFCDN---GGDLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEY 285 (1401)
Q Consensus 229 VCaIC~d---GGeLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~ 285 (1401)
+|.+|++ .+.+|.|+ .|.++||..|+ .+..+.... ....|+|++|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~-~C~~~~H~~C~--------~~~~~~~~~-~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCD-SCNRWYHQECV--------GPPEKAEEI-PSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBS-TTSCEEETTTS--------TSSHSHHSH-HSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcC-CCChhhCcccC--------CCChhhccC-CCCcEECcCCcC
Confidence 5888987 56899999 69999999943 333332222 234999999964
No 17
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.01 E-value=0.00047 Score=85.47 Aligned_cols=92 Identities=27% Similarity=0.534 Sum_probs=65.7
Q ss_pred CCCCCCcccccccccccchHHHHHHHhHhhccCCceeCCCC--------------------cccccCCCCCCCCCCCcee
Q 000595 314 TCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAGESFTCPLH--------------------KCCICKQGENKADSDLQFA 373 (1401)
Q Consensus 314 sCGRFYHpkCLa~l~~pvde~~ateLekkIaaGksFrCPlH--------------------~C~vCkqseDkn~segKLI 373 (1401)
.|.|.||..|+.+.... .....|.||.| .|..|+..+. ++
T Consensus 1 ~~~r~~~~~~~~p~~~~-------------~~~~~~k~~~~e~~~~~~~~~~~~~~~~~~e~c~ic~~~g~-------~l 60 (696)
T KOG0383|consen 1 TCPRAYHRVCLDPKLKE-------------EPEMDPKCPGCESSSAQVEAKDDDWDDAEQEACRICADGGE-------LL 60 (696)
T ss_pred CCCcccCcCCCCccccc-------------CCcCCccCcchhhcccccccccCCcchhhhhhhhhhcCCCc-------EE
Confidence 48999999999965421 11346888743 3999987764 88
Q ss_pred ecccCCccccccCCCCCccccccccccccccccccccCCCceeEeccCC--ccccccCCCCCCcccCC
Q 000595 374 VCRRCPKAYHRKCLPRKIAFEDKLEEGIITRAWEGLLPNHRILIYCLKH--EIDDEIGTPIRDHIIFP 439 (1401)
Q Consensus 374 ~CdRCPkAYH~kCLPPpIsfe~~~~EgIp~RAW~cLLpncRiLIyCpkH--eID~lLgTP~RdHIkFP 439 (1401)
.|+.||.+||.+|+.+++. ..++..|.| + | | .|+.+ .+.+ ++++++.-..+|
T Consensus 61 ~c~tC~~s~h~~cl~~pl~-------~~p~~~~~c--~--R-c-~~p~~~~k~~~-il~~~~~~~~~~ 114 (696)
T KOG0383|consen 61 WCDTCPASFHASCLGPPLT-------PQPNGEFIC--P--R-C-FCPKNAGKIEK-ILGWRWKPTPKP 114 (696)
T ss_pred EeccccHHHHHHccCCCCC-------cCCccceee--e--e-e-ccCCCcccccc-cceeEecCCCCc
Confidence 8999999999999988875 455666887 3 2 3 67766 4444 466666666666
No 18
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=96.92 E-value=0.00046 Score=87.46 Aligned_cols=119 Identities=25% Similarity=0.432 Sum_probs=70.9
Q ss_pred ccccccCCccccccCCCCceeeccccccccccCccccCcccccccCCCChhhhhccCcccccccccccccccccCCCCCC
Q 000595 220 NEEDELFDSVCSFCDNGGDLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYKQHQCFACGKLGSS 299 (1401)
Q Consensus 220 ~e~dDl~DdVCaIC~dGGeLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~gQHqCFVCGklGSS 299 (1401)
.|.....+++|.+|.+.|+++||+ +|+|.||+.|+.... | + .+...|-|.-| .+|+..|..
T Consensus 337 se~~~~~ddhcrf~~d~~~~lc~E-t~prvvhlEcv~hP~--~------~---~~s~~~e~evc-------~~hkvngvv 397 (1414)
T KOG1473|consen 337 SEGEIEYDDHCRFCHDLGDLLCCE-TCPRVVHLECVFHPR--F------A---VPSAFWECEVC-------NIHKVNGVV 397 (1414)
T ss_pred cccceeecccccccCcccceeecc-cCCceEEeeecCCcc--c------c---CCCccchhhhh-------hhhccCccc
Confidence 334556789999999999999999 899999999764322 1 1 13467877644 456555422
Q ss_pred CCC----CCCeeeecCCCCCCCCCcccccccccccchHHHHHHHhHhhccCCceeCCCCcccccCCCCCCCCCCCceeec
Q 000595 300 DKE----TGAEVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAGESFTCPLHKCCICKQGENKADSDLQFAVC 375 (1401)
Q Consensus 300 Dk~----SGaEVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLekkIaaGksFrCPlH~C~vCkqseDkn~segKLI~C 375 (1401)
|-. .....++|. +.+.+ ..+...-=-.-.|.+|.+.+ .++-|
T Consensus 398 d~vl~~~K~~~~iR~~----------------~iG~d-----------r~gr~ywfi~rrl~Ie~~de-------t~l~y 443 (1414)
T KOG1473|consen 398 DCVLPPSKNVDSIRHT----------------PIGRD-----------RYGRKYWFISRRLRIEGMDE-------TLLWY 443 (1414)
T ss_pred ccccChhhcccceecc----------------CCCcC-----------ccccchhceeeeeEEecCCC-------cEEEE
Confidence 100 001112332 00000 01111111123488888654 57888
Q ss_pred cc-CCccccc-cCCCCCc
Q 000595 376 RR-CPKAYHR-KCLPRKI 391 (1401)
Q Consensus 376 dR-CPkAYH~-kCLPPpI 391 (1401)
.- ||.+||. .||+...
T Consensus 444 ysT~pqly~ll~cLd~~~ 461 (1414)
T KOG1473|consen 444 YSTCPQLYHLLRCLDRTY 461 (1414)
T ss_pred ecCcHHHHHHHHHhchHH
Confidence 77 9999999 9999643
No 19
>PF02384 N6_Mtase: N-6 DNA Methylase; InterPro: IPR003356 This domain is fpound in N-6 adenine-specific DNA methylase (2.1.1.72 from EC) from Type I and Type IC restriction systems. These enzymes are responsible for the methylation of specific DNA sequences in order to prevent the host from digesting its own genome via its restriction enzymes. These methylases have the same sequence specificity as their corresponding restriction enzymes. The type I restriction and modification system is composed of three polypeptides R, M and S. The M and S subunits together form a methyltransferase that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. In the presence of the R subunit, the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence. When the target site is unmodified, the DNA is cut. When the target site is hemimethylated, the complex acts as a maintenance methyltransferase, modifying the DNA so that both strands become methylated.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2F8L_A 2Y7C_C 2Y7H_C 2AR0_B 3KHK_A 3LKD_A 2OKC_B.
Probab=96.87 E-value=0.0014 Score=72.79 Aligned_cols=124 Identities=24% Similarity=0.379 Sum_probs=63.1
Q ss_pred ccCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhhh---CCccccccccc-------------cCC
Q 000595 702 SFGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDET---GKNCLYKNYDI-------------LPA 765 (1401)
Q Consensus 702 s~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~~---gk~c~~kn~dl-------------~~~ 765 (1401)
+.|.+||-.+-.+-+++.| =.+++++|+|+|||+-.|.--..+.+.+. .+...+==.|+ +..
T Consensus 24 ~~G~~~TP~~i~~l~~~~~--~~~~~~~VlDPacGsG~fL~~~~~~i~~~~~~~~~~~i~G~ei~~~~~~la~~nl~l~~ 101 (311)
T PF02384_consen 24 KLGQFYTPREIVDLMVKLL--NPKKGDSVLDPACGSGGFLVAAMEYIKEKRNKIKEINIYGIEIDPEAVALAKLNLLLHG 101 (311)
T ss_dssp SCGGC---HHHHHHHHHHH--TT-TTEEEEETT-TTSHHHHHHHHHHHTCHHHHCCEEEEEEES-HHHHHHHHHHHHHTT
T ss_pred ccceeehHHHHHHHHHhhh--hccccceeechhhhHHHHHHHHHHhhcccccccccceeEeecCcHHHHHHHHhhhhhhc
Confidence 5688898887777777777 55678899999999999965554433110 01111000111 000
Q ss_pred --CCCccccccccccccCCCCCCCCeeeeeeCCCccchh--------------------hhHHHHHHhhhccCCc--EEE
Q 000595 766 --KNDFNFEKRDWMTVEPKELAPGSRLIMGLNPPFGVKA--------------------GLANKFINKALEFNPK--LLI 821 (1401)
Q Consensus 766 --kn~f~Fe~~dw~~v~~~elp~G~~LimgLnPPfg~~a--------------------~lAnkFi~kal~f~Pk--lii 821 (1401)
.+.+++...|++.-....-..-=-+|+| |||||.+. ..-.-||.+++.+=-+ .++
T Consensus 102 ~~~~~~~i~~~d~l~~~~~~~~~~~D~ii~-NPPf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fi~~~l~~Lk~~G~~~ 180 (311)
T PF02384_consen 102 IDNSNINIIQGDSLENDKFIKNQKFDVIIG-NPPFGSKEWKDEELEKDERFKKYFPPKSNAEYAFIEHALSLLKPGGRAA 180 (311)
T ss_dssp HHCBGCEEEES-TTTSHSCTST--EEEEEE-E--CTCES-STGGGCTTCCCTTCSSSTTEHHHHHHHHHHHTEEEEEEEE
T ss_pred cccccccccccccccccccccccccccccC-CCCccccccccccccccccccccCCCccchhhhhHHHHHhhccccccee
Confidence 1112244445443322211122337888 99999881 1112499999876522 678
Q ss_pred EecCCcc
Q 000595 822 LIVPPET 828 (1401)
Q Consensus 822 li~P~~t 828 (1401)
+|+|...
T Consensus 181 ~Ilp~~~ 187 (311)
T PF02384_consen 181 IILPNGF 187 (311)
T ss_dssp EEEEHHH
T ss_pred EEecchh
Confidence 8888754
No 20
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=96.75 E-value=0.00078 Score=74.98 Aligned_cols=45 Identities=31% Similarity=0.949 Sum_probs=34.6
Q ss_pred CccccccCC--CCceeeccc-cccc-cccCccccCcccccccCCCChhhhhccCccccccccc
Q 000595 227 DSVCSFCDN--GGDLLCCEG-RCLR-SFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEY 285 (1401)
Q Consensus 227 DdVCaIC~d--GGeLLCCDG-~C~R-SFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~ 285 (1401)
..+| +|.+ .|+||-||+ .|.| |||+. | .|+.. +|.+.|||++|..
T Consensus 221 ~lYC-fCqqvSyGqMVaCDn~nCkrEWFH~~--------C--VGLk~---pPKG~WYC~eCk~ 269 (271)
T COG5034 221 ELYC-FCQQVSYGQMVACDNANCKREWFHLE--------C--VGLKE---PPKGKWYCPECKK 269 (271)
T ss_pred eeEE-EecccccccceecCCCCCchhheecc--------c--cccCC---CCCCcEeCHHhHh
Confidence 4666 4887 589999996 4875 99999 5 55543 3679999999963
No 21
>TIGR02987 met_A_Alw26 type II restriction m6 adenine DNA methyltransferase, Alw26I/Eco31I/Esp3I family. Members of this family are the m6-adenine DNA methyltransferase protein, or domain of a fusion protein that also carries m5 cytosine methyltransferase activity, of type II restriction systems of the Alw26I/Eco31I/Esp3I family. A methyltransferase of this family is alway accompanied by a type II restriction endonuclease from the Alw26I/Eco31I/Esp3I family (TIGR02986) and by an adenine-specific modification methyltransferase. Members of this family are unusual in that regions of similarity to homologs outside this family are circularly permuted.
Probab=96.67 E-value=0.004 Score=74.75 Aligned_cols=49 Identities=31% Similarity=0.513 Sum_probs=40.4
Q ss_pred ccCcccchhhhHHHHHHhhccccc-----CCCcEEeccCCcchHHHHHHHHHhh
Q 000595 702 SFGRHFTKVDKLQAIVDKLHWYVN-----DGDMIVDFCCGANDFSCLMKKKLDE 750 (1401)
Q Consensus 702 s~grhftk~ekl~~i~~~Lh~yv~-----~gd~ivdfccg~n~fs~lmk~kl~~ 750 (1401)
++|.+||-..-.+.+++.+.-+.. .+.+|+|+|||+-.|..-+-+++.+
T Consensus 2 ~~GqfyTP~~ia~~mv~~~~~~~~~~~~~~~~~ilDP~cGsG~fl~~~~~~~~~ 55 (524)
T TIGR02987 2 AYGTFFTPPDIAKAMVANLVNEIGKNDKSTKTKIIDPCCGDGRLIAALLKKNEE 55 (524)
T ss_pred CCcccCCcHHHHHHHHHHHhhhcchhhcccceEEEeCCCCccHHHHHHHHHHHh
Confidence 579999999999999998865543 3458999999999999888777754
No 22
>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 KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.65 E-value=0.0017 Score=80.26 Aligned_cols=46 Identities=28% Similarity=0.618 Sum_probs=37.8
Q ss_pred CcccccCCCCCCCCCCCceeecccCCcc-ccccCCCCCccccccccccccccccccccCC
Q 000595 354 HKCCICKQGENKADSDLQFAVCRRCPKA-YHRKCLPRKIAFEDKLEEGIITRAWEGLLPN 412 (1401)
Q Consensus 354 H~C~vCkqseDkn~segKLI~CdRCPkA-YH~kCLPPpIsfe~~~~EgIp~RAW~cLLpn 412 (1401)
+.|..|..... +.-|+.|+-|..+ ||.+||+|++. +++...|-| .+
T Consensus 216 ~~C~IC~~~Dp----EdVLLLCDsCN~~~YH~YCLDPdl~-------eiP~~eWYC--~N 262 (1134)
T KOG0825|consen 216 VKCDICTVHDP----EDVLLLCDSCNKVYYHVYCLDPDLS-------ESPVNEWYC--TN 262 (1134)
T ss_pred ccceeeccCCh----HHhheeecccccceeeccccCcccc-------cccccceec--Cc
Confidence 46999998864 4469999999999 99999999874 567778886 55
No 24
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=96.64 E-value=0.00074 Score=75.73 Aligned_cols=46 Identities=26% Similarity=0.703 Sum_probs=36.3
Q ss_pred CCccccccCCCCceeeccc-ccc-ccccCccccCcccccccCCCChhhhhccCccccccccc
Q 000595 226 FDSVCSFCDNGGDLLCCEG-RCL-RSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEY 285 (1401)
Q Consensus 226 ~DdVCaIC~dGGeLLCCDG-~C~-RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~ 285 (1401)
.-.+|. |..+|+|+-||+ .|+ .|||+. | .||+. +|.+.|||+.|..
T Consensus 220 ~yC~Cn-qvsyg~Mi~CDn~~C~~eWFH~~--------C--VGL~~---~PkgkWyC~~C~~ 267 (274)
T KOG1973|consen 220 TYCICN-QVSYGKMIGCDNPGCPIEWFHFT--------C--VGLKT---KPKGKWYCPRCKA 267 (274)
T ss_pred EEEEec-ccccccccccCCCCCCcceEEEe--------c--ccccc---CCCCcccchhhhh
Confidence 346677 778999999994 399 999999 6 56764 3568899999964
No 25
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=96.43 E-value=0.0069 Score=66.20 Aligned_cols=148 Identities=22% Similarity=0.343 Sum_probs=91.6
Q ss_pred ccCccc-chhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhhhCCccc-c-ccccc-------cCCCCCccc
Q 000595 702 SFGRHF-TKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDETGKNCL-Y-KNYDI-------LPAKNDFNF 771 (1401)
Q Consensus 702 s~grhf-tk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~~gk~c~-~-kn~dl-------~~~kn~f~F 771 (1401)
+||-|| +...-+.+|++.+. +.++++|+|+.||.-.++..|.++.. ... + .|-++ +.....+.+
T Consensus 6 ~~gq~fl~d~~i~~~i~~~~~--~~~~~~VLEiG~G~G~lt~~L~~~~~----~v~~iE~d~~~~~~l~~~~~~~~~v~v 79 (253)
T TIGR00755 6 SLGQNFLIDESVIQKIVEAAN--VLEGDVVLEIGPGLGALTEPLLKRAK----KVTAIEIDPRLAEILRKLLSLYERLEV 79 (253)
T ss_pred CCCCccCCCHHHHHHHHHhcC--CCCcCEEEEeCCCCCHHHHHHHHhCC----cEEEEECCHHHHHHHHHHhCcCCcEEE
Confidence 689999 66777888888875 36899999999999999999966431 111 0 00000 111234556
Q ss_pred cccccccccCCCCCCCCeeeeeeCCCccchhhhHHHHHHhhh-ccCCcEEEEecCCc-ccccccc-----CCCceeee--
Q 000595 772 EKRDWMTVEPKELAPGSRLIMGLNPPFGVKAGLANKFINKAL-EFNPKLLILIVPPE-TERLDRK-----ESAYELVW-- 842 (1401)
Q Consensus 772 e~~dw~~v~~~elp~G~~LimgLnPPfg~~a~lAnkFi~kal-~f~Pkliili~P~~-t~rld~k-----~~~Y~liw-- 842 (1401)
...|.+.+...++.. ..+|+| |+||.+ +..++.+.| ...+..++|++..| .+||=.+ .....+++
T Consensus 80 ~~~D~~~~~~~~~d~-~~~vvs-NlPy~i----~~~il~~ll~~~~~~~~~~~~q~e~a~Rl~a~pg~~~y~~lsv~~~~ 153 (253)
T TIGR00755 80 IEGDALKVDLPDFPK-QLKVVS-NLPYNI----SSPLIFKLLEKPKFRLAVLMVQKEVAERLTAKPGSKDYGRLSVLVQY 153 (253)
T ss_pred EECchhcCChhHcCC-cceEEE-cCChhh----HHHHHHHHhccCCCceEEEEehHHHHHHHccCCCCCcccHHHHHHHH
Confidence 666666655443321 247888 999994 555555555 67778899999888 3444322 11111111
Q ss_pred ----ccccccCCcceecCCCccc
Q 000595 843 ----EDDQFLSGKSFYLPGSVDE 861 (1401)
Q Consensus 843 ----ed~~~l~gksFylPGsvd~ 861 (1401)
+--.-+...+||-|--||.
T Consensus 154 ~~~~~~~~~v~~~~F~P~PkVds 176 (253)
T TIGR00755 154 FANVEIVFKVPPSAFYPPPKVDS 176 (253)
T ss_pred HcceEEEEEEchhhCcCCCCeeE
Confidence 1123345788998888874
No 26
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=96.38 E-value=0.0027 Score=69.83 Aligned_cols=149 Identities=19% Similarity=0.247 Sum_probs=85.2
Q ss_pred ccCccc-chhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhh-hCCcccccccccc----CCCCCccccccc
Q 000595 702 SFGRHF-TKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDE-TGKNCLYKNYDIL----PAKNDFNFEKRD 775 (1401)
Q Consensus 702 s~grhf-tk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~-~gk~c~~kn~dl~----~~kn~f~Fe~~d 775 (1401)
+||.|| +...-+..|++.+. +.+|++|||+.||.-.++..|-++... ++.+..-.-++.+ ....++.|...|
T Consensus 6 ~~GQnfl~d~~~~~~iv~~~~--~~~~~~VLEIG~G~G~lt~~L~~~~~~v~~vEid~~~~~~l~~~~~~~~~v~ii~~D 83 (258)
T PRK14896 6 KLGQHFLIDDRVVDRIVEYAE--DTDGDPVLEIGPGKGALTDELAKRAKKVYAIELDPRLAEFLRDDEIAAGNVEIIEGD 83 (258)
T ss_pred cCCccccCCHHHHHHHHHhcC--CCCcCeEEEEeCccCHHHHHHHHhCCEEEEEECCHHHHHHHHHHhccCCCEEEEEec
Confidence 789999 67888889999875 678999999999999999988764110 0111110011111 111345555566
Q ss_pred cccccCCCCCCCCeeeeeeCCCccchhhhHHHHHHhhhccCCcEEEEecCCc-cccccccC-----CCceee------ec
Q 000595 776 WMTVEPKELAPGSRLIMGLNPPFGVKAGLANKFINKALEFNPKLLILIVPPE-TERLDRKE-----SAYELV------WE 843 (1401)
Q Consensus 776 w~~v~~~elp~G~~LimgLnPPfg~~a~lAnkFi~kal~f~Pkliili~P~~-t~rld~k~-----~~Y~li------we 843 (1401)
.+.+....+ .+|+| ||||.+- ...+.+.+.+...-.+|.+..| .+||=.+. ....++ .+
T Consensus 84 ~~~~~~~~~----d~Vv~-NlPy~i~----s~~~~~l~~~~~~~~~l~~q~e~A~rl~a~~g~~~yg~lsv~~~~~~~~~ 154 (258)
T PRK14896 84 ALKVDLPEF----NKVVS-NLPYQIS----SPITFKLLKHGFEPAVLMYQKEFAERMVAKPGTKEYGRLSVMVQYYADVE 154 (258)
T ss_pred cccCCchhc----eEEEE-cCCcccC----cHHHHHHHhhccceeEEEeeHHHHHHhcCCCCCccccHHHHHHHHHeeeE
Confidence 665543322 47888 9999864 4455555555554344544443 34442221 121222 12
Q ss_pred cccccCCcceecCCCccc
Q 000595 844 DDQFLSGKSFYLPGSVDE 861 (1401)
Q Consensus 844 d~~~l~gksFylPGsvd~ 861 (1401)
--..+.-+.|+-|-.||.
T Consensus 155 ~~~~v~~~~F~P~PkV~s 172 (258)
T PRK14896 155 IVEKVPPGAFSPKPKVDS 172 (258)
T ss_pred EEEEeChHhCCCCCCceE
Confidence 223345678887766673
No 27
>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=96.33 E-value=0.003 Score=53.46 Aligned_cols=45 Identities=27% Similarity=0.624 Sum_probs=34.3
Q ss_pred cccccCCCCCCCCCCCceeecccCCccccccCCCCCcccccccccccccccccc
Q 000595 355 KCCICKQGENKADSDLQFAVCRRCPKAYHRKCLPRKIAFEDKLEEGIITRAWEG 408 (1401)
Q Consensus 355 ~C~vCkqseDkn~segKLI~CdRCPkAYH~kCLPPpIsfe~~~~EgIp~RAW~c 408 (1401)
+|.+|++.++ +..++.|+.|..+||..|+.++..- +.++...|.|
T Consensus 1 ~C~vC~~~~~----~~~~i~C~~C~~~~H~~C~~~~~~~-----~~~~~~~w~C 45 (51)
T PF00628_consen 1 YCPVCGQSDD----DGDMIQCDSCNRWYHQECVGPPEKA-----EEIPSGDWYC 45 (51)
T ss_dssp EBTTTTSSCT----TSSEEEBSTTSCEEETTTSTSSHSH-----HSHHSSSBSS
T ss_pred eCcCCCCcCC----CCCeEEcCCCChhhCcccCCCChhh-----ccCCCCcEEC
Confidence 4889998543 3579999999999999999998652 2334458886
No 28
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=96.16 E-value=0.0018 Score=80.47 Aligned_cols=50 Identities=36% Similarity=0.756 Sum_probs=37.9
Q ss_pred cccCCccccccCCCCceeeccccccccccCccccCcccccccCCCChhhhhccCcccccccc
Q 000595 223 DELFDSVCSFCDNGGDLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCE 284 (1401)
Q Consensus 223 dDl~DdVCaIC~dGGeLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe 284 (1401)
++-....|.+|.++|++|||+ .|+.+||+.|+ .+.+++. +++.|.|+.|.
T Consensus 43 ~~~~~e~c~ic~~~g~~l~c~-tC~~s~h~~cl--------~~pl~~~---p~~~~~c~Rc~ 92 (696)
T KOG0383|consen 43 DDAEQEACRICADGGELLWCD-TCPASFHASCL--------GPPLTPQ---PNGEFICPRCF 92 (696)
T ss_pred chhhhhhhhhhcCCCcEEEec-cccHHHHHHcc--------CCCCCcC---Cccceeeeeec
Confidence 334467899999999999999 89999999953 3444332 34559999884
No 29
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=96.08 E-value=0.0048 Score=65.65 Aligned_cols=94 Identities=26% Similarity=0.558 Sum_probs=64.0
Q ss_pred cccccCCCCCCCCCCCCeeeecCCCCCCCCCcccccccccccchHHHHHHHhHhhccC-CceeC--------------CC
Q 000595 289 QCFACGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAG-ESFTC--------------PL 353 (1401)
Q Consensus 289 qCFVCGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLekkIaaG-ksFrC--------------Pl 353 (1401)
.|-+|+..|.+ ...+.|+.|. .|...||..||..-... +.|-.+|... ...+| |.
T Consensus 1 ~C~~C~~~g~~--~~kG~Lv~CQ--GCs~sYHk~CLG~Rs~R------eHlVTKVg~d~FVLQCr~Cig~~~kKD~~aP~ 70 (175)
T PF15446_consen 1 TCDTCGYEGDD--RNKGPLVYCQ--GCSSSYHKACLGPRSQR------EHLVTKVGDDDFVLQCRRCIGIAHKKDPRAPH 70 (175)
T ss_pred CcccccCCCCC--ccCCCeEEcC--ccChHHHhhhcCCcccc------ceeeEEEcCCceEEechhhcChhhcccCCCCC
Confidence 37778765543 2335899999 99999999999976532 1232333321 23445 44
Q ss_pred C-cccccCCCCCC----------------------------------CCCCCceeecccCCccccccCCCCCcc
Q 000595 354 H-KCCICKQGENK----------------------------------ADSDLQFAVCRRCPKAYHRKCLPRKIA 392 (1401)
Q Consensus 354 H-~C~vCkqseDk----------------------------------n~segKLI~CdRCPkAYH~kCLPPpIs 392 (1401)
| .|..|+..+.. +..+.-|++|..|-++||...||+...
T Consensus 71 ~~~C~~C~~~G~~c~pfr~r~T~kQEe~~ReeNgG~DPit~Vd~~lvnN~~nVLFRC~~C~RawH~~HLP~~~~ 144 (175)
T PF15446_consen 71 HGMCQQCKKPGPSCKPFRPRKTPKQEEKLREENGGVDPITPVDPELVNNPDNVLFRCTSCHRAWHFEHLPPPSG 144 (175)
T ss_pred CCcccccCCCCCCCcccCCCCCcHHHHHHHHHcCCCCCCccCCHHHccChhheEEecCCccceeehhhCCCCcC
Confidence 4 49999987320 145667999999999999999998643
No 30
>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 PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=95.65 E-value=0.015 Score=65.93 Aligned_cols=154 Identities=19% Similarity=0.274 Sum_probs=92.7
Q ss_pred cccccc-ccCccc-chhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhhhCCcc-cc----------ccccc
Q 000595 696 HGMRYT-SFGRHF-TKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDETGKNC-LY----------KNYDI 762 (1401)
Q Consensus 696 ~G~ryt-s~grhf-tk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~~gk~c-~~----------kn~dl 762 (1401)
||+|.. +||.|| +...-+..|++.+. +.+|++|+|+-||.-.+...+-++ ..+-. .= +|+.-
T Consensus 6 ~~~~~kk~~GQnFL~d~~i~~~Iv~~~~--~~~~~~VLEIG~G~G~LT~~Ll~~---~~~V~avEiD~~li~~l~~~~~~ 80 (294)
T PTZ00338 6 SGMVFNKKFGQHILKNPLVLDKIVEKAA--IKPTDTVLEIGPGTGNLTEKLLQL---AKKVIAIEIDPRMVAELKKRFQN 80 (294)
T ss_pred CCcCcCCCCCccccCCHHHHHHHHHhcC--CCCcCEEEEecCchHHHHHHHHHh---CCcEEEEECCHHHHHHHHHHHHh
Confidence 455543 899999 67888889999874 679999999999999998877442 11100 00 11110
Q ss_pred cCCCCCccccccccccccCCCCCCCCeeeeeeCCCccchhhhHHHHHHhhhccCCcEEEEecCCcc-ccccccC--CCc-
Q 000595 763 LPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLNPPFGVKAGLANKFINKALEFNPKLLILIVPPET-ERLDRKE--SAY- 838 (1401)
Q Consensus 763 ~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLnPPfg~~a~lAnkFi~kal~f~Pkliili~P~~t-~rld~k~--~~Y- 838 (1401)
......+.+...|++.+...++ .+|++ ||||.+-..+--+++.... ..+-.+|++-.|. +||=.++ .-|
T Consensus 81 ~~~~~~v~ii~~Dal~~~~~~~----d~Vva-NlPY~Istpil~~ll~~~~--~~~~~vlm~QkEvA~Rl~A~pg~k~y~ 153 (294)
T PTZ00338 81 SPLASKLEVIEGDALKTEFPYF----DVCVA-NVPYQISSPLVFKLLAHRP--LFRCAVLMFQKEFALRLLAQPGDELYC 153 (294)
T ss_pred cCCCCcEEEEECCHhhhccccc----CEEEe-cCCcccCcHHHHHHHhcCC--CCceeeeeehHHHHHHHhcCCCCcccC
Confidence 0002346666667766554333 26666 9999966666555554433 3346777777776 7774331 112
Q ss_pred --eeee------ccccccCCcceecCCCccc
Q 000595 839 --ELVW------EDDQFLSGKSFYLPGSVDE 861 (1401)
Q Consensus 839 --~liw------ed~~~l~gksFylPGsvd~ 861 (1401)
.++| +--.-+...+||=|=-||.
T Consensus 154 ~LSv~~q~~~~~~~~~~V~~~~F~P~PkVdS 184 (294)
T PTZ00338 154 RLSVNTQLLCRVTHLMKVSKNSFNPPPKVES 184 (294)
T ss_pred HHHHHHHHHhceEEEEEeCchhCCCCCCcEE
Confidence 1221 2223456778887777773
No 32
>PF01170 UPF0020: Putative RNA methylase family UPF0020; InterPro: IPR000241 This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains [].; PDB: 3LDU_A 3LDG_A 3K0B_A 3V8V_B 3V97_A 3TLJ_A 3TM5_B 3TM4_A 3TMA_A.
Probab=95.55 E-value=0.029 Score=59.15 Aligned_cols=107 Identities=23% Similarity=0.445 Sum_probs=56.2
Q ss_pred HHHHhhcccccCCCcEEeccCCcchHHH---HHHHHHh---------hhCCccc-------cccccccCCCCCccccccc
Q 000595 715 AIVDKLHWYVNDGDMIVDFCCGANDFSC---LMKKKLD---------ETGKNCL-------YKNYDILPAKNDFNFEKRD 775 (1401)
Q Consensus 715 ~i~~~Lh~yv~~gd~ivdfccg~n~fs~---lmk~kl~---------~~gk~c~-------~kn~dl~~~kn~f~Fe~~d 775 (1401)
.++..--| ++|++|+|.+||+-.|.. +|....- -.|.+.. -.|..-..-.+...|...|
T Consensus 19 ~ll~la~~--~~~~~vlDP~CGsGtiliEaa~~~~~~~~~~~~~~~~~~g~Di~~~~v~~a~~N~~~ag~~~~i~~~~~D 96 (179)
T PF01170_consen 19 ALLNLAGW--RPGDVVLDPFCGSGTILIEAALMGANIPPLNDINELKIIGSDIDPKAVRGARENLKAAGVEDYIDFIQWD 96 (179)
T ss_dssp HHHHHTT----TTS-EEETT-TTSHHHHHHHHHHTTTSTTTH-CH--EEEEESSHHHHHHHHHHHHHTT-CGGEEEEE--
T ss_pred HHHHHhCC--CCCCEEeecCCCCCHHHHHHHHHhhCcccccccccccEEecCCCHHHHHHHHHHHHhcccCCceEEEecc
Confidence 34444444 789999999999999862 2221111 0011111 1222222223445566666
Q ss_pred cccccCCCCCCCCeeeeeeCCCccchhh-------hHHHHHHhhhc-cCCcEEEEecCC
Q 000595 776 WMTVEPKELAPGSRLIMGLNPPFGVKAG-------LANKFINKALE-FNPKLLILIVPP 826 (1401)
Q Consensus 776 w~~v~~~elp~G~~LimgLnPPfg~~a~-------lAnkFi~kal~-f~Pkliili~P~ 826 (1401)
...+. ++.|+.=+|--|||||.+.. |-.+|++.+-. ++|++++|+...
T Consensus 97 ~~~l~---~~~~~~d~IvtnPPyG~r~~~~~~~~~ly~~~~~~~~~~l~~~~v~l~~~~ 152 (179)
T PF01170_consen 97 ARELP---LPDGSVDAIVTNPPYGRRLGSKKDLEKLYRQFLRELKRVLKPRAVFLTTSN 152 (179)
T ss_dssp GGGGG---GTTSBSCEEEEE--STTSHCHHHHHHHHHHHHHHHHHCHSTTCEEEEEESC
T ss_pred hhhcc---cccCCCCEEEECcchhhhccCHHHHHHHHHHHHHHHHHHCCCCEEEEEECC
Confidence 66665 45666656667999999855 34567777777 898666666553
No 33
>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=93.96 E-value=0.033 Score=52.65 Aligned_cols=87 Identities=22% Similarity=0.316 Sum_probs=55.5
Q ss_pred CCcEEeccCCcchHHHHHHHHH--hhhCCccc-------cccccccCCCCCccccccccccccCCCCCCCCeeeeeeCCC
Q 000595 727 GDMIVDFCCGANDFSCLMKKKL--DETGKNCL-------YKNYDILPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLNPP 797 (1401)
Q Consensus 727 gd~ivdfccg~n~fs~lmk~kl--~~~gk~c~-------~kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLnPP 797 (1401)
|++|+|+|||.-.|...+-+.. .-+|.+.. -+|+....-.....|...|+.++. .+++.+..=++-.|||
T Consensus 1 g~~vlD~~~G~G~~~~~~~~~~~~~~~gvdi~~~~~~~a~~~~~~~~~~~~~~~~~~D~~~~~-~~~~~~~~D~Iv~npP 79 (117)
T PF13659_consen 1 GDRVLDPGCGSGTFLLAALRRGAARVTGVDIDPEAVELARRNLPRNGLDDRVEVIVGDARDLP-EPLPDGKFDLIVTNPP 79 (117)
T ss_dssp TEEEEEETSTTCHHHHHHHHHCTCEEEEEESSHHHHHHHHHHCHHCTTTTTEEEEESHHHHHH-HTCTTT-EEEEEE--S
T ss_pred CCEEEEcCcchHHHHHHHHHHCCCeEEEEEECHHHHHHHHHHHHHccCCceEEEEECchhhch-hhccCceeEEEEECCC
Confidence 7899999999999999997764 11111111 134444433456888889998886 4566666644444999
Q ss_pred ccch-------hhhHHHHHHhhhc
Q 000595 798 FGVK-------AGLANKFINKALE 814 (1401)
Q Consensus 798 fg~~-------a~lAnkFi~kal~ 814 (1401)
|+.. ..++..|+.+|..
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~ 103 (117)
T PF13659_consen 80 YGPRSGDKAALRRLYSRFLEAAAR 103 (117)
T ss_dssp TTSBTT----GGCHHHHHHHHHHH
T ss_pred CccccccchhhHHHHHHHHHHHHH
Confidence 9954 2367788888764
No 34
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=93.79 E-value=0.076 Score=56.88 Aligned_cols=93 Identities=25% Similarity=0.510 Sum_probs=57.0
Q ss_pred cccccCC------CCceeeccccccccccCccccCcccccccCCCChhhhhccCcccccccccc----------cccccc
Q 000595 229 VCSFCDN------GGDLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYK----------QHQCFA 292 (1401)
Q Consensus 229 VCaIC~d------GGeLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~g----------QHqCFV 292 (1401)
+|..|.. -|-||.|.| |..+||..|+-...+- .--.|..- ...--..|..|..- +..|..
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQG-Cs~sYHk~CLG~Rs~R--eHlVTKVg-~d~FVLQCr~Cig~~~kKD~~aP~~~~C~~ 76 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQG-CSSSYHKACLGPRSQR--EHLVTKVG-DDDFVLQCRRCIGIAHKKDPRAPHHGMCQQ 76 (175)
T ss_pred CcccccCCCCCccCCCeEEcCc-cChHHHhhhcCCcccc--ceeeEEEc-CCceEEechhhcChhhcccCCCCCCCcccc
Confidence 4788853 368999996 9999999975322110 00000000 01123457777431 357999
Q ss_pred cCCCCCCCC---------------------------------CCCCeeeecCCCCCCCCCcccccccc
Q 000595 293 CGKLGSSDK---------------------------------ETGAEVFPCVSATCGHFYHPHCVSKL 327 (1401)
Q Consensus 293 CGklGSSDk---------------------------------~SGaEVfrCsvasCGRFYHpkCLa~l 327 (1401)
|+..|.+-+ -...-||+|. .|-+.+|..-|...
T Consensus 77 C~~~G~~c~pfr~r~T~kQEe~~ReeNgG~DPit~Vd~~lvnN~~nVLFRC~--~C~RawH~~HLP~~ 142 (175)
T PF15446_consen 77 CKKPGPSCKPFRPRKTPKQEEKLREENGGVDPITPVDPELVNNPDNVLFRCT--SCHRAWHFEHLPPP 142 (175)
T ss_pred cCCCCCCCcccCCCCCcHHHHHHHHHcCCCCCCccCCHHHccChhheEEecC--CccceeehhhCCCC
Confidence 998887520 0113569999 99999999888765
No 35
>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=93.50 E-value=0.061 Score=59.54 Aligned_cols=155 Identities=21% Similarity=0.329 Sum_probs=87.0
Q ss_pred cccCcccc-hhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhhh---CCccccccccccC----CCCCcccc
Q 000595 701 TSFGRHFT-KVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDET---GKNCLYKNYDILP----AKNDFNFE 772 (1401)
Q Consensus 701 ts~grhft-k~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~~---gk~c~~kn~dl~~----~kn~f~Fe 772 (1401)
-+||-||- ...-++.|++.+..- .+++|||+-.|...|++.|-++...+ .++-.| ++.+. ...++..-
T Consensus 6 k~~gQnFL~~~~~~~~Iv~~~~~~--~~~~VlEiGpG~G~lT~~L~~~~~~v~~vE~d~~~--~~~L~~~~~~~~~~~vi 81 (262)
T PF00398_consen 6 KSLGQNFLVDPNIADKIVDALDLS--EGDTVLEIGPGPGALTRELLKRGKRVIAVEIDPDL--AKHLKERFASNPNVEVI 81 (262)
T ss_dssp CGCTSSEEEHHHHHHHHHHHHTCG--TTSEEEEESSTTSCCHHHHHHHSSEEEEEESSHHH--HHHHHHHCTTCSSEEEE
T ss_pred CCCCcCeeCCHHHHHHHHHhcCCC--CCCEEEEeCCCCccchhhHhcccCcceeecCcHhH--HHHHHHHhhhcccceee
Confidence 47899997 566778899988654 99999999999999999886544110 000000 11111 12333444
Q ss_pred ccccccccCCC-CCCCCeeeeeeCCCccchhhhHHHHHHhhhccCCcEEEEecCCc-cccccccC-----CCceee----
Q 000595 773 KRDWMTVEPKE-LAPGSRLIMGLNPPFGVKAGLANKFINKALEFNPKLLILIVPPE-TERLDRKE-----SAYELV---- 841 (1401)
Q Consensus 773 ~~dw~~v~~~e-lp~G~~LimgLnPPfg~~a~lAnkFi~kal~f~Pkliili~P~~-t~rld~k~-----~~Y~li---- 841 (1401)
..|.++++..+ +.....+|+| |.||.+-..|-.+++. ...+...-++|+++.| .+||=.+. ....++
T Consensus 82 ~~D~l~~~~~~~~~~~~~~vv~-NlPy~is~~il~~ll~-~~~~g~~~~~l~vq~e~a~rl~a~pg~~~~~~lsv~~q~~ 159 (262)
T PF00398_consen 82 NGDFLKWDLYDLLKNQPLLVVG-NLPYNISSPILRKLLE-LYRFGRVRMVLMVQKEVAERLLAKPGSKRYSRLSVLAQAF 159 (262)
T ss_dssp ES-TTTSCGGGHCSSSEEEEEE-EETGTGHHHHHHHHHH-HGGGCEEEEEEEEEHHHHHHHHTSTTSTTCSHHHHHHHHH
T ss_pred ecchhccccHHhhcCCceEEEE-EecccchHHHHHHHhh-cccccccceEEEEehhhhhhccCCCCCCccchhhhhhhhh
Confidence 55666665554 4456667777 9999755555555554 1123224556666555 46665542 111122
Q ss_pred --eccccccCCcceecCCCccc
Q 000595 842 --WEDDQFLSGKSFYLPGSVDE 861 (1401)
Q Consensus 842 --wed~~~l~gksFylPGsvd~ 861 (1401)
++--.-+....||=|-.||.
T Consensus 160 ~~i~~l~~v~~~~F~P~PkVds 181 (262)
T PF00398_consen 160 FDIKLLFKVPPSCFYPPPKVDS 181 (262)
T ss_dssp EEEEEEEEE-GGGEESSSSS-E
T ss_pred hceeEecccCCccccCCCCCce
Confidence 22223344567776666674
No 36
>PRK10909 rsmD 16S rRNA m(2)G966-methyltransferase; Provisional
Probab=93.04 E-value=0.33 Score=52.58 Aligned_cols=120 Identities=18% Similarity=0.211 Sum_probs=62.3
Q ss_pred cCCCcEEeccCCcchHHHH-HHHH-HhhhCCcc-------ccccccccCCCCCccccccccccccCCCCCCCCeeeeeeC
Q 000595 725 NDGDMIVDFCCGANDFSCL-MKKK-LDETGKNC-------LYKNYDILPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLN 795 (1401)
Q Consensus 725 ~~gd~ivdfccg~n~fs~l-mk~k-l~~~gk~c-------~~kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLn 795 (1401)
..|.+|+|++||+..|+-. +... ..-++.+. .-+|.....- ++..|...|++..-+. ..+..=++-+|
T Consensus 52 ~~~~~vLDl~~GsG~l~l~~lsr~a~~V~~vE~~~~a~~~a~~Nl~~~~~-~~v~~~~~D~~~~l~~--~~~~fDlV~~D 128 (199)
T PRK10909 52 IVDARCLDCFAGSGALGLEALSRYAAGATLLEMDRAVAQQLIKNLATLKA-GNARVVNTNALSFLAQ--PGTPHNVVFVD 128 (199)
T ss_pred cCCCEEEEcCCCccHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHHHhCC-CcEEEEEchHHHHHhh--cCCCceEEEEC
Confidence 5788999999999999964 3321 01111111 1245444432 2466777777653222 12334456689
Q ss_pred CCccchhhhHHHHHHhhhc---cCCcEEEEec-CCccccccccCCCceeeeccccccCCcce
Q 000595 796 PPFGVKAGLANKFINKALE---FNPKLLILIV-PPETERLDRKESAYELVWEDDQFLSGKSF 853 (1401)
Q Consensus 796 PPfg~~a~lAnkFi~kal~---f~Pkliili~-P~~t~rld~k~~~Y~liwed~~~l~gksF 853 (1401)
|||.. .+..+-++.... ..|+=||.|- +..++ +......|.++ ..+.. |+|+
T Consensus 129 PPy~~--g~~~~~l~~l~~~~~l~~~~iv~ve~~~~~~-~~~~~~~~~~~-~~k~y--G~s~ 184 (199)
T PRK10909 129 PPFRK--GLLEETINLLEDNGWLADEALIYVESEVENG-LPTVPANWQLH-REKVA--GQVA 184 (199)
T ss_pred CCCCC--ChHHHHHHHHHHCCCcCCCcEEEEEecCCCC-cccCCCccEEE-EEecC--CCEE
Confidence 99843 344443333333 3677666665 43332 33333346554 33333 6664
No 37
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=92.76 E-value=0.016 Score=68.49 Aligned_cols=141 Identities=18% Similarity=0.419 Sum_probs=80.0
Q ss_pred ccccccCCC--CceeeccccccccccCccccCccccc-ccCCCChhhhhccCcccccccccc-cccccccCCCCCCCCCC
Q 000595 228 SVCSFCDNG--GDLLCCEGRCLRSFHATIDAGEESHC-ASLGLTKDEVEAMLNFFCKNCEYK-QHQCFACGKLGSSDKET 303 (1401)
Q Consensus 228 dVCaIC~dG--GeLLCCDG~C~RSFH~~CldGeeS~C-ltLGLTeaEvq~~~sW~C~nCe~g-QHqCFVCGklGSSDk~S 303 (1401)
.+|..|+++ |+-.-|+ -=.+.||..|..=.. | .+|.-. .--.-.++-+|..|-.. ...|.+|++.-.
T Consensus 275 ~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 275 GICAFCHKTVSGQGLAVE-AMDQLFHVQCFTCRT--CRRQLAGQ-SFYQVDGKPYCEGCYQDTLEKCNKCGEPIM----- 345 (468)
T ss_pred hhhhhcCCcccCcchHHH-HhhhhhcccceehHh--hhhhhccc-cccccCCcccchHHHHHHHHHHhhhhhHHH-----
Confidence 399999984 7777887 467999999875110 2 111110 00112467889998543 357999998753
Q ss_pred CCeeeecCCCCCCCCCcccccccccccchHHHHHHHhHhhccCCceeCCC--C-----cccccCCC---CCCCCCCCcee
Q 000595 304 GAEVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAGESFTCPL--H-----KCCICKQG---ENKADSDLQFA 373 (1401)
Q Consensus 304 GaEVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLekkIaaGksFrCPl--H-----~C~vCkqs---eDkn~segKLI 373 (1401)
..+++ .||+.||+.|..-.......++. .+ .+......+|=. | +|.+|... .+.. ...+
T Consensus 346 -d~iLr----A~GkayHp~CF~Cv~C~r~ldgi-pF--tvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~---~etv 414 (468)
T KOG1701|consen 346 -DRILR----ALGKAYHPGCFTCVVCARCLDGI-PF--TVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGK---DETV 414 (468)
T ss_pred -HHHHH----hcccccCCCceEEEEeccccCCc-cc--cccCCCceeeehhhhhhcCcchhhccCCccCCCCC---cceE
Confidence 35665 79999999987644322100000 01 122234456632 2 39999875 2221 1133
Q ss_pred ecccCCccccccCCC
Q 000595 374 VCRRCPKAYHRKCLP 388 (1401)
Q Consensus 374 ~CdRCPkAYH~kCLP 388 (1401)
+=.-=++.||..|..
T Consensus 415 Rvvamdr~fHv~CY~ 429 (468)
T KOG1701|consen 415 RVVAMDRDFHVNCYK 429 (468)
T ss_pred EEEEcccccccccee
Confidence 333346788886643
No 38
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=92.29 E-value=0.066 Score=60.52 Aligned_cols=24 Identities=21% Similarity=0.585 Sum_probs=21.4
Q ss_pred CeeeecCCCCCC-CCCccccccccc
Q 000595 305 AEVFPCVSATCG-HFYHPHCVSKLL 328 (1401)
Q Consensus 305 aEVfrCsvasCG-RFYHpkCLa~l~ 328 (1401)
++++.|+.+.|. .|||..||....
T Consensus 230 g~Mi~CDn~~C~~eWFH~~CVGL~~ 254 (274)
T KOG1973|consen 230 GKMIGCDNPGCPIEWFHFTCVGLKT 254 (274)
T ss_pred ccccccCCCCCCcceEEEecccccc
Confidence 579999999999 999999999764
No 39
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=92.21 E-value=0.078 Score=66.41 Aligned_cols=47 Identities=23% Similarity=0.662 Sum_probs=35.0
Q ss_pred CccccccCCCC---ceeecccccccc-ccCccccCcccccccCCCChhhhhccCccccccccc
Q 000595 227 DSVCSFCDNGG---DLLCCEGRCLRS-FHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEY 285 (1401)
Q Consensus 227 DdVCaIC~dGG---eLLCCDG~C~RS-FH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~ 285 (1401)
...|.||.... -||.|+ .|... ||..|++ ..+.+. +.+.|||.+|..
T Consensus 215 ~~~C~IC~~~DpEdVLLLCD-sCN~~~YH~YCLD--------Pdl~ei---P~~eWYC~NC~d 265 (1134)
T KOG0825|consen 215 EVKCDICTVHDPEDVLLLCD-SCNKVYYHVYCLD--------PDLSES---PVNEWYCTNCSL 265 (1134)
T ss_pred cccceeeccCChHHhheeec-ccccceeeccccC--------cccccc---cccceecCcchh
Confidence 46799999764 589999 59998 9999543 444332 458999999963
No 40
>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=92.17 E-value=0.22 Score=58.65 Aligned_cols=129 Identities=21% Similarity=0.365 Sum_probs=72.8
Q ss_pred hhhhHHHHHHhhccccc--CCCcEEeccCCcchHHHHHHHHHhh-hCCccc-------cccccccCCCCCcccccccccc
Q 000595 709 KVDKLQAIVDKLHWYVN--DGDMIVDFCCGANDFSCLMKKKLDE-TGKNCL-------YKNYDILPAKNDFNFEKRDWMT 778 (1401)
Q Consensus 709 k~ekl~~i~~~Lh~yv~--~gd~ivdfccg~n~fs~lmk~kl~~-~gk~c~-------~kn~dl~~~kn~f~Fe~~dw~~ 778 (1401)
..+-.+.+++++.-+++ ++++|+|++||.-.|+..|.+.... +|.+.+ =+|..... -++..|...|+..
T Consensus 273 N~~~~~~l~~~~~~~l~~~~~~~vLDl~cG~G~~sl~la~~~~~V~~vE~~~~av~~a~~n~~~~~-~~nv~~~~~d~~~ 351 (431)
T TIGR00479 273 NSGQNEKLVDRALEALELQGEELVVDAYCGVGTFTLPLAKQAKSVVGIEVVPESVEKAQQNAELNG-IANVEFLAGTLET 351 (431)
T ss_pred CHHHHHHHHHHHHHHhccCCCCEEEEcCCCcCHHHHHHHHhCCEEEEEEcCHHHHHHHHHHHHHhC-CCceEEEeCCHHH
Confidence 45666667777766654 6789999999999999888653210 111111 12222211 1235566666654
Q ss_pred ccCCC-CCCCCeeeeeeCCCccchhhhHHHHHHhhhccCCcEEEEec-CCcccccccc---CCCceee
Q 000595 779 VEPKE-LAPGSRLIMGLNPPFGVKAGLANKFINKALEFNPKLLILIV-PPETERLDRK---ESAYELV 841 (1401)
Q Consensus 779 v~~~e-lp~G~~LimgLnPPfg~~a~lAnkFi~kal~f~Pkliili~-P~~t~rld~k---~~~Y~li 841 (1401)
.-++. +..++.=++-+|||. +.++..|++.....+|+-||.|. -|.|---|-+ ..+|.+.
T Consensus 352 ~l~~~~~~~~~~D~vi~dPPr---~G~~~~~l~~l~~l~~~~ivyvsc~p~tlard~~~l~~~gy~~~ 416 (431)
T TIGR00479 352 VLPKQPWAGQIPDVLLLDPPR---KGCAAEVLRTIIELKPERIVYVSCNPATLARDLEFLCKEGYGIT 416 (431)
T ss_pred HHHHHHhcCCCCCEEEECcCC---CCCCHHHHHHHHhcCCCEEEEEcCCHHHHHHHHHHHHHCCeeEE
Confidence 32211 112222233469994 34778888887788898877765 4455433332 2356543
No 41
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=90.99 E-value=0.086 Score=63.53 Aligned_cols=51 Identities=24% Similarity=0.673 Sum_probs=36.6
Q ss_pred CccccccCCCC-----ceeeccccccccccCccccCcccccccCCCChhhh-hccCcccccccccc
Q 000595 227 DSVCSFCDNGG-----DLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEV-EAMLNFFCKNCEYK 286 (1401)
Q Consensus 227 DdVCaIC~dGG-----eLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEv-q~~~sW~C~nCe~g 286 (1401)
+..|.+|..|+ .||.|+ .|..+||..|.. | .++..+. ++...|+|..|.++
T Consensus 168 n~qc~vC~~g~~~~~NrmlqC~-~C~~~fHq~Chq-----p---~i~~~l~~D~~~~w~C~~C~~~ 224 (464)
T KOG4323|consen 168 NLQCSVCYCGGPGAGNRMLQCD-KCRQWYHQACHQ-----P---LIKDELAGDPFYEWFCDVCNRG 224 (464)
T ss_pred cceeeeeecCCcCccceeeeec-ccccHHHHHhcc-----C---CCCHhhccCccceEeehhhccc
Confidence 45599999754 799999 599999999765 3 2333322 24578999888654
No 42
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=90.90 E-value=0.22 Score=48.38 Aligned_cols=84 Identities=20% Similarity=0.364 Sum_probs=49.5
Q ss_pred cccccCCC-CceeeccccccccccCccccCcc-cccccC-CCChhhhhccCcccccccccccccccccCCCCCCCCCCCC
Q 000595 229 VCSFCDNG-GDLLCCEGRCLRSFHATIDAGEE-SHCASL-GLTKDEVEAMLNFFCKNCEYKQHQCFACGKLGSSDKETGA 305 (1401)
Q Consensus 229 VCaIC~dG-GeLLCCDG~C~RSFH~~CldGee-S~CltL-GLTeaEvq~~~sW~C~nCe~gQHqCFVCGklGSSDk~SGa 305 (1401)
.|.+|... |-|..-. -.++.|..|+--.. ....+. .+....+ .... ++ .....|.+|++.+ +
T Consensus 2 ~C~lC~~~~Galk~t~--~~~WvHv~Cal~~~~~~~~~~~~~~~v~~---~~i~-~~--~~~~~C~iC~~~~-------G 66 (110)
T PF13832_consen 2 SCVLCPKRGGALKRTS--DGQWVHVLCALWIPEVIFNNGESMEPVDI---SNIP-PS--RFKLKCSICGKSG-------G 66 (110)
T ss_pred ccEeCCCCCCcccCcc--CCcEEEeEccceeCccEEeechhcCcccc---eeec-ch--hcCCcCcCCCCCC-------c
Confidence 59999985 5554444 58999999874111 001000 0000000 0000 00 1245799998863 3
Q ss_pred eeeecCCCCCCCCCcccccccc
Q 000595 306 EVFPCVSATCGHFYHPHCVSKL 327 (1401)
Q Consensus 306 EVfrCsvasCGRFYHpkCLa~l 327 (1401)
-.++|....|.+.||+.|....
T Consensus 67 ~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 67 ACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred eeEEcCCCCCCcCCCHHHHHHC
Confidence 5899998899999999998764
No 43
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=90.90 E-value=0.089 Score=49.16 Aligned_cols=40 Identities=28% Similarity=0.506 Sum_probs=32.1
Q ss_pred ccccccCCccccccCCC-Cceeecc-ccccccccCccccCcc
Q 000595 220 NEEDELFDSVCSFCDNG-GDLLCCE-GRCLRSFHATIDAGEE 259 (1401)
Q Consensus 220 ~e~dDl~DdVCaIC~dG-GeLLCCD-G~C~RSFH~~CldGee 259 (1401)
++........|.+|+.. |-.+.|. ..|.+.||+.|+...+
T Consensus 29 ~~~~~~~~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~~~ 70 (90)
T PF13771_consen 29 KEIKRRRKLKCSICKKKGGACIGCSHPGCSRSFHVPCARKAG 70 (90)
T ss_pred HHHHHHhCCCCcCCCCCCCeEEEEeCCCCCcEEChHHHccCC
Confidence 44566778999999997 8877776 5799999999875444
No 44
>TIGR01177 conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea.
Probab=90.73 E-value=1 Score=51.56 Aligned_cols=104 Identities=21% Similarity=0.364 Sum_probs=54.0
Q ss_pred HHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhhhCCcccccccccc--------------CCCCCcccccccccc
Q 000595 713 LQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDETGKNCLYKNYDIL--------------PAKNDFNFEKRDWMT 778 (1401)
Q Consensus 713 l~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~~gk~c~~kn~dl~--------------~~kn~f~Fe~~dw~~ 778 (1401)
...+++.+. +++|++|+|++||.-.|..-+.. .|.. .--.|+- .-.+ ..|...|-..
T Consensus 171 a~~~~~l~~--~~~g~~vLDp~cGtG~~lieaa~----~~~~--v~g~Di~~~~~~~a~~nl~~~g~~~-i~~~~~D~~~ 241 (329)
T TIGR01177 171 ARAMVNLAR--VTEGDRVLDPFCGTGGFLIEAGL----MGAK--VIGCDIDWKMVAGARINLEHYGIED-FFVKRGDATK 241 (329)
T ss_pred HHHHHHHhC--CCCcCEEEECCCCCCHHHHHHHH----hCCe--EEEEcCCHHHHHHHHHHHHHhCCCC-CeEEecchhc
Confidence 344555554 48999999999999988543311 1211 1111221 1111 3344444333
Q ss_pred ccCCCCCCCCeeeeeeCCCccchhhh--------HHHHHHhhhc-cCCc-EEEEecCCcc
Q 000595 779 VEPKELAPGSRLIMGLNPPFGVKAGL--------ANKFINKALE-FNPK-LLILIVPPET 828 (1401)
Q Consensus 779 v~~~elp~G~~LimgLnPPfg~~a~l--------AnkFi~kal~-f~Pk-liili~P~~t 828 (1401)
.. ++.+..=+|-.|||||.+... -.+|++.+.. .+|. .+++++|...
T Consensus 242 l~---~~~~~~D~Iv~dPPyg~~~~~~~~~~~~l~~~~l~~~~r~Lk~gG~lv~~~~~~~ 298 (329)
T TIGR01177 242 LP---LSSESVDAIATDPPYGRSTTAAGDGLESLYERSLEEFHEVLKSEGWIVYAVPTRI 298 (329)
T ss_pred CC---cccCCCCEEEECCCCcCcccccCCchHHHHHHHHHHHHHHccCCcEEEEEEcCCC
Confidence 21 123443344459999986533 3566666654 4554 3556666653
No 45
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=90.61 E-value=0.1 Score=62.98 Aligned_cols=47 Identities=26% Similarity=0.572 Sum_probs=36.7
Q ss_pred cccccCCCCCCCCCCCceeecccCCccccccCCCCCcccccccccccccccccc
Q 000595 355 KCCICKQGENKADSDLQFAVCRRCPKAYHRKCLPRKIAFEDKLEEGIITRAWEG 408 (1401)
Q Consensus 355 ~C~vCkqseDkn~segKLI~CdRCPkAYH~kCLPPpIsfe~~~~EgIp~RAW~c 408 (1401)
.|-+|+++.+.- .+++|+.|.+.||..||.||++..... ..+-.|-|
T Consensus 546 sCgiCkks~dQH----ll~~CDtC~lhYHlGCL~PPLTR~Pkk---~kn~gWqC 592 (707)
T KOG0957|consen 546 SCGICKKSTDQH----LLTQCDTCHLHYHLGCLSPPLTRLPKK---NKNFGWQC 592 (707)
T ss_pred eeeeeccchhhH----HHhhcchhhceeeccccCCccccCccc---ccCcceee
Confidence 499999987753 688999999999999999999754322 23456776
No 46
>smart00650 rADc Ribosomal RNA adenine dimethylases.
Probab=90.33 E-value=0.27 Score=50.70 Aligned_cols=141 Identities=18% Similarity=0.223 Sum_probs=72.9
Q ss_pred HHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHh-hhCCcccccccccc----CCCCCccccccccccccCCCCCCC
Q 000595 713 LQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLD-ETGKNCLYKNYDIL----PAKNDFNFEKRDWMTVEPKELAPG 787 (1401)
Q Consensus 713 l~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~-~~gk~c~~kn~dl~----~~kn~f~Fe~~dw~~v~~~elp~G 787 (1401)
++.|++.+.+ .+|++|+|+.||.-.++..+-++.. -++.+-.-+-.++. ...+.+.|...|.+.+...+. .
T Consensus 2 ~~~i~~~~~~--~~~~~vLEiG~G~G~lt~~l~~~~~~v~~vE~~~~~~~~~~~~~~~~~~v~ii~~D~~~~~~~~~--~ 77 (169)
T smart00650 2 IDKIVRAANL--RPGDTVLEIGPGKGALTEELLERAARVTAIEIDPRLAPRLREKFAAADNLTVIHGDALKFDLPKL--Q 77 (169)
T ss_pred HHHHHHhcCC--CCcCEEEEECCCccHHHHHHHhcCCeEEEEECCHHHHHHHHHHhccCCCEEEEECchhcCCcccc--C
Confidence 3567777764 6789999999999999988755310 00111110011111 112345566667766643321 1
Q ss_pred CeeeeeeCCCccchhhhHHHHHHhhhccCCcEEEEecCCc-cccccccC--CCc---------eeeeccccccCCcceec
Q 000595 788 SRLIMGLNPPFGVKAGLANKFINKALEFNPKLLILIVPPE-TERLDRKE--SAY---------ELVWEDDQFLSGKSFYL 855 (1401)
Q Consensus 788 ~~LimgLnPPfg~~a~lAnkFi~kal~f~Pkliili~P~~-t~rld~k~--~~Y---------~liwed~~~l~gksFyl 855 (1401)
--+|++ ||||.+...+-.+++.... ..+..+ |++-.| .+||-.+. .-| ..-|+--.-+...+||=
T Consensus 78 ~d~vi~-n~Py~~~~~~i~~~l~~~~-~~~~~~-l~~q~e~a~rl~~~~~~~~y~~lsv~~~~~~~~~~~~~v~~~~F~P 154 (169)
T smart00650 78 PYKVVG-NLPYNISTPILFKLLEEPP-AFRDAV-LMVQKEVARRLAAKPGSKDYGRLSVLLQPYFDVKILFKVPPEAFRP 154 (169)
T ss_pred CCEEEE-CCCcccHHHHHHHHHhcCC-CcceEE-EEEEHHHhHHhcCCCCCCcccHHHHHHHHHeeEEEEEEEChhhCCC
Confidence 246777 9999864444444444332 223444 455444 45666652 122 23344444455566654
Q ss_pred CCCcc
Q 000595 856 PGSVD 860 (1401)
Q Consensus 856 PGsvd 860 (1401)
|=-||
T Consensus 155 ~PkV~ 159 (169)
T smart00650 155 PPKVD 159 (169)
T ss_pred CCCce
Confidence 44443
No 47
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=90.33 E-value=0.21 Score=48.53 Aligned_cols=102 Identities=25% Similarity=0.454 Sum_probs=58.4
Q ss_pred cccccCCCCCCCCCCCCeeeecCCCCCCCCCcccccccccccchHHHHHHHh----HhhccCCceeCCCCcccccCCCCC
Q 000595 289 QCFACGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLA----KSIIAGESFTCPLHKCCICKQGEN 364 (1401)
Q Consensus 289 qCFVCGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLe----kkIaaGksFrCPlH~C~vCkqseD 364 (1401)
.|.+|.+.|. .++-. .-+.|.|..|....+........ .++ ..+.. .. -.-.|..|+...
T Consensus 2 ~C~lC~~~~G--------alk~t--~~~~WvHv~Cal~~~~~~~~~~~-~~~~v~~~~i~~-~~---~~~~C~iC~~~~- 65 (110)
T PF13832_consen 2 SCVLCPKRGG--------ALKRT--SDGQWVHVLCALWIPEVIFNNGE-SMEPVDISNIPP-SR---FKLKCSICGKSG- 65 (110)
T ss_pred ccEeCCCCCC--------cccCc--cCCcEEEeEccceeCccEEeech-hcCcccceeecc-hh---cCCcCcCCCCCC-
Confidence 5889988753 23333 35889999998865432111000 000 00111 01 123599998873
Q ss_pred CCCCCCceeeccc--CCccccccCCCC-CccccccccccccccccccccCCCceeEeccCC
Q 000595 365 KADSDLQFAVCRR--CPKAYHRKCLPR-KIAFEDKLEEGIITRAWEGLLPNHRILIYCLKH 422 (1401)
Q Consensus 365 kn~segKLI~CdR--CPkAYH~kCLPP-pIsfe~~~~EgIp~RAW~cLLpncRiLIyCpkH 422 (1401)
+..++|.. |.++||..|.-. ++.++. ..+.. +....++|.+|
T Consensus 66 -----G~~i~C~~~~C~~~fH~~CA~~~g~~~~~--------~~~~~---~~~~~~~C~~H 110 (110)
T PF13832_consen 66 -----GACIKCSHPGCSTAFHPTCARKAGLYFEI--------ENEED---NVQFIAYCPKH 110 (110)
T ss_pred -----ceeEEcCCCCCCcCCCHHHHHHCCCeEEe--------eecCC---CceEEEECCCC
Confidence 46899999 999999999754 332211 11110 23568899988
No 48
>TIGR02085 meth_trns_rumB 23S rRNA (uracil-5-)-methyltransferase RumB. This family consists of RNA methyltransferases designated RumB, formerly YbjF. Members act on 23S rRNA U747 and the equivalent position in other proteobacterial species. This family is homologous to the other 23S rRNA methyltransferase RumA and to the tRNA methyltransferase TrmA.
Probab=89.56 E-value=0.34 Score=56.67 Aligned_cols=115 Identities=16% Similarity=0.229 Sum_probs=64.0
Q ss_pred chhhhHHHHHHhhcccc--cCCCcEEeccCCcchHHHHHHHHHh-hhCCccc-------cccccccCCCCCccccccccc
Q 000595 708 TKVDKLQAIVDKLHWYV--NDGDMIVDFCCGANDFSCLMKKKLD-ETGKNCL-------YKNYDILPAKNDFNFEKRDWM 777 (1401)
Q Consensus 708 tk~ekl~~i~~~Lh~yv--~~gd~ivdfccg~n~fs~lmk~kl~-~~gk~c~-------~kn~dl~~~kn~f~Fe~~dw~ 777 (1401)
|..+-.+.+++.+.-++ .++.+|+|++||...|+..+-.+.. -+|.+.+ -+|.....- ++..|...|..
T Consensus 213 ~n~~~~~~l~~~~~~~l~~~~~~~vLDL~cG~G~~~l~la~~~~~v~~vE~~~~av~~a~~N~~~~~~-~~~~~~~~d~~ 291 (374)
T TIGR02085 213 TNPKVAAQLYATARQWVREIPVTQMWDLFCGVGGFGLHCAGPDTQLTGIEIESEAIACAQQSAQMLGL-DNLSFAALDSA 291 (374)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCCEEEEccCCccHHHHHHhhcCCeEEEEECCHHHHHHHHHHHHHcCC-CcEEEEECCHH
Confidence 44444455555544443 3578999999999999987754321 1122221 122222211 13445555543
Q ss_pred cccCCCCCCCCeeeeeeCCCccchhhhHHHHHHhhhccCCcEEEEe-cCCcc
Q 000595 778 TVEPKELAPGSRLIMGLNPPFGVKAGLANKFINKALEFNPKLLILI-VPPET 828 (1401)
Q Consensus 778 ~v~~~elp~G~~LimgLnPPfg~~a~lAnkFi~kal~f~Pkliili-~P~~t 828 (1401)
+.-+. + .+..=++-+|||. +.+..++|+.++.++|+-||.| .-|.|
T Consensus 292 ~~~~~-~-~~~~D~vi~DPPr---~G~~~~~l~~l~~~~p~~ivyvsc~p~T 338 (374)
T TIGR02085 292 KFATA-Q-MSAPELVLVNPPR---RGIGKELCDYLSQMAPKFILYSSCNAQT 338 (374)
T ss_pred HHHHh-c-CCCCCEEEECCCC---CCCcHHHHHHHHhcCCCeEEEEEeCHHH
Confidence 32211 1 1222345569996 4788999999999999655554 44444
No 49
>PF05175 MTS: Methyltransferase small domain; InterPro: IPR007848 This domain is found in ribosomal RNA small subunit methyltransferase C and in other methyltransferases.; GO: 0008168 methyltransferase activity; PDB: 1WY7_A 1DUS_A 2OZV_A 2PJD_A 1VQ1_A 1NV9_A 1SG9_C 1NV8_A 3Q87_B 3DMF_A ....
Probab=88.34 E-value=0.44 Score=49.45 Aligned_cols=84 Identities=23% Similarity=0.344 Sum_probs=53.6
Q ss_pred CCCcEEeccCCcchHHHHHHHHHhhhC----------CccccccccccCCCCCccccccccccccCCCCCCCCeeeeeeC
Q 000595 726 DGDMIVDFCCGANDFSCLMKKKLDETG----------KNCLYKNYDILPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLN 795 (1401)
Q Consensus 726 ~gd~ivdfccg~n~fs~lmk~kl~~~g----------k~c~~kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLn 795 (1401)
.+..|+|++||+--.+-++.++..... ..|.-+|.....-.+ ..+...||+. .++.+..=++-.|
T Consensus 31 ~~~~vLDlG~G~G~i~~~la~~~~~~~v~~vDi~~~a~~~a~~n~~~n~~~~-v~~~~~d~~~----~~~~~~fD~Iv~N 105 (170)
T PF05175_consen 31 KGGRVLDLGCGSGVISLALAKRGPDAKVTAVDINPDALELAKRNAERNGLEN-VEVVQSDLFE----ALPDGKFDLIVSN 105 (170)
T ss_dssp TTCEEEEETSTTSHHHHHHHHTSTCEEEEEEESBHHHHHHHHHHHHHTTCTT-EEEEESSTTT----TCCTTCEEEEEE-
T ss_pred cCCeEEEecCChHHHHHHHHHhCCCCEEEEEcCCHHHHHHHHHHHHhcCccc-cccccccccc----cccccceeEEEEc
Confidence 788999999999999999877544311 123345555554444 6777788764 3444555455559
Q ss_pred CCccchhh----hHHHHHHhhhc
Q 000595 796 PPFGVKAG----LANKFINKALE 814 (1401)
Q Consensus 796 PPfg~~a~----lAnkFi~kal~ 814 (1401)
|||--... +..+||..|..
T Consensus 106 PP~~~~~~~~~~~~~~~i~~a~~ 128 (170)
T PF05175_consen 106 PPFHAGGDDGLDLLRDFIEQARR 128 (170)
T ss_dssp --SBTTSHCHHHHHHHHHHHHHH
T ss_pred cchhcccccchhhHHHHHHHHHH
Confidence 99965444 77899988754
No 50
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=87.55 E-value=0.33 Score=58.72 Aligned_cols=48 Identities=27% Similarity=0.549 Sum_probs=35.8
Q ss_pred ccccCCCCCCCCCCCceeecccCCccccccCCCCCcccccccccccccccccc
Q 000595 356 CCICKQGENKADSDLQFAVCRRCPKAYHRKCLPRKIAFEDKLEEGIITRAWEG 408 (1401)
Q Consensus 356 C~vCkqseDkn~segKLI~CdRCPkAYH~kCLPPpIsfe~~~~EgIp~RAW~c 408 (1401)
|.+|..+.... .+ +|++|++|-.+||..|..+.+.-+ ..+-+...|.|
T Consensus 171 c~vC~~g~~~~-~N-rmlqC~~C~~~fHq~Chqp~i~~~---l~~D~~~~w~C 218 (464)
T KOG4323|consen 171 CSVCYCGGPGA-GN-RMLQCDKCRQWYHQACHQPLIKDE---LAGDPFYEWFC 218 (464)
T ss_pred eeeeecCCcCc-cc-eeeeecccccHHHHHhccCCCCHh---hccCccceEee
Confidence 88888765431 12 799999999999999999987522 22447788987
No 51
>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed
Probab=87.20 E-value=0.62 Score=53.07 Aligned_cols=93 Identities=15% Similarity=0.237 Sum_probs=51.8
Q ss_pred CCCcEEeccCCcchHHHHHHHHHh-hhCCcccc-------ccccccCCCCCccccccccccccCCCCCCCCeeeeeeCCC
Q 000595 726 DGDMIVDFCCGANDFSCLMKKKLD-ETGKNCLY-------KNYDILPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLNPP 797 (1401)
Q Consensus 726 ~gd~ivdfccg~n~fs~lmk~kl~-~~gk~c~~-------kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLnPP 797 (1401)
++++|+|++||.-.|+..+-++.. -+|.+.+- +|.....- ++..|...|..+..+. ..+..=++-+|||
T Consensus 173 ~~~~VLDl~cG~G~~sl~la~~~~~V~gvD~s~~av~~A~~n~~~~~l-~~v~~~~~D~~~~~~~--~~~~~D~Vv~dPP 249 (315)
T PRK03522 173 PPRSMWDLFCGVGGFGLHCATPGMQLTGIEISAEAIACAKQSAAELGL-TNVQFQALDSTQFATA--QGEVPDLVLVNPP 249 (315)
T ss_pred CCCEEEEccCCCCHHHHHHHhcCCEEEEEeCCHHHHHHHHHHHHHcCC-CceEEEEcCHHHHHHh--cCCCCeEEEECCC
Confidence 579999999999999987765321 11222211 12211111 2345666665443221 1122223446999
Q ss_pred ccchhhhHHHHHHhhhccCCcEEEEec
Q 000595 798 FGVKAGLANKFINKALEFNPKLLILIV 824 (1401)
Q Consensus 798 fg~~a~lAnkFi~kal~f~Pkliili~ 824 (1401)
++.+..+.+.-....+|+-||.|.
T Consensus 250 ---r~G~~~~~~~~l~~~~~~~ivyvs 273 (315)
T PRK03522 250 ---RRGIGKELCDYLSQMAPRFILYSS 273 (315)
T ss_pred ---CCCccHHHHHHHHHcCCCeEEEEE
Confidence 455667777777778888777653
No 52
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=86.70 E-value=0.87 Score=54.28 Aligned_cols=124 Identities=21% Similarity=0.307 Sum_probs=68.2
Q ss_pred HHHHHHhhcccc--cCCCcEEeccCCcchHHHHHHHHHhh-hCCccc-------cccccccCCCCCccccccccccccCC
Q 000595 713 LQAIVDKLHWYV--NDGDMIVDFCCGANDFSCLMKKKLDE-TGKNCL-------YKNYDILPAKNDFNFEKRDWMTVEPK 782 (1401)
Q Consensus 713 l~~i~~~Lh~yv--~~gd~ivdfccg~n~fs~lmk~kl~~-~gk~c~-------~kn~dl~~~kn~f~Fe~~dw~~v~~~ 782 (1401)
.+.+++.+.-++ .+|++|+|++||.-.|+..|-++... +|.+.+ -+|.....-+ +..|...||...-++
T Consensus 282 ~e~l~~~vl~~l~~~~~~~VLDlgcGtG~~sl~la~~~~~V~gvD~s~~al~~A~~n~~~~~~~-~v~~~~~d~~~~l~~ 360 (443)
T PRK13168 282 NQKMVARALEWLDPQPGDRVLDLFCGLGNFTLPLARQAAEVVGVEGVEAMVERARENARRNGLD-NVTFYHANLEEDFTD 360 (443)
T ss_pred HHHHHHHHHHHhcCCCCCEEEEEeccCCHHHHHHHHhCCEEEEEeCCHHHHHHHHHHHHHcCCC-ceEEEEeChHHhhhh
Confidence 344444444333 58899999999999999988654211 111111 1333322222 367888887653221
Q ss_pred -CCCCCCeeeeeeCCCccchhhhHHHHHHhhhccCCcEEEEec-CCcccccccc---CCCceee
Q 000595 783 -ELAPGSRLIMGLNPPFGVKAGLANKFINKALEFNPKLLILIV-PPETERLDRK---ESAYELV 841 (1401)
Q Consensus 783 -elp~G~~LimgLnPPfg~~a~lAnkFi~kal~f~Pkliili~-P~~t~rld~k---~~~Y~li 841 (1401)
.++.++.=++-+|||..- +.+.+......+|+-||.|. -|.|---|-+ ..+|.|.
T Consensus 361 ~~~~~~~fD~Vi~dPPr~g----~~~~~~~l~~~~~~~ivyvSCnp~tlaRDl~~L~~~gY~l~ 420 (443)
T PRK13168 361 QPWALGGFDKVLLDPPRAG----AAEVMQALAKLGPKRIVYVSCNPATLARDAGVLVEAGYRLK 420 (443)
T ss_pred hhhhcCCCCEEEECcCCcC----hHHHHHHHHhcCCCeEEEEEeChHHhhccHHHHhhCCcEEE
Confidence 122332223346999863 23556666666887777665 5555433432 2467664
No 53
>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=86.17 E-value=2.3 Score=46.92 Aligned_cols=99 Identities=23% Similarity=0.366 Sum_probs=56.7
Q ss_pred HHHhhcccc-----cCCCcEEeccCCcchHHHHHH--------------HHHhhhCCccccccccccCCCCCcccccccc
Q 000595 716 IVDKLHWYV-----NDGDMIVDFCCGANDFSCLMK--------------KKLDETGKNCLYKNYDILPAKNDFNFEKRDW 776 (1401)
Q Consensus 716 i~~~Lh~yv-----~~gd~ivdfccg~n~fs~lmk--------------~kl~~~gk~c~~kn~dl~~~kn~f~Fe~~dw 776 (1401)
++..+.|.+ ..|-+|+|++||.--|+.-.. +.++....+|.= + ..++.|...|=
T Consensus 30 ~Aa~il~~a~~~g~l~g~~V~DlG~GTG~La~ga~~lGa~~V~~vdiD~~a~ei~r~N~~~----l---~g~v~f~~~dv 102 (198)
T COG2263 30 LAAYILWVAYLRGDLEGKTVLDLGAGTGILAIGAALLGASRVLAVDIDPEALEIARANAEE----L---LGDVEFVVADV 102 (198)
T ss_pred HHHHHHHHHHHcCCcCCCEEEEcCCCcCHHHHHHHhcCCcEEEEEecCHHHHHHHHHHHHh----h---CCceEEEEcch
Confidence 666677766 345579999999999886432 112211111110 0 13444544443
Q ss_pred ccccCCCCCCCCeeeeeeCCCccchhhhH-HHHHHhhhccCCcEEEEecCCcc
Q 000595 777 MTVEPKELAPGSRLIMGLNPPFGVKAGLA-NKFINKALEFNPKLLILIVPPET 828 (1401)
Q Consensus 777 ~~v~~~elp~G~~LimgLnPPfg~~a~lA-nkFi~kal~f~Pkliili~P~~t 828 (1401)
-.+..+ -. ..| .|||||.+..=| ..|+++||+-. +.|--|---.+
T Consensus 103 ~~~~~~---~d-tvi--mNPPFG~~~rhaDr~Fl~~Ale~s-~vVYsiH~a~~ 148 (198)
T COG2263 103 SDFRGK---FD-TVI--MNPPFGSQRRHADRPFLLKALEIS-DVVYSIHKAGS 148 (198)
T ss_pred hhcCCc---cc-eEE--ECCCCccccccCCHHHHHHHHHhh-heEEEeecccc
Confidence 222222 11 233 399999986655 36999999998 77666654443
No 54
>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=85.24 E-value=1.4 Score=49.92 Aligned_cols=72 Identities=17% Similarity=0.241 Sum_probs=43.4
Q ss_pred cCCCcEEeccCCcchHHHHHHHHHh---hhCCcc-------ccccccccCCCCCccccccccccccCCCCCCCC-eeeee
Q 000595 725 NDGDMIVDFCCGANDFSCLMKKKLD---ETGKNC-------LYKNYDILPAKNDFNFEKRDWMTVEPKELAPGS-RLIMG 793 (1401)
Q Consensus 725 ~~gd~ivdfccg~n~fs~lmk~kl~---~~gk~c-------~~kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~-~Limg 793 (1401)
.++..|+|++||+--++..+.++.. -++.+. .-+|.....-.+...|...|+++. ++.+. -+|+.
T Consensus 120 ~~~~~vLDlG~GsG~i~~~la~~~~~~~v~avDis~~al~~A~~n~~~~~~~~~i~~~~~D~~~~----~~~~~fD~Iv~ 195 (284)
T TIGR03533 120 EPVKRILDLCTGSGCIAIACAYAFPEAEVDAVDISPDALAVAEINIERHGLEDRVTLIQSDLFAA----LPGRKYDLIVS 195 (284)
T ss_pred CCCCEEEEEeCchhHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEECchhhc----cCCCCccEEEE
Confidence 4567899999999999988876532 111111 123333222235677888888642 34333 35554
Q ss_pred eCCCccch
Q 000595 794 LNPPFGVK 801 (1401)
Q Consensus 794 LnPPfg~~ 801 (1401)
||||.-.
T Consensus 196 -NPPy~~~ 202 (284)
T TIGR03533 196 -NPPYVDA 202 (284)
T ss_pred -CCCCCCc
Confidence 9999643
No 55
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=84.37 E-value=0.69 Score=60.72 Aligned_cols=58 Identities=29% Similarity=0.606 Sum_probs=40.4
Q ss_pred cccccCCCCCCCCCCCceeecccCCccccccCCCCCcccccccccccccccccc---ccCCCc--eeEeccCCc
Q 000595 355 KCCICKQGENKADSDLQFAVCRRCPKAYHRKCLPRKIAFEDKLEEGIITRAWEG---LLPNHR--ILIYCLKHE 423 (1401)
Q Consensus 355 ~C~vCkqseDkn~segKLI~CdRCPkAYH~kCLPPpIsfe~~~~EgIp~RAW~c---LLpncR--iLIyCpkHe 423 (1401)
+|.+|...+-.+ ...++.|+.|..++|.+|.- +. -|+.+.|.| +....+ .|+.||.+.
T Consensus 221 ~C~iC~~~~~~n--~n~ivfCD~Cnl~VHq~Cyg--i~-------~ipeg~WlCr~Cl~s~~~~v~c~~cp~~~ 283 (1051)
T KOG0955|consen 221 VCCICLDGECQN--SNVIVFCDGCNLAVHQECYG--IP-------FIPEGQWLCRRCLQSPQRPVRCLLCPSKG 283 (1051)
T ss_pred cceeecccccCC--CceEEEcCCCcchhhhhccC--CC-------CCCCCcEeehhhccCcCcccceEeccCCC
Confidence 599999876432 23699999999999999987 32 367789987 222112 266677663
No 56
>PF07669 Eco57I: Eco57I restriction-modification methylase; InterPro: IPR011639 This entry contains restriction modification methylases, which in the case of endonuclease Eco57I is found adjacent to the DNA cleavage domain, which recognises asymmetric DNA sequence 5'-CTGAAG [, ]. The methylase causes specific methylation on A-5 on one strand, the other strand being methylated by the Eco57IB methylase []. ; GO: 0003677 DNA binding, 0003824 catalytic activity, 0006304 DNA modification
Probab=84.32 E-value=0.84 Score=44.71 Aligned_cols=39 Identities=31% Similarity=0.498 Sum_probs=30.8
Q ss_pred eeeeeCCCccchhhhH-------------HHHHHhhhccCCcEEEEecCCccc
Q 000595 790 LIMGLNPPFGVKAGLA-------------NKFINKALEFNPKLLILIVPPETE 829 (1401)
Q Consensus 790 LimgLnPPfg~~a~lA-------------nkFi~kal~f~Pkliili~P~~t~ 829 (1401)
+|+| |||++....+. .-||.+|++.-.-.+.+|+|...=
T Consensus 5 ~VIG-NPPY~~~~~~~~~~~~~~~~~dlY~~Fie~~~~ll~G~~~~I~P~~~l 56 (106)
T PF07669_consen 5 VVIG-NPPYIKIKSLSKKKKKKKKKSDLYILFIEKSLNLLNGYLSFITPNSFL 56 (106)
T ss_pred EEEE-CCCChhhccccchhhcccccCcHHHHHHHHHHHHhCCeEEEEeChHHh
Confidence 8999 99998765322 129999988888999999997654
No 57
>PHA03411 putative methyltransferase; Provisional
Probab=83.97 E-value=0.73 Score=52.93 Aligned_cols=40 Identities=20% Similarity=0.253 Sum_probs=30.5
Q ss_pred cCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHH
Q 000595 703 FGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKK 746 (1401)
Q Consensus 703 ~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~ 746 (1401)
.|-+||-..-+..++ +....+.+|+|++||...|+.++-+
T Consensus 45 ~G~FfTP~~i~~~f~----~~~~~~grVLDLGcGsGilsl~la~ 84 (279)
T PHA03411 45 SGAFFTPEGLAWDFT----IDAHCTGKVLDLCAGIGRLSFCMLH 84 (279)
T ss_pred ceeEcCCHHHHHHHH----hccccCCeEEEcCCCCCHHHHHHHH
Confidence 499999877765543 2344678999999999999887754
No 58
>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=83.73 E-value=2.1 Score=45.93 Aligned_cols=70 Identities=24% Similarity=0.441 Sum_probs=41.0
Q ss_pred ccCCCcEEeccCCcchHHHHHHHHHhhhCCccccccccccC-------------CCCCccccccccccccCCCCCCCC-e
Q 000595 724 VNDGDMIVDFCCGANDFSCLMKKKLDETGKNCLYKNYDILP-------------AKNDFNFEKRDWMTVEPKELAPGS-R 789 (1401)
Q Consensus 724 v~~gd~ivdfccg~n~fs~lmk~kl~~~gk~c~~kn~dl~~-------------~kn~f~Fe~~dw~~v~~~elp~G~-~ 789 (1401)
-..+.+|+|++||...|...+.+.+. .+.+--.|+-+ .-++..|...|+.+. ++.++ -
T Consensus 85 ~~~~~~ilDig~G~G~~~~~l~~~~~----~~~v~~iD~~~~~~~~a~~~~~~~~~~~~~~~~~d~~~~----~~~~~fD 156 (251)
T TIGR03534 85 KKGPLRVLDLGTGSGAIALALAKERP----DARVTAVDISPEALAVARKNAARLGLDNVTFLQSDWFEP----LPGGKFD 156 (251)
T ss_pred ccCCCeEEEEeCcHhHHHHHHHHHCC----CCEEEEEECCHHHHHHHHHHHHHcCCCeEEEEECchhcc----CcCCcee
Confidence 34556899999999999888876432 12222222110 011366777777652 33343 3
Q ss_pred eeeeeCCCccchh
Q 000595 790 LIMGLNPPFGVKA 802 (1401)
Q Consensus 790 LimgLnPPfg~~a 802 (1401)
+|+. ||||....
T Consensus 157 ~Vi~-npPy~~~~ 168 (251)
T TIGR03534 157 LIVS-NPPYIPEA 168 (251)
T ss_pred EEEE-CCCCCchh
Confidence 5555 99998543
No 59
>COG2265 TrmA SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=83.43 E-value=1.9 Score=52.15 Aligned_cols=116 Identities=19% Similarity=0.449 Sum_probs=77.9
Q ss_pred cccccccCcccchh--hhHHHHHHhhccccc--CCCcEEeccCCcchHHHHHHHH-------------HhhhCCcc---c
Q 000595 697 GMRYTSFGRHFTKV--DKLQAIVDKLHWYVN--DGDMIVDFCCGANDFSCLMKKK-------------LDETGKNC---L 756 (1401)
Q Consensus 697 G~ryts~grhftk~--ekl~~i~~~Lh~yv~--~gd~ivdfccg~n~fs~lmk~k-------------l~~~gk~c---~ 756 (1401)
|..|.=..|.|+++ +-.+.+++...-+++ .+|+++|+.||.-.|+-.|-++ .++...+. .
T Consensus 260 ~~~~~~~~~sF~Q~N~~~~ekl~~~a~~~~~~~~~~~vlDlYCGvG~f~l~lA~~~~~V~gvEi~~~aV~~A~~NA~~n~ 339 (432)
T COG2265 260 GVSFQISPRSFFQVNPAVAEKLYETALEWLELAGGERVLDLYCGVGTFGLPLAKRVKKVHGVEISPEAVEAAQENAAANG 339 (432)
T ss_pred ceEEEeCCCCceecCHHHHHHHHHHHHHHHhhcCCCEEEEeccCCChhhhhhcccCCEEEEEecCHHHHHHHHHHHHHcC
Confidence 56677778899865 344555555555566 5789999999999999887632 22222222 2
Q ss_pred cccccccCCCCCccccccccccccCCCCCCCCeeeeeeCCCccchhhhHHHHHHhhhccCCcEEEEec
Q 000595 757 YKNYDILPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLNPPFGVKAGLANKFINKALEFNPKLLILIV 824 (1401)
Q Consensus 757 ~kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLnPPfg~~a~lAnkFi~kal~f~Pkliili~ 824 (1401)
..| --|..-..+.|..+-|..-.|+ +|+ ++|| ++-+...|++..++++|+-||-|.
T Consensus 340 i~N-~~f~~~~ae~~~~~~~~~~~~d-------~Vv-vDPP---R~G~~~~~lk~l~~~~p~~IvYVS 395 (432)
T COG2265 340 IDN-VEFIAGDAEEFTPAWWEGYKPD-------VVV-VDPP---RAGADREVLKQLAKLKPKRIVYVS 395 (432)
T ss_pred CCc-EEEEeCCHHHHhhhccccCCCC-------EEE-ECCC---CCCCCHHHHHHHHhcCCCcEEEEe
Confidence 334 3444555666666656333333 444 5999 567899999999999999998885
No 60
>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]
Probab=83.33 E-value=1.3 Score=49.69 Aligned_cols=58 Identities=26% Similarity=0.441 Sum_probs=47.4
Q ss_pred hhHhHHHHHhhccccccccccccccccccCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHH
Q 000595 675 EVLSQIFKWKNKLKVYLAPFLHGMRYTSFGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 675 ~vl~ql~~wk~kL~vylaP~l~G~ryts~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~k 747 (1401)
++-.++.++.|... +--|||.|.+-...|.+....- +|+.|+|.|||.-|+..++.+.
T Consensus 15 ~vF~~ia~~YD~~n----------~~~S~g~~~~Wr~~~i~~~~~~-----~g~~vLDva~GTGd~a~~~~k~ 72 (238)
T COG2226 15 KVFDKVAKKYDLMN----------DLMSFGLHRLWRRALISLLGIK-----PGDKVLDVACGTGDMALLLAKS 72 (238)
T ss_pred HHHHhhHHHHHhhc----------ccccCcchHHHHHHHHHhhCCC-----CCCEEEEecCCccHHHHHHHHh
Confidence 56778888988875 4459999999998887654332 9999999999999999998773
No 61
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=82.70 E-value=0.49 Score=57.40 Aligned_cols=49 Identities=24% Similarity=0.612 Sum_probs=34.8
Q ss_pred CCccccccCCCC---ceeeccccccccccCccccCcccccccCCCChhhhhc-cCccccccc
Q 000595 226 FDSVCSFCDNGG---DLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEA-MLNFFCKNC 283 (1401)
Q Consensus 226 ~DdVCaIC~dGG---eLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~-~~sW~C~nC 283 (1401)
...-|.||.+.- -|+.|| .|...||+- |+++.+|..+... .-.|.|.+|
T Consensus 543 ~~ysCgiCkks~dQHll~~CD-tC~lhYHlG--------CL~PPLTR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 543 MNYSCGICKKSTDQHLLTQCD-TCHLHYHLG--------CLSPPLTRLPKKNKNFGWQCSEC 595 (707)
T ss_pred cceeeeeeccchhhHHHhhcc-hhhceeecc--------ccCCccccCcccccCcceeeccc
Confidence 345699999864 489999 799999999 5556676544322 346876655
No 62
>PRK11805 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=82.59 E-value=2.2 Score=49.05 Aligned_cols=69 Identities=17% Similarity=0.257 Sum_probs=41.0
Q ss_pred CcEEeccCCcchHHHHHHHHHh---hhCCccc-------cccccccCCCCCccccccccccccCCCCCCCC-eeeeeeCC
Q 000595 728 DMIVDFCCGANDFSCLMKKKLD---ETGKNCL-------YKNYDILPAKNDFNFEKRDWMTVEPKELAPGS-RLIMGLNP 796 (1401)
Q Consensus 728 d~ivdfccg~n~fs~lmk~kl~---~~gk~c~-------~kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~-~LimgLnP 796 (1401)
.+|+|+|||+-.++..+.++.. -++.+.+ =+|.....-.+...|...||.+. +|.++ -+|+. ||
T Consensus 135 ~~VLDlG~GsG~iai~la~~~p~~~V~avDis~~al~~A~~n~~~~~l~~~i~~~~~D~~~~----l~~~~fDlIvs-NP 209 (307)
T PRK11805 135 TRILDLCTGSGCIAIACAYAFPDAEVDAVDISPDALAVAEINIERHGLEDRVTLIESDLFAA----LPGRRYDLIVS-NP 209 (307)
T ss_pred CEEEEEechhhHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHHHHHhCCCCcEEEEECchhhh----CCCCCccEEEE-CC
Confidence 7899999999999988866431 1111111 12322222234577888888653 33333 36665 99
Q ss_pred Cccch
Q 000595 797 PFGVK 801 (1401)
Q Consensus 797 Pfg~~ 801 (1401)
||--.
T Consensus 210 Pyi~~ 214 (307)
T PRK11805 210 PYVDA 214 (307)
T ss_pred CCCCc
Confidence 99643
No 63
>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional
Probab=82.23 E-value=7.6 Score=42.24 Aligned_cols=65 Identities=22% Similarity=0.253 Sum_probs=44.4
Q ss_pred hhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhhhCCccccccccccC--CCCCcccccccccc
Q 000595 710 VDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDETGKNCLYKNYDILP--AKNDFNFEKRDWMT 778 (1401)
Q Consensus 710 ~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~~gk~c~~kn~dl~~--~kn~f~Fe~~dw~~ 778 (1401)
..||.+|.+++. ++.+|++|||++||.-.|+..+-++ .+..+..--.|+-+ +..+..|-.-|..+
T Consensus 36 ~~kl~~~~~~~~-~~~~~~~VLDlG~GtG~~t~~l~~~---~~~~~~V~aVDi~~~~~~~~v~~i~~D~~~ 102 (209)
T PRK11188 36 WFKLDEIQQSDK-LFKPGMTVVDLGAAPGGWSQYAVTQ---IGDKGRVIACDILPMDPIVGVDFLQGDFRD 102 (209)
T ss_pred HHhhHHHHHHhc-cCCCCCEEEEEcccCCHHHHHHHHH---cCCCceEEEEecccccCCCCcEEEecCCCC
Confidence 457888888865 6789999999999999999987553 34445555555543 11234555556554
No 64
>PRK14967 putative methyltransferase; Provisional
Probab=81.12 E-value=5.3 Score=43.21 Aligned_cols=34 Identities=15% Similarity=0.322 Sum_probs=26.3
Q ss_pred hhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHH
Q 000595 711 DKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKK 746 (1401)
Q Consensus 711 ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~ 746 (1401)
+.|.+++.++ .+.+|++|+|++||.--|+..+.+
T Consensus 23 ~~l~~~l~~~--~~~~~~~vLDlGcG~G~~~~~la~ 56 (223)
T PRK14967 23 QLLADALAAE--GLGPGRRVLDLCTGSGALAVAAAA 56 (223)
T ss_pred HHHHHHHHhc--ccCCCCeEEEecCCHHHHHHHHHH
Confidence 4455666554 368899999999999999888765
No 65
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=80.89 E-value=0.83 Score=42.78 Aligned_cols=34 Identities=26% Similarity=0.617 Sum_probs=28.6
Q ss_pred cccccccCCC-CCCCCCCCCeeeecCCCCCCCCCccccccccc
Q 000595 287 QHQCFACGKL-GSSDKETGAEVFPCVSATCGHFYHPHCVSKLL 328 (1401)
Q Consensus 287 QHqCFVCGkl-GSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~ 328 (1401)
...|.+|++. | -.+.|....|.+.||+.|.....
T Consensus 36 ~~~C~~C~~~~G--------a~i~C~~~~C~~~fH~~CA~~~~ 70 (90)
T PF13771_consen 36 KLKCSICKKKGG--------ACIGCSHPGCSRSFHVPCARKAG 70 (90)
T ss_pred CCCCcCCCCCCC--------eEEEEeCCCCCcEEChHHHccCC
Confidence 3579999987 4 47999999999999999998653
No 66
>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=78.55 E-value=0.71 Score=50.45 Aligned_cols=101 Identities=27% Similarity=0.366 Sum_probs=49.0
Q ss_pred hccccccccccccccccccCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhhhCCccccc------
Q 000595 685 NKLKVYLAPFLHGMRYTSFGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDETGKNCLYK------ 758 (1401)
Q Consensus 685 ~kL~vylaP~l~G~ryts~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~~gk~c~~k------ 758 (1401)
|--|||.+|-|-+.|- ||-=.|.+|++|+|++||-.-|+-.+-+. ++.+..-
T Consensus 78 D~~kvyfs~rl~~Er~------------------Ri~~~v~~~e~VlD~faGIG~f~l~~ak~----~~~~~V~A~d~Np 135 (200)
T PF02475_consen 78 DLSKVYFSPRLSTERR------------------RIANLVKPGEVVLDMFAGIGPFSLPIAKH----GKAKRVYAVDLNP 135 (200)
T ss_dssp ETTTS---GGGHHHHH------------------HHHTC--TT-EEEETT-TTTTTHHHHHHH----T-SSEEEEEES-H
T ss_pred ccceEEEccccHHHHH------------------HHHhcCCcceEEEEccCCccHHHHHHhhh----cCccEEEEecCCH
Confidence 3346677776655532 33345999999999999999999988551 2333221
Q ss_pred --------cccccCCCCCccccccccccccCCCCCCCCeeeeeeCCCccchhhhHHHHHHhhhccC
Q 000595 759 --------NYDILPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLNPPFGVKAGLANKFINKALEFN 816 (1401)
Q Consensus 759 --------n~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLnPPfg~~a~lAnkFi~kal~f~ 816 (1401)
|-.+=.-++....-.-|..++-+ -..-+.+|||| |+. |..|++.|+...
T Consensus 136 ~a~~~L~~Ni~lNkv~~~i~~~~~D~~~~~~--~~~~drvim~l-p~~------~~~fl~~~~~~~ 192 (200)
T PF02475_consen 136 DAVEYLKENIRLNKVENRIEVINGDAREFLP--EGKFDRVIMNL-PES------SLEFLDAALSLL 192 (200)
T ss_dssp HHHHHHHHHHHHTT-TTTEEEEES-GGG-----TT-EEEEEE---TSS------GGGGHHHHHHHE
T ss_pred HHHHHHHHHHHHcCCCCeEEEEcCCHHHhcC--ccccCEEEECC-hHH------HHHHHHHHHHHh
Confidence 11111112333233334433333 23346899995 664 457888887654
No 67
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=76.70 E-value=1.5 Score=49.85 Aligned_cols=35 Identities=23% Similarity=0.574 Sum_probs=28.0
Q ss_pred CeeeecCCCCCC-CCCcccccccccccchHHHHHHHhHhhccCCceeCCCC
Q 000595 305 AEVFPCVSATCG-HFYHPHCVSKLLLRDDEVAADQLAKSIIAGESFTCPLH 354 (1401)
Q Consensus 305 aEVfrCsvasCG-RFYHpkCLa~l~~pvde~~ateLekkIaaGksFrCPlH 354 (1401)
++++-|+.++|. -|||..||..-..| ...|+||.|
T Consensus 232 GqMVaCDn~nCkrEWFH~~CVGLk~pP---------------KG~WYC~eC 267 (271)
T COG5034 232 GQMVACDNANCKREWFHLECVGLKEPP---------------KGKWYCPEC 267 (271)
T ss_pred ccceecCCCCCchhheeccccccCCCC---------------CCcEeCHHh
Confidence 589999999996 79999999965322 357999865
No 68
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=76.66 E-value=5.4 Score=45.68 Aligned_cols=116 Identities=20% Similarity=0.340 Sum_probs=73.2
Q ss_pred cccCcccchhhh-HHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhh-----hCCcc---------ccccccccCC
Q 000595 701 TSFGRHFTKVDK-LQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDE-----TGKNC---------LYKNYDILPA 765 (1401)
Q Consensus 701 ts~grhftk~ek-l~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~-----~gk~c---------~~kn~dl~~~ 765 (1401)
-+||.||..-.. +..||+... ++++|+||+.-+|--.+-.-|-++... ....+ .+.|+.||+
T Consensus 6 K~~GQnFL~d~~v~~kIv~~a~--~~~~d~VlEIGpG~GaLT~~Ll~~~~~v~aiEiD~~l~~~L~~~~~~~~n~~vi~- 82 (259)
T COG0030 6 KRLGQNFLIDKNVIDKIVEAAN--ISPGDNVLEIGPGLGALTEPLLERAARVTAIEIDRRLAEVLKERFAPYDNLTVIN- 82 (259)
T ss_pred CCcccccccCHHHHHHHHHhcC--CCCCCeEEEECCCCCHHHHHHHhhcCeEEEEEeCHHHHHHHHHhcccccceEEEe-
Confidence 479999976544 677888765 567999999999999887665432211 00000 356666664
Q ss_pred CCCccccccccccccCCCCCCCCeeeeeeCCCccchhhhHHHHHHhhhccCCc--EEEEecCCc-cccccc
Q 000595 766 KNDFNFEKRDWMTVEPKELAPGSRLIMGLNPPFGVKAGLANKFINKALEFNPK--LLILIVPPE-TERLDR 833 (1401)
Q Consensus 766 kn~f~Fe~~dw~~v~~~elp~G~~LimgLnPPfg~~a~lAnkFi~kal~f~Pk--liili~P~~-t~rld~ 833 (1401)
.|-|.++..+|- +...|+| |.||. .+..+|-|.|+..+. -.++.+=.| .+||=.
T Consensus 83 --------~DaLk~d~~~l~-~~~~vVa-NlPY~----Isspii~kll~~~~~~~~~v~M~QkEva~Rl~A 139 (259)
T COG0030 83 --------GDALKFDFPSLA-QPYKVVA-NLPYN----ISSPILFKLLEEKFIIQDMVLMVQKEVAERLVA 139 (259)
T ss_pred --------CchhcCcchhhc-CCCEEEE-cCCCc----ccHHHHHHHHhccCccceEEEEeHHHHHHHHhC
Confidence 444555555554 6668888 99999 566666666666654 444444333 344433
No 69
>TIGR00095 RNA methyltransferase, RsmD family. This model represents a family of uncharacterized bacterial proteins. Members are present in nearly every complete bacterial genome, always in a single copy. PSI-BLAST analysis shows homology to several families of SAM-dependent methyltransferases, including ribosomal RNA adenine dimethylases.
Probab=75.84 E-value=8.8 Score=41.25 Aligned_cols=107 Identities=14% Similarity=0.147 Sum_probs=55.1
Q ss_pred HHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHh--hhCCccc-------cccccccCCCCCccccccccccccCCC
Q 000595 713 LQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLD--ETGKNCL-------YKNYDILPAKNDFNFEKRDWMTVEPKE 783 (1401)
Q Consensus 713 l~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~--~~gk~c~-------~kn~dl~~~kn~f~Fe~~dw~~v~~~e 783 (1401)
++.+...|.-++ .|..|+|++||+..|+-..-.+.. -+..+.. -+|.....-.+...|.+.|-+..-. .
T Consensus 37 rea~f~~l~~~~-~g~~vLDLfaGsG~lglea~srga~~v~~vE~~~~a~~~~~~N~~~~~~~~~~~~~~~D~~~~l~-~ 114 (189)
T TIGR00095 37 RELFFNILRPEI-QGAHLLDVFAGSGLLGEEALSRGAKVAFLEEDDRKANQTLKENLALLKSGEQAEVVRNSALRALK-F 114 (189)
T ss_pred HHHHHHHHHHhc-CCCEEEEecCCCcHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHhCCcccEEEEehhHHHHHH-H
Confidence 444666665444 488999999999999877644321 1111111 2444444322334455555433211 1
Q ss_pred CC-CCC-eeeeeeCCCccchhhhHHHHHH---hhhccCCcEEEEe
Q 000595 784 LA-PGS-RLIMGLNPPFGVKAGLANKFIN---KALEFNPKLLILI 823 (1401)
Q Consensus 784 lp-~G~-~LimgLnPPfg~~a~lAnkFi~---kal~f~Pkliili 823 (1401)
+. .+. -.|+=++|||+... -.+-+. +.--.++.-||++
T Consensus 115 ~~~~~~~~dvv~~DPPy~~~~--~~~~l~~l~~~~~l~~~~iiv~ 157 (189)
T TIGR00095 115 LAKKPTFDNVIYLDPPFFNGA--LQALLELCENNWILEDTVLIVV 157 (189)
T ss_pred hhccCCCceEEEECcCCCCCc--HHHHHHHHHHCCCCCCCeEEEE
Confidence 21 222 47777899998532 222222 2222566766655
No 70
>TIGR03704 PrmC_rel_meth putative protein-(glutamine-N5) methyltransferase, unknown substrate-specific. This protein family is closely related to two different families of protein-(glutamine-N5) methyltransferase. The first is PrmB, which modifies ribosomal protein L3 in some bacteria. The second is PrmC (HemK), which modifies peptide chain release factors 1 and 2 in most bacteria and also in eukaryotes. The glutamine side chain-binding motif NPPY shared by PrmB and PrmC is N[VAT]PY in this family. The protein substrate is unknown.
Probab=75.14 E-value=1.9 Score=48.07 Aligned_cols=68 Identities=22% Similarity=0.361 Sum_probs=38.6
Q ss_pred CCcEEeccCCcchHHHHHHHHHh---hhCCccc-------cccccccCCCCCccccccccccccCCCCCCCCeeeeeeCC
Q 000595 727 GDMIVDFCCGANDFSCLMKKKLD---ETGKNCL-------YKNYDILPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLNP 796 (1401)
Q Consensus 727 gd~ivdfccg~n~fs~lmk~kl~---~~gk~c~-------~kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLnP 796 (1401)
+..|+|+|||+--|+..+.++.. -++.+.+ -+|... |...|...||...-++.+. +..=++-+||
T Consensus 87 ~~~vLDlg~GsG~i~l~la~~~~~~~v~~vDis~~al~~A~~N~~~----~~~~~~~~D~~~~l~~~~~-~~fDlVv~NP 161 (251)
T TIGR03704 87 TLVVVDLCCGSGAVGAALAAALDGIELHAADIDPAAVRCARRNLAD----AGGTVHEGDLYDALPTALR-GRVDILAANA 161 (251)
T ss_pred CCEEEEecCchHHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHH----cCCEEEEeechhhcchhcC-CCEeEEEECC
Confidence 35799999999999988765432 1122211 233322 2246777888764443332 3322344599
Q ss_pred Ccc
Q 000595 797 PFG 799 (1401)
Q Consensus 797 Pfg 799 (1401)
||-
T Consensus 162 Py~ 164 (251)
T TIGR03704 162 PYV 164 (251)
T ss_pred CCC
Confidence 985
No 71
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=75.08 E-value=1.1 Score=56.19 Aligned_cols=41 Identities=24% Similarity=0.689 Sum_probs=28.4
Q ss_pred ccccCCccccccCCC--------Cceeecc-ccccccccCccccCccccc
Q 000595 222 EDELFDSVCSFCDNG--------GDLLCCE-GRCLRSFHATIDAGEESHC 262 (1401)
Q Consensus 222 ~dDl~DdVCaIC~dG--------GeLLCCD-G~C~RSFH~~CldGeeS~C 262 (1401)
-.|.+...|.||+.- |.-+.|. -.|.++||.+|+.-.+..|
T Consensus 112 P~dRfnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLC 161 (900)
T KOG0956|consen 112 PHDRFNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLC 161 (900)
T ss_pred chhhhcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccce
Confidence 355678899999864 3345555 4699999999876444333
No 72
>PRK05785 hypothetical protein; Provisional
Probab=74.83 E-value=3.7 Score=44.97 Aligned_cols=59 Identities=20% Similarity=0.324 Sum_probs=41.4
Q ss_pred hHhHHHHHhhccccccccccccccccccCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHH
Q 000595 676 VLSQIFKWKNKLKVYLAPFLHGMRYTSFGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 676 vl~ql~~wk~kL~vylaP~l~G~ryts~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~k 747 (1401)
.-+.+..+.|.+. +..|||++--- -+++++.|..+..++.+|+|++||..++...+.++
T Consensus 14 ~f~~iA~~YD~~n----------~~~s~g~~~~w---r~~~~~~l~~~~~~~~~VLDlGcGtG~~~~~l~~~ 72 (226)
T PRK05785 14 AYNKIPKAYDRAN----------RFISFNQDVRW---RAELVKTILKYCGRPKKVLDVAAGKGELSYHFKKV 72 (226)
T ss_pred HHHhhhHHHHHhh----------hhccCCCcHHH---HHHHHHHHHHhcCCCCeEEEEcCCCCHHHHHHHHh
Confidence 4455566666543 45677877322 23566666667677999999999999999998776
No 73
>PRK05031 tRNA (uracil-5-)-methyltransferase; Validated
Probab=73.39 E-value=4.5 Score=47.44 Aligned_cols=115 Identities=12% Similarity=0.215 Sum_probs=61.8
Q ss_pred hhhhHHHHHHhhcccccC-CCcEEeccCCcchHHHHHHHHHhh-hCC-------ccccccccccCCCCCccccccccccc
Q 000595 709 KVDKLQAIVDKLHWYVND-GDMIVDFCCGANDFSCLMKKKLDE-TGK-------NCLYKNYDILPAKNDFNFEKRDWMTV 779 (1401)
Q Consensus 709 k~ekl~~i~~~Lh~yv~~-gd~ivdfccg~n~fs~lmk~kl~~-~gk-------~c~~kn~dl~~~kn~f~Fe~~dw~~v 779 (1401)
+.+-.+.+++.+.-+++. +..|+|++||...|+..+.++... +|. .+.=+|..+..- ++..|...|..+.
T Consensus 188 N~~~~e~l~~~v~~~~~~~~~~vLDl~~G~G~~sl~la~~~~~v~~vE~~~~ai~~a~~N~~~~~~-~~v~~~~~d~~~~ 266 (362)
T PRK05031 188 NAAVNEKMLEWALDATKGSKGDLLELYCGNGNFTLALARNFRRVLATEISKPSVAAAQYNIAANGI-DNVQIIRMSAEEF 266 (362)
T ss_pred CHHHHHHHHHHHHHHhhcCCCeEEEEeccccHHHHHHHhhCCEEEEEECCHHHHHHHHHHHHHhCC-CcEEEEECCHHHH
Confidence 344566677776666653 457999999999999888764220 000 111133222211 1344555554432
Q ss_pred cCC-----CC--CC-----C-CeeeeeeCCCccchhhhHHHHHHhhhccCCcEEEEecCCcc
Q 000595 780 EPK-----EL--AP-----G-SRLIMGLNPPFGVKAGLANKFINKALEFNPKLLILIVPPET 828 (1401)
Q Consensus 780 ~~~-----el--p~-----G-~~LimgLnPPfg~~a~lAnkFi~kal~f~Pkliili~P~~t 828 (1401)
-++ ++ +. + ..=++-|+||. +.+..+.|...++. .++|++=.-|.|
T Consensus 267 l~~~~~~~~~~~~~~~~~~~~~~D~v~lDPPR---~G~~~~~l~~l~~~-~~ivyvSC~p~t 324 (362)
T PRK05031 267 TQAMNGVREFNRLKGIDLKSYNFSTIFVDPPR---AGLDDETLKLVQAY-ERILYISCNPET 324 (362)
T ss_pred HHHHhhcccccccccccccCCCCCEEEECCCC---CCCcHHHHHHHHcc-CCEEEEEeCHHH
Confidence 111 00 01 1 11255579995 67889998888773 355544444444
No 74
>COG2520 Predicted methyltransferase [General function prediction only]
Probab=72.51 E-value=1.6 Score=51.40 Aligned_cols=102 Identities=30% Similarity=0.404 Sum_probs=58.6
Q ss_pred ccccccccccccccccCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhhh----CCc-----cccc
Q 000595 688 KVYLAPFLHGMRYTSFGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDET----GKN-----CLYK 758 (1401)
Q Consensus 688 ~vylaP~l~G~ryts~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~~----gk~-----c~~k 758 (1401)
|||.+|=|.+.|. |+-=.|.+|++|||+-+|---||-.+-++-... .++ +.=+
T Consensus 168 Kv~Fsprl~~ER~------------------Rva~~v~~GE~V~DmFAGVGpfsi~~Ak~g~~~V~A~diNP~A~~~L~e 229 (341)
T COG2520 168 KVYFSPRLSTERA------------------RVAELVKEGETVLDMFAGVGPFSIPIAKKGRPKVYAIDINPDAVEYLKE 229 (341)
T ss_pred HeEECCCchHHHH------------------HHHhhhcCCCEEEEccCCcccchhhhhhcCCceEEEEecCHHHHHHHHH
Confidence 4666666666654 444557789999999999999998876643331 111 1112
Q ss_pred cccccCCCCCccccccccccccCCCCCCCCeeeeeeCCCccchhhhHHHHHHhhhcc
Q 000595 759 NYDILPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLNPPFGVKAGLANKFINKALEF 815 (1401)
Q Consensus 759 n~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLnPPfg~~a~lAnkFi~kal~f 815 (1401)
|--|=.-++....---|=-.| +.+++..+.+||| +|+ .|-+|+..|++.
T Consensus 230 Ni~LN~v~~~v~~i~gD~rev-~~~~~~aDrIim~-~p~------~a~~fl~~A~~~ 278 (341)
T COG2520 230 NIRLNKVEGRVEPILGDAREV-APELGVADRIIMG-LPK------SAHEFLPLALEL 278 (341)
T ss_pred HHHhcCccceeeEEeccHHHh-hhccccCCEEEeC-CCC------cchhhHHHHHHH
Confidence 222211112111111111111 1223778999999 555 678999999864
No 75
>PLN02672 methionine S-methyltransferase
Probab=71.77 E-value=10 Score=50.77 Aligned_cols=165 Identities=15% Similarity=0.162 Sum_probs=87.9
Q ss_pred chHHHHHhhccCCccccccccchhhhHhHhhHHHHHHHHhhhcCCCChHHHhhhcChhhHhHHHHHh------------h
Q 000595 618 VRMEEILKRHKIPSTHAYASKSAVDKAITLGKAIRTALKKLDVDGSSIEDAKAVCEPEVLSQIFKWK------------N 685 (1401)
Q Consensus 618 ~t~~~~~k~~~~~st~~~~~~~~~~k~it~gkAvr~AL~kLe~~g~siedAkAvc~p~vl~ql~~wk------------~ 685 (1401)
-++++|...|+..--.+| -|+|..|++|+ +-.+.-+|.+.- ..|...+.=+ .
T Consensus 6 ~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~-~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~ 69 (1082)
T PLN02672 6 AEVDEFLDQCKQSGDAAY-------------GAFKGVLERLE-DPTTRSDARKLL--SAVEKRVAASEAGEDCFATYHFR 69 (1082)
T ss_pred HHHHHHHHHhhcCcHHHH-------------HHHHHHHHHhc-CccccHHHHHHH--HHHHHHhcccCcccchhhhcceE
Confidence 356677777773322222 16677788887 666666665543 1222222211 0
Q ss_pred ccccccccccccccccccCcccc----------hhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhh---hC
Q 000595 686 KLKVYLAPFLHGMRYTSFGRHFT----------KVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDE---TG 752 (1401)
Q Consensus 686 kL~vylaP~l~G~ryts~grhft----------k~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~---~g 752 (1401)
-=.|+|.|.- |.++ =||+-|. -.|.|.+..++...-.-.|.+|+|+|||+--.+..+.++... ++
T Consensus 70 ~~~~~~~~~~-G~~~-F~~l~~~V~p~VLIPRpeTE~lve~L~~~~~~~~~~~~VLDlG~GSG~Iai~La~~~~~~~v~a 147 (1082)
T PLN02672 70 IHDLVLDDYE-GFRN-RKKLTMMEIPSIFIPEDWSFTFYEGLNRHPDSIFRDKTVAELGCGNGWISIAIAEKWLPSKVYG 147 (1082)
T ss_pred EeeEEEcCCC-CeEE-ecCCceeeCCCcccCchhHHHHHHHHHhcccccCCCCEEEEEecchHHHHHHHHHHCCCCEEEE
Confidence 1146788765 6553 4566553 123343333322111113568999999999999988775431 11
Q ss_pred Ccc-------cccccccc---------------CCCCCccccccccccccCCCCCCCCeeeeeeCCCccchh
Q 000595 753 KNC-------LYKNYDIL---------------PAKNDFNFEKRDWMTVEPKELAPGSRLIMGLNPPFGVKA 802 (1401)
Q Consensus 753 k~c-------~~kn~dl~---------------~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLnPPfg~~a 802 (1401)
.+. --+|-.+- ...+...|...||++.-+. ...-=-||++ |||+=..+
T Consensus 148 vDis~~Al~~A~~Na~~n~l~~~~~~~~~~~~~~l~~rV~f~~sDl~~~~~~-~~~~fDlIVS-NPPYI~~~ 217 (1082)
T PLN02672 148 LDINPRAVKVAWINLYLNALDDDGLPVYDGEGKTLLDRVEFYESDLLGYCRD-NNIELDRIVG-CIPQILNP 217 (1082)
T ss_pred EECCHHHHHHHHHHHHHcCcccccccccccccccccccEEEEECchhhhccc-cCCceEEEEE-CCCcCCCc
Confidence 111 12333221 0124689999999864321 1001248888 99986544
No 76
>TIGR02143 trmA_only tRNA (uracil-5-)-methyltransferase. This family consists exclusively of proteins believed to act as tRNA (uracil-5-)-methyltransferase. All members of far are proteobacterial. The seed alignment was taken directly from pfam05958 in Pfam 12.0, but higher cutoffs are used to select only functionally equivalent proteins. Homologous proteins excluded by the higher cutoff scores of this model include other uracil methyltransferases, such as RumA, active on rRNA.
Probab=71.64 E-value=3.9 Score=47.90 Aligned_cols=115 Identities=16% Similarity=0.250 Sum_probs=61.0
Q ss_pred HHHHHhhccccc-CCCcEEeccCCcchHHHHHHHHHhh-hCC-------ccccccccccCCCCCccccccccccccCC--
Q 000595 714 QAIVDKLHWYVN-DGDMIVDFCCGANDFSCLMKKKLDE-TGK-------NCLYKNYDILPAKNDFNFEKRDWMTVEPK-- 782 (1401)
Q Consensus 714 ~~i~~~Lh~yv~-~gd~ivdfccg~n~fs~lmk~kl~~-~gk-------~c~~kn~dl~~~kn~f~Fe~~dw~~v~~~-- 782 (1401)
+.+++.+.-++. .++.|+|++||.-.|+-.+.++... +|. .+.=+|..+-.-+ +..|...|....-+.
T Consensus 184 ~~l~~~v~~~~~~~~~~vlDl~~G~G~~sl~la~~~~~v~~vE~~~~av~~a~~n~~~~~~~-~v~~~~~d~~~~~~~~~ 262 (353)
T TIGR02143 184 IKMLEWACEVTQGSKGDLLELYCGNGNFSLALAQNFRRVLATEIAKPSVNAAQYNIAANNID-NVQIIRMSAEEFTQAMN 262 (353)
T ss_pred HHHHHHHHHHhhcCCCcEEEEeccccHHHHHHHHhCCEEEEEECCHHHHHHHHHHHHHcCCC-cEEEEEcCHHHHHHHHh
Confidence 333333333344 3457999999999999988764210 000 1112344333222 255666665442221
Q ss_pred ---CCC--CC----C--eeeeeeCCCccchhhhHHHHHHhhhccCCcEEEEecCCccccccc
Q 000595 783 ---ELA--PG----S--RLIMGLNPPFGVKAGLANKFINKALEFNPKLLILIVPPETERLDR 833 (1401)
Q Consensus 783 ---elp--~G----~--~LimgLnPPfg~~a~lAnkFi~kal~f~Pkliili~P~~t~rld~ 833 (1401)
.++ .| . .=++-|+|| ++.+..++++-.+.. .++|.+=.-|.|=-=|-
T Consensus 263 ~~~~~~~~~~~~~~~~~~d~v~lDPP---R~G~~~~~l~~l~~~-~~ivYvsC~p~tlaRDl 320 (353)
T TIGR02143 263 GVREFRRLKGIDLKSYNCSTIFVDPP---RAGLDPDTCKLVQAY-ERILYISCNPETLKANL 320 (353)
T ss_pred hccccccccccccccCCCCEEEECCC---CCCCcHHHHHHHHcC-CcEEEEEcCHHHHHHHH
Confidence 110 11 0 124567999 678888998877772 35555555665543343
No 77
>PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=70.90 E-value=5.7 Score=43.52 Aligned_cols=74 Identities=20% Similarity=0.349 Sum_probs=42.6
Q ss_pred ccCCCcEEeccCCcchHHHHHHHHHhhh---CC-------ccccccccccCCCCCccccccccccccCCCCCCCCe-eee
Q 000595 724 VNDGDMIVDFCCGANDFSCLMKKKLDET---GK-------NCLYKNYDILPAKNDFNFEKRDWMTVEPKELAPGSR-LIM 792 (1401)
Q Consensus 724 v~~gd~ivdfccg~n~fs~lmk~kl~~~---gk-------~c~~kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~-Lim 792 (1401)
..++.+|+|++||+-.++..|.+.+... |. ...-+|+. ....+...|...||+.- ++.+.. +|+
T Consensus 106 ~~~~~~vLDiG~GsG~~~~~la~~~~~~~v~~iDis~~~l~~a~~n~~-~~~~~~i~~~~~d~~~~----~~~~~fD~Iv 180 (275)
T PRK09328 106 LKEPLRVLDLGTGSGAIALALAKERPDAEVTAVDISPEALAVARRNAK-HGLGARVEFLQGDWFEP----LPGGRFDLIV 180 (275)
T ss_pred ccCCCEEEEEcCcHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHH-hCCCCcEEEEEccccCc----CCCCceeEEE
Confidence 3577899999999999988886654110 10 01112222 11234567777787542 223433 555
Q ss_pred eeCCCccchhh
Q 000595 793 GLNPPFGVKAG 803 (1401)
Q Consensus 793 gLnPPfg~~a~ 803 (1401)
. ||||.-...
T Consensus 181 ~-npPy~~~~~ 190 (275)
T PRK09328 181 S-NPPYIPEAD 190 (275)
T ss_pred E-CCCcCCcch
Confidence 5 999975443
No 78
>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=67.49 E-value=4.7 Score=42.91 Aligned_cols=21 Identities=19% Similarity=0.476 Sum_probs=18.7
Q ss_pred cccccCCCCCcccccccccccccccccc
Q 000595 381 AYHRKCLPRKIAFEDKLEEGIITRAWEG 408 (1401)
Q Consensus 381 AYH~kCLPPpIsfe~~~~EgIp~RAW~c 408 (1401)
.||..||.|++. .+|.+.|.|
T Consensus 1 g~H~~CL~Ppl~-------~~P~g~W~C 21 (148)
T cd04718 1 GFHLCCLRPPLK-------EVPEGDWIC 21 (148)
T ss_pred CcccccCCCCCC-------CCCCCCcCC
Confidence 599999999996 688899996
No 79
>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=66.56 E-value=6.3 Score=42.76 Aligned_cols=51 Identities=12% Similarity=0.051 Sum_probs=44.8
Q ss_pred cccccccCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHH
Q 000595 697 GMRYTSFGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 697 G~ryts~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~k 747 (1401)
|.+|+.-+|...-+.+.-+.+.++...+.++++|+|+.||.-.++..|.+.
T Consensus 14 g~~~~~rn~~~~~~~~~~~~~~~~l~~~~~~~~VLDiGCG~G~~~~~L~~~ 64 (204)
T TIGR03587 14 GKEYIDRNSRQSLVAAKLAMFARALNRLPKIASILELGANIGMNLAALKRL 64 (204)
T ss_pred cchhhhccccHHHHHHHHHHHHHHHHhcCCCCcEEEEecCCCHHHHHHHHh
Confidence 778999999888777777788888888999999999999999999988664
No 80
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=64.00 E-value=1.8 Score=58.76 Aligned_cols=60 Identities=20% Similarity=0.478 Sum_probs=42.5
Q ss_pred ccCCccccccCCCC---ceeeccccccccccCccccCcccccccCCCChhhhhccCccccccccccc---ccccccCC
Q 000595 224 ELFDSVCSFCDNGG---DLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYKQ---HQCFACGK 295 (1401)
Q Consensus 224 Dl~DdVCaIC~dGG---eLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~gQ---HqCFVCGk 295 (1401)
+...-.|.+|...+ .++.|++ |...||..| ..+.++.. +.+.|+|+.|...+ -+|..|+.
T Consensus 1105 s~~~~~c~~cr~k~~~~~m~lc~~-c~~~~h~~C--------~rp~~~~~---~~~dW~C~~c~~e~~~rr~~~~~~~ 1170 (1404)
T KOG1245|consen 1105 SAVNALCKVCRRKKQDEKMLLCDE-CLSGFHLFC--------LRPALSSV---PPGDWMCPSCRKEHRARRQKRFRKE 1170 (1404)
T ss_pred ccchhhhhhhhhcccchhhhhhHh-hhhhHHHHh--------hhhhhccC---CcCCccCCccchhhhhhhhhhhhcc
Confidence 34467899999854 6899995 999999985 44444432 46889999997654 24555544
No 81
>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=60.98 E-value=6.6 Score=44.28 Aligned_cols=68 Identities=16% Similarity=0.214 Sum_probs=40.0
Q ss_pred CcEEeccCCcchHHHHHHHHHhh---hCCccc-------cccccccCCCCCccccccccccccCCCCCCC-CeeeeeeCC
Q 000595 728 DMIVDFCCGANDFSCLMKKKLDE---TGKNCL-------YKNYDILPAKNDFNFEKRDWMTVEPKELAPG-SRLIMGLNP 796 (1401)
Q Consensus 728 d~ivdfccg~n~fs~lmk~kl~~---~gk~c~-------~kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G-~~LimgLnP 796 (1401)
..|+|+|||+--+...+...+.. ++.+.+ -+|.....-.+...|...||+.. ++.. =-+|+. ||
T Consensus 116 ~~vLDlG~GsG~i~l~la~~~~~~~v~avDis~~al~~a~~n~~~~~~~~~v~~~~~d~~~~----~~~~~fDlIvs-NP 190 (284)
T TIGR00536 116 LHILDLGTGSGCIALALAYEFPNAEVIAVDISPDALAVAEENAEKNQLEHRVEFIQSNLFEP----LAGQKIDIIVS-NP 190 (284)
T ss_pred CEEEEEeccHhHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEECchhcc----CcCCCccEEEE-CC
Confidence 68999999999998888664321 111111 13332222234578888898753 3322 235555 99
Q ss_pred Cccc
Q 000595 797 PFGV 800 (1401)
Q Consensus 797 Pfg~ 800 (1401)
||--
T Consensus 191 Pyi~ 194 (284)
T TIGR00536 191 PYID 194 (284)
T ss_pred CCCC
Confidence 9863
No 82
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=58.30 E-value=5.8 Score=52.55 Aligned_cols=42 Identities=21% Similarity=0.623 Sum_probs=35.2
Q ss_pred cccccCCCCCCCCCCCceeecccCCccccccCCCCCcccccccccccccccccccc
Q 000595 355 KCCICKQGENKADSDLQFAVCRRCPKAYHRKCLPRKIAFEDKLEEGIITRAWEGLL 410 (1401)
Q Consensus 355 ~C~vCkqseDkn~segKLI~CdRCPkAYH~kCLPPpIsfe~~~~EgIp~RAW~cLL 410 (1401)
.|.+|...++ ++.|..||+.||..|+.++.- ..+..-|.|.+
T Consensus 346 hcrf~~d~~~-------~lc~Et~prvvhlEcv~hP~~-------~~~s~~~e~ev 387 (1414)
T KOG1473|consen 346 HCRFCHDLGD-------LLCCETCPRVVHLECVFHPRF-------AVPSAFWECEV 387 (1414)
T ss_pred cccccCcccc-------eeecccCCceEEeeecCCccc-------cCCCccchhhh
Confidence 3999988765 889999999999999999863 56778899855
No 83
>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=58.25 E-value=48 Score=37.54 Aligned_cols=94 Identities=21% Similarity=0.344 Sum_probs=65.5
Q ss_pred hHHHHHHHHhhhcCCCChHHHhhhcChhhHhHHHHHhhcccccccc---------------------------cc--ccc
Q 000595 648 GKAIRTALKKLDVDGSSIEDAKAVCEPEVLSQIFKWKNKLKVYLAP---------------------------FL--HGM 698 (1401)
Q Consensus 648 gkAvr~AL~kLe~~g~siedAkAvc~p~vl~ql~~wk~kL~vylaP---------------------------~l--~G~ 698 (1401)
|-.|..|.++++ +|.+++ +++.+|..++++..+|+.| +| ..-
T Consensus 122 g~~v~~a~~~~~-~G~s~~--------eI~~~l~~~~~~~~~~f~v~~L~~L~~gGRis~~~~~~g~lL~ikPIi~~~~G 192 (275)
T TIGR00762 122 GLLVLEAAKLAE-EGKSLE--------EILAKLEELRERTKLYFVVDTLEYLVKGGRISKAAALIGSLLNIKPILTVDDG 192 (275)
T ss_pred HHHHHHHHHHHH-cCCCHH--------HHHHHHHHHHhhcEEEEEECcHHHHHhcCCccHHHHHHHHhhcceeEEEEeCC
Confidence 448888999999 999988 4677788888888777544 22 223
Q ss_pred cccccCcccchhhhHHHHHHhhcccccCCC-cEEe-ccCCcchHHHHHHHHHhh
Q 000595 699 RYTSFGRHFTKVDKLQAIVDKLHWYVNDGD-MIVD-FCCGANDFSCLMKKKLDE 750 (1401)
Q Consensus 699 ryts~grhftk~ekl~~i~~~Lh~yv~~gd-~ivd-fccg~n~fs~lmk~kl~~ 750 (1401)
....+|+.++..-.++++++.+.=++.+++ -.|. ..+|..+=...++++|.+
T Consensus 193 ~i~~~~k~Rg~kka~~~l~~~~~~~~~~~~~~~i~i~~~~~~e~~~~l~~~l~~ 246 (275)
T TIGR00762 193 KLVPIEKVRGRKKAIKKLVELVKEDIKDGKPKRVAIIHADAEEEAEELKEKLKE 246 (275)
T ss_pred EEEEeeccccHHHHHHHHHHHHHHhhccCCCcEEEEEeCCCHHHHHHHHHHHHh
Confidence 456788888888888889988887776543 2333 345555555566666665
No 84
>PF13679 Methyltransf_32: Methyltransferase domain
Probab=57.76 E-value=54 Score=33.47 Aligned_cols=108 Identities=17% Similarity=0.264 Sum_probs=63.2
Q ss_pred hhhHHHHHHhhccc---ccCCCcEEeccCCcchHHHHHHHHHhhhCCccccccccccC----------------CCCCcc
Q 000595 710 VDKLQAIVDKLHWY---VNDGDMIVDFCCGANDFSCLMKKKLDETGKNCLYKNYDILP----------------AKNDFN 770 (1401)
Q Consensus 710 ~ekl~~i~~~Lh~y---v~~gd~ivdfccg~n~fs~lmk~kl~~~gk~c~~kn~dl~~----------------~kn~f~ 770 (1401)
++.+.++++.+.-. ..+..+|||||||-.-.++++-..|......+..--.|.=+ -.+.+.
T Consensus 6 i~~~~~~i~~~~~~~~~~~~~~~vvD~GsG~GyLs~~La~~l~~~~~~~~v~~iD~~~~~~~~a~~~~~~~~~~~~~~~~ 85 (141)
T PF13679_consen 6 IERMAELIDSLCDSVGESKRCITVVDLGSGKGYLSRALAHLLCNSSPNLRVLGIDCNESLVESAQKRAQKLGSDLEKRLS 85 (141)
T ss_pred HHHHHHHHHHHHHHhhccCCCCEEEEeCCChhHHHHHHHHHHHhcCCCCeEEEEECCcHHHHHHHHHHHHhcchhhccch
Confidence 44455555555433 46788999999999999999988665554344333222211 113344
Q ss_pred ccccccccccCCCCCCCCeeeeeeCCCccchhhhHHHHHHhhhccCCcEEEEecC
Q 000595 771 FEKRDWMTVEPKELAPGSRLIMGLNPPFGVKAGLANKFINKALEFNPKLLILIVP 825 (1401)
Q Consensus 771 Fe~~dw~~v~~~elp~G~~LimgLnPPfg~~a~lAnkFi~kal~f~Pkliili~P 825 (1401)
|...+.-... ...+..+++||-. =+.|+-.-|..+..-+.+.|+ +||
T Consensus 86 ~~~~~~~~~~---~~~~~~~~vgLHa----CG~Ls~~~l~~~~~~~~~~l~-~vp 132 (141)
T PF13679_consen 86 FIQGDIADES---SSDPPDILVGLHA----CGDLSDRALRLFIRPNARFLV-LVP 132 (141)
T ss_pred hhccchhhhc---ccCCCeEEEEeec----ccchHHHHHHHHHHcCCCEEE-EcC
Confidence 4433222211 2556678888764 345888888888883344443 344
No 85
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=56.51 E-value=7.3 Score=42.70 Aligned_cols=46 Identities=22% Similarity=0.437 Sum_probs=35.3
Q ss_pred cccccccccccccccCCCCCCCCCCCCeeeecCCCCCCCCCccccccc
Q 000595 279 FCKNCEYKQHQCFACGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSK 326 (1401)
Q Consensus 279 ~C~nCe~gQHqCFVCGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~ 326 (1401)
.|.-|..+-..|.+|...+..--+....+.+|. .|+..||..|...
T Consensus 144 ~C~lC~~kGfiCe~C~~~~~IfPF~~~~~~~C~--~C~~v~H~~C~~~ 189 (202)
T PF13901_consen 144 SCELCQQKGFICEICNSDDIIFPFQIDTTVRCP--KCKSVFHKSCFRK 189 (202)
T ss_pred HhHHHHhCCCCCccCCCCCCCCCCCCCCeeeCC--cCccccchhhcCC
Confidence 788888888889999875432112224789998 9999999999984
No 86
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=56.03 E-value=6.5 Score=50.23 Aligned_cols=43 Identities=16% Similarity=0.537 Sum_probs=32.1
Q ss_pred cccccCCCCCCCCCCCceeecccCCccccccCCCCCcccccccccccccccccc
Q 000595 355 KCCICKQGENKADSDLQFAVCRRCPKAYHRKCLPRKIAFEDKLEEGIITRAWEG 408 (1401)
Q Consensus 355 ~C~vCkqseDkn~segKLI~CdRCPkAYH~kCLPPpIsfe~~~~EgIp~RAW~c 408 (1401)
.|-+|..+.-. ....|++|+.|....|..|.-- +.+|...|.|
T Consensus 273 iCDvCrspD~e--~~neMVfCd~Cn~cVHqaCyGI---------le~p~gpWlC 315 (893)
T KOG0954|consen 273 ICDVCRSPDSE--EANEMVFCDKCNICVHQACYGI---------LEVPEGPWLC 315 (893)
T ss_pred eeceecCCCcc--ccceeEEeccchhHHHHhhhce---------eecCCCCeee
Confidence 49999887321 2347999999999999999543 2466788987
No 87
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=55.86 E-value=7.2 Score=36.32 Aligned_cols=39 Identities=26% Similarity=0.563 Sum_probs=16.6
Q ss_pred cccccCCCCCCCCCCCCeeeecCCCCCCCCCcccccccccc
Q 000595 289 QCFACGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKLLL 329 (1401)
Q Consensus 289 qCFVCGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~~ 329 (1401)
.|.||...-..+ .....+.|..+.|++.||..||..|+.
T Consensus 4 ~C~IC~~~~~~~--~~~p~~~C~n~~C~~~fH~~CL~~wf~ 42 (70)
T PF11793_consen 4 ECGICYSYRLDD--GEIPDVVCPNPSCGKKFHLLCLSEWFL 42 (70)
T ss_dssp S-SSS--SS-TT-------B--S-TT----B-SGGGHHHHH
T ss_pred CCCcCCcEecCC--CCcCceEcCCcccCCHHHHHHHHHHHH
Confidence 577886542211 122468899999999999999999974
No 88
>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=55.37 E-value=15 Score=36.23 Aligned_cols=36 Identities=19% Similarity=0.433 Sum_probs=30.3
Q ss_pred hhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHH
Q 000595 711 DKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKK 746 (1401)
Q Consensus 711 ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~ 746 (1401)
+.+.+++.+|..+..++..|+|+-||...|+..|.+
T Consensus 7 ~~~~~~~~~~~~~~~~~~~vLDiGcG~G~~~~~l~~ 42 (161)
T PF13489_consen 7 RAYADLLERLLPRLKPGKRVLDIGCGTGSFLRALAK 42 (161)
T ss_dssp HCHHHHHHHHHTCTTTTSEEEEESSTTSHHHHHHHH
T ss_pred HHHHHHHHHHhcccCCCCEEEEEcCCCCHHHHHHHH
Confidence 345677777777789999999999999999999955
No 89
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=55.12 E-value=22 Score=32.67 Aligned_cols=46 Identities=11% Similarity=0.330 Sum_probs=36.9
Q ss_pred hHHHHHHHHHHhhhcc-cchHHHHHhhccCCccccccccchhhhHhHhhHHHHHHHHhhhcCCC
Q 000595 601 EDSKRRLSSLMKDAAS-SVRMEEILKRHKIPSTHAYASKSAVDKAITLGKAIRTALKKLDVDGS 663 (1401)
Q Consensus 601 ~~~erR~~~~~k~~~s-s~t~~~~~k~~~~~st~~~~~~~~~~k~it~gkAvr~AL~kLe~~g~ 663 (1401)
.+++++||.++++... .+|..+|.+...++.. +|+.+|..|+.+|.
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~-----------------~v~r~L~~L~~~G~ 51 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNLGLPKK-----------------EVNRVLYSLEKKGK 51 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHH-----------------HHHHHHHHHHHCCC
Confidence 4678999999999866 5999999998885432 57888999986664
No 90
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.14 E-value=6.9 Score=46.51 Aligned_cols=69 Identities=17% Similarity=0.299 Sum_probs=36.8
Q ss_pred cCCceeeeecceeecccccCCCCcceeEEEeecCCCCcEEEEEEEEEEeecCCCcceEEEEecCCceEEeCCccch-HHH
Q 000595 28 QKEIISFSALPIQWNENERTGGCKELIYLRGAADSGLQKIFKPVIAWKFDLTNVIPEIFVLSKENSWIKLQKPRKC-YEE 106 (1401)
Q Consensus 28 ~~~pVsFs~LPi~w~~~e~~~~~k~~vfLrG~~dnGlq~i~k~V~AWr~~L~~~~PeIsVLs~e~~WI~L~KPrks-Yee 106 (1401)
++.-.+|..||-.|+-+=...+ -.++.+.-..+|+=.+|+.- |+- -+....|+-|..=-.| |++
T Consensus 30 ~n~S~sf~d~~a~f~~s~~~e~-~~G~l~~~ep~~aC~~i~~~------------p~~--~~~~~~~laLI~Rg~CsFe~ 94 (348)
T KOG4628|consen 30 RNTSLSFADLPALFGPSLPSEG-NLGVLVVAEPLNACNPITNF------------PEH--STRSTSFLALIRRGGCSFED 94 (348)
T ss_pred ccccccccCCccccCCcccccc-ceeeeecCCCccccCccccC------------ccC--CCCCcceEEEEEccCCchHH
Confidence 4445578888888877332111 12233322223444444442 111 2333577777665556 999
Q ss_pred HHHHH
Q 000595 107 IYRTI 111 (1401)
Q Consensus 107 ~iRtv 111 (1401)
+||.+
T Consensus 95 Kv~~A 99 (348)
T KOG4628|consen 95 KVLNA 99 (348)
T ss_pred HHhhc
Confidence 99875
No 91
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=54.11 E-value=3.6 Score=56.08 Aligned_cols=43 Identities=19% Similarity=0.634 Sum_probs=36.3
Q ss_pred cccccCCCCCCCCCCCceeecccCCccccccCCCCCcccccccccccccccccc
Q 000595 355 KCCICKQGENKADSDLQFAVCRRCPKAYHRKCLPRKIAFEDKLEEGIITRAWEG 408 (1401)
Q Consensus 355 ~C~vCkqseDkn~segKLI~CdRCPkAYH~kCLPPpIsfe~~~~EgIp~RAW~c 408 (1401)
.|.+|...... ..++.|+-|..+||..|+.+-+. ..+-+.|.|
T Consensus 1110 ~c~~cr~k~~~----~~m~lc~~c~~~~h~~C~rp~~~-------~~~~~dW~C 1152 (1404)
T KOG1245|consen 1110 LCKVCRRKKQD----EKMLLCDECLSGFHLFCLRPALS-------SVPPGDWMC 1152 (1404)
T ss_pred hhhhhhhcccc----hhhhhhHhhhhhHHHHhhhhhhc-------cCCcCCccC
Confidence 59999997654 25899999999999999999875 567788997
No 92
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=53.15 E-value=11 Score=46.49 Aligned_cols=72 Identities=19% Similarity=0.422 Sum_probs=46.8
Q ss_pred cccccCCCCCCCCCCCceeecccCCccccccCCCCCcccccccccccccccccc---ccCCC--ceeEeccCCcccc-cc
Q 000595 355 KCCICKQGENKADSDLQFAVCRRCPKAYHRKCLPRKIAFEDKLEEGIITRAWEG---LLPNH--RILIYCLKHEIDD-EI 428 (1401)
Q Consensus 355 ~C~vCkqseDkn~segKLI~CdRCPkAYH~kCLPPpIsfe~~~~EgIp~RAW~c---LLpnc--RiLIyCpkHeID~-lL 428 (1401)
.|.+|..+.+.+ ...++.|+-|..+.|..|.- +.| +|.+-|.| ++.-+ +.|..||.|.-.= ..
T Consensus 195 ~C~~c~~t~~eN--~naiVfCdgC~i~VHq~CYG--I~f-------~peG~WlCrkCi~~~~~i~~C~fCps~dGaFkqT 263 (669)
T COG5141 195 ICTKCTSTHNEN--SNAIVFCDGCEICVHQSCYG--IQF-------LPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQT 263 (669)
T ss_pred hhHhccccccCC--cceEEEecCcchhhhhhccc--cee-------cCcchhhhhhhcccccceeEEEeccCCCCceeec
Confidence 388888876543 34799999999999999964 443 56788987 22222 4478888883221 11
Q ss_pred CCCCCCccc
Q 000595 429 GTPIRDHII 437 (1401)
Q Consensus 429 gTP~RdHIk 437 (1401)
.+-+|.|..
T Consensus 264 ~dgrW~H~i 272 (669)
T COG5141 264 SDGRWGHVI 272 (669)
T ss_pred cCCchHhHh
Confidence 334566644
No 93
>COG0286 HsdM Type I restriction-modification system methyltransferase subunit [Defense mechanisms]
Probab=53.08 E-value=15 Score=45.15 Aligned_cols=49 Identities=22% Similarity=0.278 Sum_probs=43.6
Q ss_pred ccCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhhhC
Q 000595 702 SFGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDETG 752 (1401)
Q Consensus 702 s~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~~g 752 (1401)
+.|.+||-.+--+=||+.|-. +++++|.|.|||+..|.....+.+.+..
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 9999999999999999988888776543
No 94
>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=52.51 E-value=8.2 Score=42.94 Aligned_cols=56 Identities=21% Similarity=0.421 Sum_probs=19.7
Q ss_pred hHhHHHHHhhccccccccccccccccccCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHH
Q 000595 676 VLSQIFKWKNKLKVYLAPFLHGMRYTSFGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKK 746 (1401)
Q Consensus 676 vl~ql~~wk~kL~vylaP~l~G~ryts~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~ 746 (1401)
..+++....|.+. +--|||.|---..++.+++ -+.+|++|+|+|||.-+++..+-+
T Consensus 12 ~Fd~ia~~YD~~n----------~~ls~g~~~~wr~~~~~~~-----~~~~g~~vLDv~~GtG~~~~~l~~ 67 (233)
T PF01209_consen 12 MFDRIAPRYDRMN----------DLLSFGQDRRWRRKLIKLL-----GLRPGDRVLDVACGTGDVTRELAR 67 (233)
T ss_dssp -----------------------------------SHHHHHH-----T--S--EEEEET-TTSHHHHHHGG
T ss_pred HHHHHHHHhCCCc----------cccCCcHHHHHHHHHHhcc-----CCCCCCEEEEeCCChHHHHHHHHH
Confidence 4455666666553 4457887755555544443 368999999999999999988744
No 95
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=51.42 E-value=9.3 Score=47.89 Aligned_cols=27 Identities=22% Similarity=0.369 Sum_probs=19.3
Q ss_pred CccccccCC--CCceeeccccccccccCcccc
Q 000595 227 DSVCSFCDN--GGDLLCCEGRCLRSFHATIDA 256 (1401)
Q Consensus 227 DdVCaIC~d--GGeLLCCDG~C~RSFH~~Cld 256 (1401)
--.|..|.. .|+.|. .|...||..|..
T Consensus 16 ~i~c~~c~~kc~gevlr---v~d~~fhi~cf~ 44 (670)
T KOG1044|consen 16 GIKCDKCRKKCSGEVLR---VNDNHFHINCFQ 44 (670)
T ss_pred ceehhhhCCccccceeE---eeccccceeeee
Confidence 356999987 466553 466899999875
No 96
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=51.07 E-value=3.3 Score=34.46 Aligned_cols=35 Identities=29% Similarity=0.790 Sum_probs=17.2
Q ss_pred CceeeccccccccccCccccCcccccccCCCChhhhhccCcccccccc
Q 000595 237 GDLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCE 284 (1401)
Q Consensus 237 GeLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe 284 (1401)
..||.|+ .|.-++|.. | +|+...+ ....|+|..|+
T Consensus 2 n~ll~C~-~C~v~VH~~--------C--YGv~~~~--~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCD-NCNVAVHQS--------C--YGVSEVP--DGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-S-SS--EEEHH--------H--HT-SS----SS-----HHH-
T ss_pred CceEEeC-CCCCcCChh--------h--CCcccCC--CCCcEECCcCC
Confidence 3589999 699999998 5 7776532 23469998773
No 97
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=50.71 E-value=12 Score=46.60 Aligned_cols=38 Identities=32% Similarity=0.524 Sum_probs=32.3
Q ss_pred cCCccccccCCccccccCCCCceeeccccccccccCccc
Q 000595 217 DESNEEDELFDSVCSFCDNGGDLLCCEGRCLRSFHATID 255 (1401)
Q Consensus 217 d~s~e~dDl~DdVCaIC~dGGeLLCCDG~C~RSFH~~Cl 255 (1401)
+...+...+.+.+|+-|.-.|..|.|. .|.|+||-.|.
T Consensus 50 ~~~~~~~~N~d~~cfechlpg~vl~c~-vc~Rs~h~~c~ 87 (588)
T KOG3612|consen 50 KVSRLPSSNIDPFCFECHLPGAVLKCI-VCHRSFHENCQ 87 (588)
T ss_pred ccccccccCCCcccccccCCcceeeee-hhhcccccccc
Confidence 335556677789999999999999999 79999999964
No 98
>TIGR00080 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt.
Probab=50.34 E-value=21 Score=38.44 Aligned_cols=45 Identities=9% Similarity=0.300 Sum_probs=36.3
Q ss_pred cCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHh
Q 000595 703 FGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLD 749 (1401)
Q Consensus 703 ~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~ 749 (1401)
+|++++.+.-...+++.|- +++|+.|+|+.||.--++.+|-+...
T Consensus 56 ~~~~~~~p~~~~~~~~~l~--~~~~~~VLDiG~GsG~~a~~la~~~~ 100 (215)
T TIGR00080 56 YGQTISAPHMVAMMTELLE--LKPGMKVLEIGTGSGYQAAVLAEIVG 100 (215)
T ss_pred CCCEechHHHHHHHHHHhC--CCCcCEEEEECCCccHHHHHHHHHhC
Confidence 3677777766777777774 78999999999999999998877543
No 99
>PRK15001 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional
Probab=50.08 E-value=22 Score=42.62 Aligned_cols=123 Identities=15% Similarity=0.133 Sum_probs=67.2
Q ss_pred cccccccCcccchhhhHHHHHHhhcccccC--CCcEEeccCCcchHHHHHHHHH---hhhCCccccc-------cccccC
Q 000595 697 GMRYTSFGRHFTKVDKLQAIVDKLHWYVND--GDMIVDFCCGANDFSCLMKKKL---DETGKNCLYK-------NYDILP 764 (1401)
Q Consensus 697 G~ryts~grhftk~ekl~~i~~~Lh~yv~~--gd~ivdfccg~n~fs~lmk~kl---~~~gk~c~~k-------n~dl~~ 764 (1401)
+..+.+..--|.. ++|-.=.+-|.-++.. +..|||+.||.-..+..+.++. .-++.+.++. |+..-.
T Consensus 198 ~~~~~~~~gVFs~-~~LD~GtrllL~~lp~~~~~~VLDLGCGtGvi~i~la~~~P~~~V~~vD~S~~Av~~A~~N~~~n~ 276 (378)
T PRK15001 198 DWTIHNHANVFSR-TGLDIGARFFMQHLPENLEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDESPMAVASSRLNVETNM 276 (378)
T ss_pred eEEEEecCCccCC-CCcChHHHHHHHhCCcccCCeEEEEeccccHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcC
Confidence 3445566667764 3343333333333322 4589999999999998887753 2223333333 332222
Q ss_pred CC--CCccccccccccccCCCCCCCCeeeeeeCCCccch----hhhHHHHHHhhhc-cCCcEEEEec
Q 000595 765 AK--NDFNFEKRDWMTVEPKELAPGSRLIMGLNPPFGVK----AGLANKFINKALE-FNPKLLILIV 824 (1401)
Q Consensus 765 ~k--n~f~Fe~~dw~~v~~~elp~G~~LimgLnPPfg~~----a~lAnkFi~kal~-f~Pkliili~ 824 (1401)
+. ...+|...|.++ .++.++.=++-.||||-.. ..+|.+|+..|.. -+|.=.++||
T Consensus 277 ~~~~~~v~~~~~D~l~----~~~~~~fDlIlsNPPfh~~~~~~~~ia~~l~~~a~~~LkpGG~L~iV 339 (378)
T PRK15001 277 PEALDRCEFMINNALS----GVEPFRFNAVLCNPPFHQQHALTDNVAWEMFHHARRCLKINGELYIV 339 (378)
T ss_pred cccCceEEEEEccccc----cCCCCCEEEEEECcCcccCccCCHHHHHHHHHHHHHhcccCCEEEEE
Confidence 11 245666666654 2333343333449999643 2578889877663 3555444444
No 100
>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=48.90 E-value=14 Score=39.57 Aligned_cols=35 Identities=26% Similarity=0.384 Sum_probs=27.1
Q ss_pred HHHHHHhhccccc----CCCcEEeccCCcchHHHHHHHH
Q 000595 713 LQAIVDKLHWYVN----DGDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 713 l~~i~~~Lh~yv~----~gd~ivdfccg~n~fs~lmk~k 747 (1401)
...+++++.++++ .+++|+|+.||...|+..+.+.
T Consensus 38 ~~~~~~~~~~~l~~~~~~~~~vLDiGcG~G~~~~~la~~ 76 (219)
T TIGR02021 38 RAAMRRKLLDWLPKDPLKGKRVLDAGCGTGLLSIELAKR 76 (219)
T ss_pred HHHHHHHHHHHHhcCCCCCCEEEEEeCCCCHHHHHHHHC
Confidence 3455666777766 5889999999999999888653
No 101
>KOG3420 consensus Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=48.75 E-value=4.8 Score=43.40 Aligned_cols=105 Identities=26% Similarity=0.344 Sum_probs=53.9
Q ss_pred chhhhHHHHHHhhccccc--CCCcEEeccCCcchHH--HHHHHHHhhhCCccccccccccCCCCCccccc------cccc
Q 000595 708 TKVDKLQAIVDKLHWYVN--DGDMIVDFCCGANDFS--CLMKKKLDETGKNCLYKNYDILPAKNDFNFEK------RDWM 777 (1401)
Q Consensus 708 tk~ekl~~i~~~Lh~yv~--~gd~ivdfccg~n~fs--~lmk~kl~~~gk~c~~kn~dl~~~kn~f~Fe~------~dw~ 777 (1401)
|.++-....+.-+|=-.- .|-.+.|+|||-.+.| +-|.+-=.=.|-+.-=-... |...|-..||- -|..
T Consensus 28 T~p~iAasM~~~Ih~TygdiEgkkl~DLgcgcGmLs~a~sm~~~e~vlGfDIdpeALE-If~rNaeEfEvqidlLqcdil 106 (185)
T KOG3420|consen 28 TRPHIAASMLYTIHNTYGDIEGKKLKDLGCGCGMLSIAFSMPKNESVLGFDIDPEALE-IFTRNAEEFEVQIDLLQCDIL 106 (185)
T ss_pred CcHHHHHHHHHHHHhhhccccCcchhhhcCchhhhHHHhhcCCCceEEeeecCHHHHH-HHhhchHHhhhhhheeeeecc
Confidence 445555555555553222 3555899999987765 22211000011111101111 12245555552 2333
Q ss_pred cccCCCCCCCCeeeeeeCCCccchhhhH-HHHHHhhhccC
Q 000595 778 TVEPKELAPGSRLIMGLNPPFGVKAGLA-NKFINKALEFN 816 (1401)
Q Consensus 778 ~v~~~elp~G~~LimgLnPPfg~~a~lA-nkFi~kal~f~ 816 (1401)
+. |+..|-.=.-..|||||-|-.=| -.||++||+.-
T Consensus 107 dl---e~~~g~fDtaviNppFGTk~~~aDm~fv~~al~~~ 143 (185)
T KOG3420|consen 107 DL---ELKGGIFDTAVINPPFGTKKKGADMEFVSAALKVA 143 (185)
T ss_pred ch---hccCCeEeeEEecCCCCcccccccHHHHHHHHHHH
Confidence 32 33345555566799999875545 57999999865
No 102
>COG3802 GguC Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.37 E-value=9.1 Score=44.06 Aligned_cols=66 Identities=33% Similarity=0.630 Sum_probs=55.7
Q ss_pred CccchhhhHHHHHHhhh----------------ccCCcEEEEecCCccccccccCCCceeeeccccccCCcc--------
Q 000595 797 PFGVKAGLANKFINKAL----------------EFNPKLLILIVPPETERLDRKESAYELVWEDDQFLSGKS-------- 852 (1401)
Q Consensus 797 Pfg~~a~lAnkFi~kal----------------~f~Pkliili~P~~t~rld~k~~~Y~liwed~~~l~gks-------- 852 (1401)
||-+--+|||.|-||.- .|-|.|+|=-+|.+.+-.-++.+.=++||| +-||||..
T Consensus 186 p~RlGfal~NEfSDHvtEr~NYL~LAHSKLR~as~GPEl~vG~lP~~vrG~SRI~Rdg~viwe-k~FlSGE~nMsHs~aN 264 (333)
T COG3802 186 PYRLGFALANEFSDHVTERVNYLYLAHSKLRNASFGPELLVGALPEDVRGVSRILRDGEVIWE-KPFLSGEANMSHSIAN 264 (333)
T ss_pred eeEEeeeecchhhhhhhhccceEEeehhhhhccccCcceeeccCchhhcCceeeecCCEEEEe-cccccCccchhhhhhh
Confidence 99999999999999974 589999999999998877778888899998 46888874
Q ss_pred ----------eecCCCcccch
Q 000595 853 ----------FYLPGSVDEND 863 (1401)
Q Consensus 853 ----------FylPGsvd~nd 863 (1401)
|--||.|+|+.
T Consensus 265 LEhhHFkY~lfrrpGDvHvh~ 285 (333)
T COG3802 265 LEHHHFKYALFRRPGDVHVHF 285 (333)
T ss_pred hhhhhhhhhhhcCCCceEEEE
Confidence 45688888754
No 103
>PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=47.97 E-value=21 Score=38.75 Aligned_cols=45 Identities=9% Similarity=0.372 Sum_probs=38.6
Q ss_pred ccCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHH
Q 000595 702 SFGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKL 748 (1401)
Q Consensus 702 s~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl 748 (1401)
-+|++-+.+.-...+++.|. +++|++|+|+.||+--++.+|.+.+
T Consensus 54 ~~g~~~~~p~~~~~~~~~l~--~~~g~~VLdIG~GsG~~t~~la~~~ 98 (212)
T PRK13942 54 GYGQTISAIHMVAIMCELLD--LKEGMKVLEIGTGSGYHAAVVAEIV 98 (212)
T ss_pred CCCCEeCcHHHHHHHHHHcC--CCCcCEEEEECCcccHHHHHHHHhc
Confidence 46788888888888888886 6899999999999999999997744
No 104
>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=47.35 E-value=10 Score=40.53 Aligned_cols=26 Identities=27% Similarity=0.560 Sum_probs=19.2
Q ss_pred ccCccccCcccccccCCCChhhhhccCcccccccccc
Q 000595 250 FHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYK 286 (1401)
Q Consensus 250 FH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~g 286 (1401)
||+. |+++.++.. |.+.|+|+.|..+
T Consensus 2 ~H~~--------CL~Ppl~~~---P~g~W~Cp~C~~~ 27 (148)
T cd04718 2 FHLC--------CLRPPLKEV---PEGDWICPFCEVE 27 (148)
T ss_pred cccc--------cCCCCCCCC---CCCCcCCCCCcCC
Confidence 8998 555666542 5699999999754
No 105
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=46.90 E-value=33 Score=28.94 Aligned_cols=43 Identities=19% Similarity=0.478 Sum_probs=31.8
Q ss_pred HHHHHHHHHHhhhcccchHHHHHhhccCCccccccccchhhhHhHhhHHHHHHHHhhhcCC
Q 000595 602 DSKRRLSSLMKDAASSVRMEEILKRHKIPSTHAYASKSAVDKAITLGKAIRTALKKLDVDG 662 (1401)
Q Consensus 602 ~~erR~~~~~k~~~ss~t~~~~~k~~~~~st~~~~~~~~~~k~it~gkAvr~AL~kLe~~g 662 (1401)
+++++|+.++.+.. .+|..++.++..+..+ +|+..|++|+.+|
T Consensus 3 ~~~~~Il~~l~~~~-~~t~~ela~~~~is~~-----------------tv~~~l~~L~~~g 45 (48)
T PF13412_consen 3 ETQRKILNYLRENP-RITQKELAEKLGISRS-----------------TVNRYLKKLEEKG 45 (48)
T ss_dssp HHHHHHHHHHHHCT-TS-HHHHHHHHTS-HH-----------------HHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHcC-CCCHHHHHHHhCCCHH-----------------HHHHHHHHHHHCc
Confidence 67899999999965 4999999988884332 4567788887565
No 106
>PRK14968 putative methyltransferase; Provisional
Probab=46.37 E-value=51 Score=33.79 Aligned_cols=23 Identities=17% Similarity=0.367 Sum_probs=20.0
Q ss_pred cCCCcEEeccCCcchHHHHHHHH
Q 000595 725 NDGDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 725 ~~gd~ivdfccg~n~fs~lmk~k 747 (1401)
.+|+.|+|+.||.--++..+.+.
T Consensus 22 ~~~~~vLd~G~G~G~~~~~l~~~ 44 (188)
T PRK14968 22 KKGDRVLEVGTGSGIVAIVAAKN 44 (188)
T ss_pred cCCCEEEEEccccCHHHHHHHhh
Confidence 78999999999999998887553
No 107
>PRK14966 unknown domain/N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase fusion protein; Provisional
Probab=46.12 E-value=17 Score=44.46 Aligned_cols=82 Identities=16% Similarity=0.256 Sum_probs=44.9
Q ss_pred HHHHhhcccccCCCcEEeccCCcchHHHHHHHHHh---hhCCccc-------cccccccCCCCCccccccccccccCCCC
Q 000595 715 AIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLD---ETGKNCL-------YKNYDILPAKNDFNFEKRDWMTVEPKEL 784 (1401)
Q Consensus 715 ~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~---~~gk~c~-------~kn~dl~~~kn~f~Fe~~dw~~v~~~el 784 (1401)
.+++.+.=.+.++.+|+|++||+..++..+..+.- -++.+.+ =+|..... .+..|...||++.. +
T Consensus 240 ~LVe~aL~~l~~~~rVLDLGcGSG~IaiaLA~~~p~a~VtAVDiS~~ALe~AreNa~~~g--~rV~fi~gDl~e~~---l 314 (423)
T PRK14966 240 HLVEAVLARLPENGRVWDLGTGSGAVAVTVALERPDAFVRASDISPPALETARKNAADLG--ARVEFAHGSWFDTD---M 314 (423)
T ss_pred HHHHHhhhccCCCCEEEEEeChhhHHHHHHHHhCCCCEEEEEECCHHHHHHHHHHHHHcC--CcEEEEEcchhccc---c
Confidence 34444333345778999999999999987654321 1122221 12222111 24678888886532 2
Q ss_pred C-CCCeeeeeeCCCccch
Q 000595 785 A-PGSRLIMGLNPPFGVK 801 (1401)
Q Consensus 785 p-~G~~LimgLnPPfg~~ 801 (1401)
+ .++.=++-.||||-..
T Consensus 315 ~~~~~FDLIVSNPPYI~~ 332 (423)
T PRK14966 315 PSEGKWDIIVSNPPYIEN 332 (423)
T ss_pred ccCCCccEEEECCCCCCc
Confidence 2 2333344469999643
No 108
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=46.06 E-value=24 Score=39.70 Aligned_cols=50 Identities=16% Similarity=0.401 Sum_probs=37.2
Q ss_pred cccccccc---------ccCcccchh---hhHHHHHHhhcccccCCCcEEeccCCcchHHHHHH
Q 000595 694 FLHGMRYT---------SFGRHFTKV---DKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMK 745 (1401)
Q Consensus 694 ~l~G~ryt---------s~grhftk~---ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk 745 (1401)
||.-.+|| -||..|-.+ +-..+++++| -+.+|.+|+|+.||.-.++..|.
T Consensus 10 ~~~~~~y~~~~~~~~e~~~g~~~~~~gg~~~~~~~l~~l--~l~~~~~VLDiGcG~G~~a~~la 71 (263)
T PTZ00098 10 YLENNQYSDEGIKAYEFIFGEDYISSGGIEATTKILSDI--ELNENSKVLDIGSGLGGGCKYIN 71 (263)
T ss_pred hhhccccccccchhHHHHhCCCCCCCCchHHHHHHHHhC--CCCCCCEEEEEcCCCChhhHHHH
Confidence 56667777 477777766 4455566554 57899999999999999887774
No 109
>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=45.74 E-value=24 Score=37.37 Aligned_cols=30 Identities=23% Similarity=0.672 Sum_probs=23.5
Q ss_pred HHHHHHhhcccccCCCcEEeccCCcchHHHHHHH
Q 000595 713 LQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKK 746 (1401)
Q Consensus 713 l~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~ 746 (1401)
|+++.+. +.++++|+|+.||...|...+.+
T Consensus 4 ~~~i~~~----i~~~~~iLDiGcG~G~~~~~l~~ 33 (194)
T TIGR02081 4 LESILNL----IPPGSRVLDLGCGDGELLALLRD 33 (194)
T ss_pred HHHHHHh----cCCCCEEEEeCCCCCHHHHHHHh
Confidence 4455554 46899999999999999988754
No 110
>COG0293 FtsJ 23S rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=45.74 E-value=24 Score=39.50 Aligned_cols=43 Identities=28% Similarity=0.386 Sum_probs=39.7
Q ss_pred hhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhhhCC
Q 000595 710 VDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDETGK 753 (1401)
Q Consensus 710 ~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~~gk 753 (1401)
..||.||.+|- -.+.+|+.|||+|+-=-.||+...+++...++
T Consensus 30 a~KL~el~~k~-~i~~~~~~ViDLGAAPGgWsQva~~~~~~~~~ 72 (205)
T COG0293 30 AYKLLELNEKF-KLFKPGMVVVDLGAAPGGWSQVAAKKLGAGGK 72 (205)
T ss_pred HHHHHHHHHhc-CeecCCCEEEEcCCCCCcHHHHHHHHhCCCCc
Confidence 67999999998 88999999999999999999999998888766
No 111
>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=44.50 E-value=22 Score=38.11 Aligned_cols=43 Identities=28% Similarity=0.554 Sum_probs=30.2
Q ss_pred ccccCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHH
Q 000595 700 YTSFGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 700 yts~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~k 747 (1401)
+.||+++.... ++++.+| -+++|++|+|+.||...+...|.+.
T Consensus 24 ~~~~~~~~~~~---~~~l~~l--~~~~~~~vLDiGcG~G~~~~~la~~ 66 (231)
T TIGR02752 24 VISFQRHKKWR---KDTMKRM--NVQAGTSALDVCCGTADWSIALAEA 66 (231)
T ss_pred HhcCCchHHHH---HHHHHhc--CCCCCCEEEEeCCCcCHHHHHHHHH
Confidence 34566654443 3344444 3678999999999999999988664
No 112
>PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional
Probab=44.04 E-value=63 Score=38.23 Aligned_cols=21 Identities=24% Similarity=0.564 Sum_probs=18.3
Q ss_pred CCcEEeccCCcchHHHHHHHH
Q 000595 727 GDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 727 gd~ivdfccg~n~fs~lmk~k 747 (1401)
...|+||.||...++..+.++
T Consensus 197 ~g~VLDlGCG~G~ls~~la~~ 217 (342)
T PRK09489 197 KGKVLDVGCGAGVLSAVLARH 217 (342)
T ss_pred CCeEEEeccCcCHHHHHHHHh
Confidence 457999999999999988775
No 113
>PRK00312 pcm protein-L-isoaspartate O-methyltransferase; Reviewed
Probab=43.43 E-value=78 Score=33.95 Aligned_cols=44 Identities=11% Similarity=0.293 Sum_probs=34.4
Q ss_pred ccCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHH
Q 000595 702 SFGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 702 s~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~k 747 (1401)
.+|++.+.++-...+.+.|. +++|+.|+|++||.-.++.+|.+.
T Consensus 56 ~~~~~~~~p~~~~~l~~~l~--~~~~~~VLeiG~GsG~~t~~la~~ 99 (212)
T PRK00312 56 GCGQTISQPYMVARMTELLE--LKPGDRVLEIGTGSGYQAAVLAHL 99 (212)
T ss_pred CCCCeeCcHHHHHHHHHhcC--CCCCCEEEEECCCccHHHHHHHHH
Confidence 45666677777777776665 578999999999999999887653
No 114
>PRK13944 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=43.18 E-value=30 Score=37.32 Aligned_cols=45 Identities=9% Similarity=0.203 Sum_probs=35.8
Q ss_pred cCcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHh
Q 000595 703 FGRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLD 749 (1401)
Q Consensus 703 ~grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~ 749 (1401)
+|++++.+..+..+.+.|- +.+|+.|+|+.||.--++.+|.+++.
T Consensus 51 ~~~~~~~p~~~~~~~~~l~--~~~~~~VLDiG~GsG~~~~~la~~~~ 95 (205)
T PRK13944 51 AGATISAPHMVAMMCELIE--PRPGMKILEVGTGSGYQAAVCAEAIE 95 (205)
T ss_pred CCCEechHHHHHHHHHhcC--CCCCCEEEEECcCccHHHHHHHHhcC
Confidence 5677777776777777664 57899999999999999999877553
No 115
>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]
Probab=42.48 E-value=25 Score=40.96 Aligned_cols=35 Identities=26% Similarity=0.500 Sum_probs=31.2
Q ss_pred hhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHH
Q 000595 711 DKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 711 ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~k 747 (1401)
-||+.|.++|+ +++|++|+||=||--..+..|-++
T Consensus 59 ~k~~~~~~kl~--L~~G~~lLDiGCGWG~l~~~aA~~ 93 (283)
T COG2230 59 AKLDLILEKLG--LKPGMTLLDIGCGWGGLAIYAAEE 93 (283)
T ss_pred HHHHHHHHhcC--CCCCCEEEEeCCChhHHHHHHHHH
Confidence 36888999998 899999999999999999888665
No 116
>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=42.43 E-value=35 Score=32.29 Aligned_cols=35 Identities=17% Similarity=0.287 Sum_probs=26.2
Q ss_pred hhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHH
Q 000595 710 VDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKK 746 (1401)
Q Consensus 710 ~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~ 746 (1401)
.+....+++.| ++.++++|+|+.||...++..+-+
T Consensus 5 ~~~~~~~~~~~--~~~~~~~vldlG~G~G~~~~~l~~ 39 (124)
T TIGR02469 5 REVRALTLSKL--RLRPGDVLWDIGAGSGSITIEAAR 39 (124)
T ss_pred HHHHHHHHHHc--CCCCCCEEEEeCCCCCHHHHHHHH
Confidence 34444455555 567889999999999999887754
No 117
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=41.71 E-value=17 Score=44.90 Aligned_cols=72 Identities=11% Similarity=0.119 Sum_probs=41.3
Q ss_pred CCCcEEeccCCcchHHHHHHHHHh---hhCCcccc-------ccccccCCCCCccccccccccccCCCCCCCCeeeeeeC
Q 000595 726 DGDMIVDFCCGANDFSCLMKKKLD---ETGKNCLY-------KNYDILPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLN 795 (1401)
Q Consensus 726 ~gd~ivdfccg~n~fs~lmk~kl~---~~gk~c~~-------kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLn 795 (1401)
.+..|+|++||+.-++..+...+. -++.+.+- +|.....-.+...|...||++. ++.+..=++-.|
T Consensus 138 ~~~~VLDlG~GsG~iai~la~~~p~~~v~avDis~~al~~A~~N~~~~~l~~~v~~~~~D~~~~----~~~~~fDlIvsN 213 (506)
T PRK01544 138 KFLNILELGTGSGCIAISLLCELPNANVIATDISLDAIEVAKSNAIKYEVTDRIQIIHSNWFEN----IEKQKFDFIVSN 213 (506)
T ss_pred CCCEEEEccCchhHHHHHHHHHCCCCeEEEEECCHHHHHHHHHHHHHcCCccceeeeecchhhh----CcCCCccEEEEC
Confidence 456899999999999987755431 12222222 2221111124567888888752 333333334469
Q ss_pred CCccch
Q 000595 796 PPFGVK 801 (1401)
Q Consensus 796 PPfg~~ 801 (1401)
|||-..
T Consensus 214 PPYi~~ 219 (506)
T PRK01544 214 PPYISH 219 (506)
T ss_pred CCCCCc
Confidence 999744
No 118
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=41.25 E-value=14 Score=33.72 Aligned_cols=32 Identities=31% Similarity=0.804 Sum_probs=25.2
Q ss_pred cccccCCCCCCCCCCCceeecccCCccccccCCCC
Q 000595 355 KCCICKQGENKADSDLQFAVCRRCPKAYHRKCLPR 389 (1401)
Q Consensus 355 ~C~vCkqseDkn~segKLI~CdRCPkAYH~kCLPP 389 (1401)
.|..|++.-. .+..+++|..|.+-||+.|-..
T Consensus 7 ~C~~Cg~~~~---~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 7 KCPVCGKKFK---DGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cChhhCCccc---CCCCEEECCCCCCcccHHHHhh
Confidence 5999988642 1235999999999999999755
No 119
>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=40.40 E-value=17 Score=32.95 Aligned_cols=19 Identities=42% Similarity=1.097 Sum_probs=12.6
Q ss_pred EeccCCcchHHHHHHHHHhhhC
Q 000595 731 VDFCCGANDFSCLMKKKLDETG 752 (1401)
Q Consensus 731 vdfccg~n~fs~lmk~kl~~~g 752 (1401)
+|||||.|. -+.+...+.|
T Consensus 24 IDfCCgG~~---~L~eA~~~~~ 42 (56)
T PF04405_consen 24 IDFCCGGNR---SLEEACEEKG 42 (56)
T ss_pred CcccCCCCc---hHHHHHHHcC
Confidence 899999985 4444444433
No 120
>TIGR00438 rrmJ cell division protein FtsJ.
Probab=40.26 E-value=34 Score=36.01 Aligned_cols=36 Identities=19% Similarity=0.421 Sum_probs=29.8
Q ss_pred hHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHH
Q 000595 712 KLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKL 748 (1401)
Q Consensus 712 kl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl 748 (1401)
+|.++.+++. .+++|++|+|++||.-.++.++.++.
T Consensus 19 ~~~~~~~~~~-~i~~g~~VLDiG~GtG~~~~~l~~~~ 54 (188)
T TIGR00438 19 KLLQLNQKFK-LIKPGDTVLDLGAAPGGWSQVAVEQV 54 (188)
T ss_pred HHHHHHHHhc-ccCCCCEEEEecCCCCHHHHHHHHHh
Confidence 6777777765 45789999999999999999887655
No 121
>KOG2824 consensus Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=39.74 E-value=28 Score=40.64 Aligned_cols=26 Identities=15% Similarity=0.331 Sum_probs=17.8
Q ss_pred cccccccCCchhhhhhHHH---HHHHhhc
Q 000595 140 FCLYEVRPSQNDLVDHMDL---IKEALER 165 (1401)
Q Consensus 140 Fs~fdVrPSq~DL~~H~sL---IkeaakR 165 (1401)
|.+|.|+-.+.|+.=|..- +++.+..
T Consensus 157 lesf~V~v~ERDVSMd~~fr~EL~~~lg~ 185 (281)
T KOG2824|consen 157 LESFRVKVDERDVSMDSEFREELQELLGE 185 (281)
T ss_pred HHhCceEEEEecccccHHHHHHHHHHHhc
Confidence 7889999888888765543 4444444
No 122
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.56 E-value=16 Score=43.67 Aligned_cols=28 Identities=29% Similarity=0.550 Sum_probs=22.0
Q ss_pred ccccccCC---CCceeeccccccccccCcccc
Q 000595 228 SVCSFCDN---GGDLLCCEGRCLRSFHATIDA 256 (1401)
Q Consensus 228 dVCaIC~d---GGeLLCCDG~C~RSFH~~Cld 256 (1401)
+.|+||-+ .|+.|.=- +|.-.||..|.+
T Consensus 230 ~~CaIClEdY~~GdklRiL-PC~H~FH~~CID 260 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRIL-PCSHKFHVNCID 260 (348)
T ss_pred ceEEEeecccccCCeeeEe-cCCCchhhccch
Confidence 78999986 47665555 799999999654
No 123
>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=38.04 E-value=23 Score=36.87 Aligned_cols=38 Identities=18% Similarity=0.268 Sum_probs=30.4
Q ss_pred hhHHHHHHhhccccc-CCCcEEeccCCcchHHHHHHHHH
Q 000595 711 DKLQAIVDKLHWYVN-DGDMIVDFCCGANDFSCLMKKKL 748 (1401)
Q Consensus 711 ekl~~i~~~Lh~yv~-~gd~ivdfccg~n~fs~lmk~kl 748 (1401)
.||.||.++..++-. .+.+|||+||+--.|+..+-+++
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 589999999985533 45889999999999999996644
No 124
>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=37.55 E-value=38 Score=38.62 Aligned_cols=38 Identities=21% Similarity=0.181 Sum_probs=28.1
Q ss_pred CcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHH
Q 000595 704 GRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMK 745 (1401)
Q Consensus 704 grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk 745 (1401)
|.|-|..-.|+.+ .-|+.+|++|+|+.||+--++..+.
T Consensus 141 G~h~tt~l~l~~l----~~~~~~g~~VLDvGcGsG~lai~aa 178 (288)
T TIGR00406 141 GTHPTTSLCLEWL----EDLDLKDKNVIDVGCGSGILSIAAL 178 (288)
T ss_pred CCCHHHHHHHHHH----HhhcCCCCEEEEeCCChhHHHHHHH
Confidence 4777766555543 3357899999999999988876654
No 125
>PLN02585 magnesium protoporphyrin IX methyltransferase
Probab=37.50 E-value=26 Score=41.02 Aligned_cols=22 Identities=18% Similarity=0.412 Sum_probs=19.0
Q ss_pred CCCcEEeccCCcchHHHHHHHH
Q 000595 726 DGDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 726 ~gd~ivdfccg~n~fs~lmk~k 747 (1401)
+|.+|+|++||.-.++..+.++
T Consensus 144 ~~~~VLDlGcGtG~~a~~la~~ 165 (315)
T PLN02585 144 AGVTVCDAGCGTGSLAIPLALE 165 (315)
T ss_pred CCCEEEEecCCCCHHHHHHHHC
Confidence 5789999999999999887653
No 126
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=36.96 E-value=33 Score=42.02 Aligned_cols=75 Identities=19% Similarity=0.266 Sum_probs=41.1
Q ss_pred cccccccCccccCccccccc----CCCChhhhhccCcccccccccccc--cccccCCCCCCCCCCCCeeeecCCCCCCCC
Q 000595 245 RCLRSFHATIDAGEESHCAS----LGLTKDEVEAMLNFFCKNCEYKQH--QCFACGKLGSSDKETGAEVFPCVSATCGHF 318 (1401)
Q Consensus 245 ~C~RSFH~~CldGeeS~Clt----LGLTeaEvq~~~sW~C~nCe~gQH--qCFVCGklGSSDk~SGaEVfrCsvasCGRF 318 (1401)
-|.++||..|.. |+. |+-..-.++...+.+|..|-+++. .|.+|++..-... ...+.++-. .=.|-
T Consensus 351 A~GkayHp~CF~-----Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~-G~~etvRvv--amdr~ 422 (468)
T KOG1701|consen 351 ALGKAYHPGCFT-----CVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRD-GKDETVRVV--AMDRD 422 (468)
T ss_pred hcccccCCCceE-----EEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCC-CCcceEEEE--Ecccc
Confidence 356889988865 421 111111133456788888876653 7999987543210 011233322 23688
Q ss_pred Ccccccccc
Q 000595 319 YHPHCVSKL 327 (1401)
Q Consensus 319 YHpkCLa~l 327 (1401)
||..|..-.
T Consensus 423 fHv~CY~CE 431 (468)
T KOG1701|consen 423 FHVNCYKCE 431 (468)
T ss_pred ccccceehh
Confidence 888877643
No 127
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=36.44 E-value=26 Score=43.19 Aligned_cols=36 Identities=25% Similarity=0.507 Sum_probs=26.5
Q ss_pred CccccccCCccccccCCCCceeeccccccccccCccc
Q 000595 219 SNEEDELFDSVCSFCDNGGDLLCCEGRCLRSFHATID 255 (1401)
Q Consensus 219 s~e~dDl~DdVCaIC~dGGeLLCCDG~C~RSFH~~Cl 255 (1401)
+........++|++|.+||.+++|+ +|..++|-.|.
T Consensus 81 ~~~~~~~~~~~c~vc~~ggs~v~~~-s~~~~~~r~c~ 116 (463)
T KOG1081|consen 81 SRRHPKIEPSECFVCFKGGSLVTCK-SRIQAPHRKCK 116 (463)
T ss_pred chhccCCCcchhccccCCCccceec-cccccccccCc
Confidence 4444555678999999999999999 45555566654
No 128
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=36.13 E-value=13 Score=43.92 Aligned_cols=64 Identities=22% Similarity=0.466 Sum_probs=36.4
Q ss_pred CccccccCC----CCceeeccccccccccCccccCcccccccCCCChhhhhccCcccccccccccccccccCCCCCCCCC
Q 000595 227 DSVCSFCDN----GGDLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYKQHQCFACGKLGSSDKE 302 (1401)
Q Consensus 227 DdVCaIC~d----GGeLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~gQHqCFVCGklGSSDk~ 302 (1401)
-.+|..|+. .|.|+-|+ |..|++ |..+ ...-+|+.|..+...=..|. +
T Consensus 90 VHfCd~Cd~PI~IYGRmIPCk-------HvFCl~-----CAr~---------~~dK~Cp~C~d~VqrIeq~~-~------ 141 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPCK-------HVFCLE-----CARS---------DSDKICPLCDDRVQRIEQIM-M------ 141 (389)
T ss_pred eEeecccCCcceeeecccccc-------hhhhhh-----hhhc---------CccccCcCcccHHHHHHHhc-c------
Confidence 367999987 48898776 444443 4211 12346777765533222232 2
Q ss_pred CCCeeeecCCCC-CCCCCc
Q 000595 303 TGAEVFPCVSAT-CGHFYH 320 (1401)
Q Consensus 303 SGaEVfrCsvas-CGRFYH 320 (1401)
+.+|.|.... |.|.|.
T Consensus 142 --g~iFmC~~~~GC~RTyL 158 (389)
T KOG2932|consen 142 --GGIFMCAAPHGCLRTYL 158 (389)
T ss_pred --cceEEeecchhHHHHHh
Confidence 3589997444 666554
No 129
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=35.24 E-value=43 Score=39.18 Aligned_cols=34 Identities=24% Similarity=0.337 Sum_probs=29.4
Q ss_pred hHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHH
Q 000595 712 KLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 712 kl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~k 747 (1401)
.|+|+++.|- +++|+++||..||.--++..+-++
T Consensus 7 ll~Evl~~L~--~~pg~~vlD~TlG~GGhS~~il~~ 40 (296)
T PRK00050 7 LLDEVVDALA--IKPDGIYVDGTFGGGGHSRAILER 40 (296)
T ss_pred cHHHHHHhhC--CCCCCEEEEeCcCChHHHHHHHHh
Confidence 4788999886 589999999999999999999543
No 130
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=34.99 E-value=20 Score=43.96 Aligned_cols=35 Identities=26% Similarity=0.504 Sum_probs=22.2
Q ss_pred ccccccCCCCCCCCCCCCeeeecCCCCCCCCCccccccccc
Q 000595 288 HQCFACGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKLL 328 (1401)
Q Consensus 288 HqCFVCGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~ 328 (1401)
..|.||-..-+++ ++ .++. ..|.+.||-.|+..|.
T Consensus 176 PTCpVCLERMD~s--~~-gi~t---~~c~Hsfh~~cl~~w~ 210 (493)
T KOG0804|consen 176 PTCPVCLERMDSS--TT-GILT---ILCNHSFHCSCLMKWW 210 (493)
T ss_pred CCcchhHhhcCcc--cc-ceee---eecccccchHHHhhcc
Confidence 4678886554321 22 2222 2688999999999875
No 131
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=34.86 E-value=25 Score=32.18 Aligned_cols=34 Identities=35% Similarity=0.784 Sum_probs=26.3
Q ss_pred ccccccCCCCCCCCCCCCeeeecCCCCCCCCCcccccccc
Q 000595 288 HQCFACGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKL 327 (1401)
Q Consensus 288 HqCFVCGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l 327 (1401)
..|.+|++.-. .+..++.|. .|+.-||..|....
T Consensus 6 ~~C~~Cg~~~~----~~dDiVvCp--~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 6 CKCPVCGKKFK----DGDDIVVCP--ECGAPYHRDCWEKA 39 (54)
T ss_pred ccChhhCCccc----CCCCEEECC--CCCCcccHHHHhhC
Confidence 35888987532 245799998 99999999998754
No 132
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=34.76 E-value=74 Score=40.94 Aligned_cols=66 Identities=20% Similarity=0.320 Sum_probs=35.0
Q ss_pred ChhhHhHHHHHhhccccccccccccc-----cccccCcccchhhhHH-HHHHhhcccccCCCcEEeccCCcchHH
Q 000595 673 EPEVLSQIFKWKNKLKVYLAPFLHGM-----RYTSFGRHFTKVDKLQ-AIVDKLHWYVNDGDMIVDFCCGANDFS 741 (1401)
Q Consensus 673 ~p~vl~ql~~wk~kL~vylaP~l~G~-----ryts~grhftk~ekl~-~i~~~Lh~yv~~gd~ivdfccg~n~fs 741 (1401)
.|++.-.+..-++++-|||-- .|. -|-.+.---.-.|.|- .++..-.|. .+|+.+||..||+--|.
T Consensus 134 ~pdv~i~~~~~~~~~~l~ld~--sg~~L~rRgyr~~~~~Apl~etlAaa~l~~a~w~-~~~~~l~DP~CGSGTil 205 (702)
T PRK11783 134 QPDIRINARLNKGEATISLDL--SGESLHQRGYRQATGEAPLKENLAAAILLRSGWP-QEGTPLLDPMCGSGTLL 205 (702)
T ss_pred CCCEEEEEEEeCCEEEEEEEC--CCCchhhccCccCCCCCCCcHHHHHHHHHHcCCC-CCCCeEEccCCCccHHH
Confidence 345544444445666666542 232 2322211222333333 344444453 57899999999998875
No 133
>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=34.11 E-value=6.5 Score=32.76 Aligned_cols=33 Identities=30% Similarity=0.725 Sum_probs=21.8
Q ss_pred cccccCCCCCCCCCCCCeeeecCCCCCCCCCccccccccc
Q 000595 289 QCFACGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKLL 328 (1401)
Q Consensus 289 qCFVCGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~ 328 (1401)
.|.+|...-. .+..++.. .|+..||..|+..+.
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 4667754321 12345544 499999999999875
No 134
>cd00315 Cyt_C5_DNA_methylase Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Probab=34.08 E-value=1e+02 Score=35.07 Aligned_cols=89 Identities=20% Similarity=0.303 Sum_probs=56.5
Q ss_pred cEEeccCCcchHHHHHHHHHhhhCCcccc-------------ccccccCCCCCccccccccccccCCCCCCCCeeeeeeC
Q 000595 729 MIVDFCCGANDFSCLMKKKLDETGKNCLY-------------KNYDILPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLN 795 (1401)
Q Consensus 729 ~ivdfccg~n~fs~lmk~kl~~~gk~c~~-------------kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLn 795 (1401)
+|+|++||.--++.=+++ .|-.+.+ +||.- . +...|.-++.+.+++..--||+| -
T Consensus 2 ~v~dLFsG~Gg~~~gl~~----~G~~~v~a~e~~~~a~~~~~~N~~~-----~--~~~~Di~~~~~~~~~~~~D~l~~-g 69 (275)
T cd00315 2 RVIDLFAGIGGFRLGLEK----AGFEIVAANEIDKSAAETYEANFPN-----K--LIEGDITKIDEKDFIPDIDLLTG-G 69 (275)
T ss_pred cEEEEccCcchHHHHHHH----cCCEEEEEEeCCHHHHHHHHHhCCC-----C--CccCccccCchhhcCCCCCEEEe-C
Confidence 589999999999876654 4544432 34321 1 23456666666664333446666 5
Q ss_pred CCc-------------cchhhhHHHHHHhhhccCCcEEEEecCCccc
Q 000595 796 PPF-------------GVKAGLANKFINKALEFNPKLLILIVPPETE 829 (1401)
Q Consensus 796 PPf-------------g~~a~lAnkFi~kal~f~Pkliili~P~~t~ 829 (1401)
||- +-++.|.-.|++-+-.++|+++|+==-+...
T Consensus 70 pPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~P~~~v~ENV~g~~ 116 (275)
T cd00315 70 FPCQPFSIAGKRKGFEDTRGTLFFEIIRILKEKKPKYFLLENVKGLL 116 (275)
T ss_pred CCChhhhHHhhcCCCCCchHHHHHHHHHHHHhcCCCEEEEEcCcchh
Confidence 653 2356688889998889999999885444443
No 135
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=33.26 E-value=15 Score=43.67 Aligned_cols=26 Identities=38% Similarity=0.929 Sum_probs=20.7
Q ss_pred CccccccCC--CC---ceeeccccccccccCc
Q 000595 227 DSVCSFCDN--GG---DLLCCEGRCLRSFHAT 253 (1401)
Q Consensus 227 DdVCaIC~d--GG---eLLCCDG~C~RSFH~~ 253 (1401)
+..|.+|++ .| .||.|+ .|...|--+
T Consensus 15 ~ElCPVCGDkVSGYHYGLLTCE-SCKGFFKRT 45 (475)
T KOG4218|consen 15 GELCPVCGDKVSGYHYGLLTCE-SCKGFFKRT 45 (475)
T ss_pred ccccccccCccccceeeeeehh-hhhhHHHHH
Confidence 468999998 34 699999 799888544
No 136
>KOG1169 consensus Diacylglycerol kinase [Lipid transport and metabolism; Signal transduction mechanisms]
Probab=32.29 E-value=19 Score=45.85 Aligned_cols=141 Identities=22% Similarity=0.384 Sum_probs=78.0
Q ss_pred cccccCCC--CceeeccccccccccCccccCccccccc---CCCChh--h------hhcc---Ccccccccccccccccc
Q 000595 229 VCSFCDNG--GDLLCCEGRCLRSFHATIDAGEESHCAS---LGLTKD--E------VEAM---LNFFCKNCEYKQHQCFA 292 (1401)
Q Consensus 229 VCaIC~dG--GeLLCCDG~C~RSFH~~CldGeeS~Clt---LGLTea--E------vq~~---~sW~C~nCe~gQHqCFV 292 (1401)
+|.+|... -.-+-|+ .|.-.+|..|..+..+.|.- +++... . ..+. ..-+|..| ...|.+
T Consensus 46 ~~~~~~~~~~~~~~~~~-~~g~~~~~~~~~~~~s~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~c~~c---~~~c~~ 121 (634)
T KOG1169|consen 46 VCCVCLWSEMAPSVDCD-VDGGVSHEECVSGAASDCPLLVLLGFENQRHKTDGDHVWRPKHLWKPAYCFVC---PKSCGS 121 (634)
T ss_pred hhhhhhhccccccccee-ccccchhhhhhcccccchHHHHHHHhhhhhhhccCceeccCCCCCCCceEEec---cccccc
Confidence 99999873 2467899 69999999998766654421 121110 0 0011 12233333 235666
Q ss_pred cCCCCCCCCCCCCeeeecCCCCCCCCCcccccccccccchHHHHHHHhHhhccCCceeCCCC---------cccccCCCC
Q 000595 293 CGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAGESFTCPLH---------KCCICKQGE 363 (1401)
Q Consensus 293 CGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLekkIaaGksFrCPlH---------~C~vCkqse 363 (1401)
|+..+. .-+.|. .|++--|..|+......-. ... . ....+.-.|+.+ .|..|...-
T Consensus 122 ~~~~~~-------~g~~C~--~C~~~vh~~C~~~~~~~~~-~~~-~----~~~~r~~v~~~~~~~~~~~~~~~~~~~~~~ 186 (634)
T KOG1169|consen 122 CGVGIK-------QGLCCD--WCGRTVHERCVRRADPECQ-CKC-D----LGRLRKIVLDHPWVKGNAGEAKCDQCLKSV 186 (634)
T ss_pred hhhccc-------Cceeec--cccchHHHHHHhhcCcccc-ccc-c----cccccceeecCcccccccCCccchhhhccc
Confidence 665542 458898 8999999999987643200 000 0 000112222211 144444432
Q ss_pred CCCCCCCceeecccCCccccccCCCC
Q 000595 364 NKADSDLQFAVCRRCPKAYHRKCLPR 389 (1401)
Q Consensus 364 Dkn~segKLI~CdRCPkAYH~kCLPP 389 (1401)
.. ....+...|..|-..+|..|...
T Consensus 187 ~~-~~~~~~~~c~~~~~~~h~~~~~~ 211 (634)
T KOG1169|consen 187 KA-DQGLTGPRCGWCQIRVHDKCKSE 211 (634)
T ss_pred cc-cccccccccceeeeeeecchHHH
Confidence 11 12345778999999999999773
No 137
>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=32.18 E-value=28 Score=36.21 Aligned_cols=50 Identities=20% Similarity=0.336 Sum_probs=23.6
Q ss_pred cccccccccccccc----CcccchhhhHHHHHHh-hcccccCCCcEEeccCCcchHH
Q 000595 690 YLAPFLHGMRYTSF----GRHFTKVDKLQAIVDK-LHWYVNDGDMIVDFCCGANDFS 741 (1401)
Q Consensus 690 ylaP~l~G~ryts~----grhftk~ekl~~i~~~-Lh~yv~~gd~ivdfccg~n~fs 741 (1401)
+..+.+...+..+- +.|-|.. =.+++++ +..+-.+||+|+|+.||+..=.
T Consensus 152 w~~~~~~~~~~~~~~~~~~~h~~~k--P~~l~~~lI~~~t~~gdiVlDpF~GSGTT~ 206 (231)
T PF01555_consen 152 WPFSIIPPSRKNSKGNTKGKHPTQK--PVELIERLIKASTNPGDIVLDPFAGSGTTA 206 (231)
T ss_dssp EE-SEEETTSTT--CHH----TT-S---HHHHHHHHHHHS-TT-EEEETT-TTTHHH
T ss_pred cccccccccccccccccccceeecC--CHHHHHHHHHhhhccceeeehhhhccChHH
Confidence 33445555555554 3465532 1222333 3467899999999999997543
No 138
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=31.91 E-value=23 Score=39.35 Aligned_cols=41 Identities=20% Similarity=0.143 Sum_probs=24.7
Q ss_pred cccCCccccccCCccccccCCCCceeeccccccccccCcccc
Q 000595 215 EEDESNEEDELFDSVCSFCDNGGDLLCCEGRCLRSFHATIDA 256 (1401)
Q Consensus 215 ~Ed~s~e~dDl~DdVCaIC~dGGeLLCCDG~C~RSFH~~Cld 256 (1401)
+||+....+...+..|.||.+.-.-..-. .|.-.|+..|+.
T Consensus 6 ~~~~~~~~~~~~~~~CpICld~~~dPVvT-~CGH~FC~~CI~ 46 (193)
T PLN03208 6 DEDDTTLVDSGGDFDCNICLDQVRDPVVT-LCGHLFCWPCIH 46 (193)
T ss_pred ccccceeccCCCccCCccCCCcCCCcEEc-CCCchhHHHHHH
Confidence 44434444555567899999854222223 588888887653
No 139
>PRK08287 cobalt-precorrin-6Y C(15)-methyltransferase; Validated
Probab=31.83 E-value=67 Score=33.80 Aligned_cols=41 Identities=17% Similarity=0.186 Sum_probs=33.5
Q ss_pred CcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHH
Q 000595 704 GRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKK 746 (1401)
Q Consensus 704 grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~ 746 (1401)
.+..|+.+--..+++.|. +.+|.+|+|++||.-.++..+.+
T Consensus 11 ~~~~~~~~~r~~~~~~l~--~~~~~~vLDiG~G~G~~~~~la~ 51 (187)
T PRK08287 11 KVPMTKEEVRALALSKLE--LHRAKHLIDVGAGTGSVSIEAAL 51 (187)
T ss_pred CCCCchHHHHHHHHHhcC--CCCCCEEEEECCcCCHHHHHHHH
Confidence 456788877777778885 45899999999999999988855
No 140
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=31.79 E-value=34 Score=38.53 Aligned_cols=41 Identities=5% Similarity=0.039 Sum_probs=28.0
Q ss_pred cchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHH
Q 000595 707 FTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKL 748 (1401)
Q Consensus 707 ftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl 748 (1401)
|+-.+..-.++-.+. -+++|++|+|+|||...++..|-+.+
T Consensus 53 ~~~qd~~s~~~~~~l-~~~~g~~VLDl~ag~G~kt~~la~~~ 93 (264)
T TIGR00446 53 YYIQEASSMIPPLAL-EPDPPERVLDMAAAPGGKTTQISALM 93 (264)
T ss_pred EEEECHHHHHHHHHh-CCCCcCEEEEECCCchHHHHHHHHHc
Confidence 333344444433222 56899999999999999998886644
No 141
>PRK07402 precorrin-6B methylase; Provisional
Probab=30.71 E-value=71 Score=33.91 Aligned_cols=41 Identities=15% Similarity=0.231 Sum_probs=32.4
Q ss_pred CcccchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHH
Q 000595 704 GRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKK 746 (1401)
Q Consensus 704 grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~ 746 (1401)
|.-.|+.+....+++.|. +.+|++|+|++||.-.|...+.+
T Consensus 20 ~~p~t~~~v~~~l~~~l~--~~~~~~VLDiG~G~G~~~~~la~ 60 (196)
T PRK07402 20 GIPLTKREVRLLLISQLR--LEPDSVLWDIGAGTGTIPVEAGL 60 (196)
T ss_pred CCCCCHHHHHHHHHHhcC--CCCCCEEEEeCCCCCHHHHHHHH
Confidence 334677777777888874 57899999999999999887754
No 142
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=30.42 E-value=17 Score=46.00 Aligned_cols=48 Identities=21% Similarity=0.364 Sum_probs=34.4
Q ss_pred ccccccccccccccccCCCCCCCCCCCCeeeecCCCCCCCCCcccccccc
Q 000595 278 FFCKNCEYKQHQCFACGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKL 327 (1401)
Q Consensus 278 W~C~nCe~gQHqCFVCGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l 327 (1401)
--|.-|..+-..|.+|...+-.--+...++.+|. .|+..||..|+...
T Consensus 502 ~~C~lC~~~gfiCe~Cq~~~iiyPF~~~~~~rC~--~C~avfH~~C~~r~ 549 (580)
T KOG1829|consen 502 KECDLCTGKGFICELCQHNDIIYPFETRNTRRCS--TCLAVFHKKCLRRK 549 (580)
T ss_pred hhchhhccCeeeeeeccCCCcccccccccceeHH--HHHHHHHHHHHhcc
Confidence 4499998888889999443321111134679998 99999999999854
No 143
>TIGR01712 phage_N6A_met phage N-6-adenine-methyltransferase. This is a model for a phage-borne DNA N-6-adenine-methyltransferase.
Probab=29.28 E-value=43 Score=36.52 Aligned_cols=35 Identities=23% Similarity=0.494 Sum_probs=26.1
Q ss_pred eeeeCCCccchhhhHHHHHHhhhcc---CCcEEEEecCCccc
Q 000595 791 IMGLNPPFGVKAGLANKFINKALEF---NPKLLILIVPPETE 829 (1401)
Q Consensus 791 imgLnPPfg~~a~lAnkFi~kal~f---~Pkliili~P~~t~ 829 (1401)
-+=+||||+- +..||.||.++ +=..+|+.+|-.|.
T Consensus 64 ~vf~NPPYS~----~~~~v~kaae~~~~~g~~~VmLlpa~ts 101 (166)
T TIGR01712 64 AVWLNPPYSR----PDIFVNKTAWFTEARQAAEVILIEADLS 101 (166)
T ss_pred eEEecCCCCc----HHHHHHHHHHHHHhhCCeEEEEEecCCc
Confidence 4556999993 47999999765 22468888888875
No 144
>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=29.20 E-value=55 Score=37.56 Aligned_cols=34 Identities=26% Similarity=0.545 Sum_probs=24.4
Q ss_pred hHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHH
Q 000595 712 KLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 712 kl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~k 747 (1401)
|++-++++| -+++|++|+|+-||--.|+..|-++
T Consensus 50 k~~~~~~~~--~l~~G~~vLDiGcGwG~~~~~~a~~ 83 (273)
T PF02353_consen 50 KLDLLCEKL--GLKPGDRVLDIGCGWGGLAIYAAER 83 (273)
T ss_dssp HHHHHHTTT--T--TT-EEEEES-TTSHHHHHHHHH
T ss_pred HHHHHHHHh--CCCCCCEEEEeCCCccHHHHHHHHH
Confidence 455566666 3899999999999999999999776
No 145
>PTZ00146 fibrillarin; Provisional
Probab=29.15 E-value=41 Score=39.40 Aligned_cols=28 Identities=4% Similarity=0.084 Sum_probs=24.5
Q ss_pred cccCCCcEEeccCCcchHHHHHHHHHhh
Q 000595 723 YVNDGDMIVDFCCGANDFSCLMKKKLDE 750 (1401)
Q Consensus 723 yv~~gd~ivdfccg~n~fs~lmk~kl~~ 750 (1401)
++++|++|+|+|||.-.|+..|-+.+..
T Consensus 129 ~IkpG~~VLDLGaG~G~~t~~lAdiVG~ 156 (293)
T PTZ00146 129 PIKPGSKVLYLGAASGTTVSHVSDLVGP 156 (293)
T ss_pred ccCCCCEEEEeCCcCCHHHHHHHHHhCC
Confidence 5899999999999999999999775533
No 146
>PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed
Probab=28.71 E-value=31 Score=37.22 Aligned_cols=29 Identities=21% Similarity=0.308 Sum_probs=23.1
Q ss_pred hcccccCCCcEEeccCCcchHHHHHHHHH
Q 000595 720 LHWYVNDGDMIVDFCCGANDFSCLMKKKL 748 (1401)
Q Consensus 720 Lh~yv~~gd~ivdfccg~n~fs~lmk~kl 748 (1401)
+-.|.+++..|||++||.-.++..|.+++
T Consensus 34 ~~~~~~~~~~VLDiGcGtG~~~~~la~~~ 62 (202)
T PRK00121 34 AELFGNDAPIHLEIGFGKGEFLVEMAKAN 62 (202)
T ss_pred HHHcCCCCCeEEEEccCCCHHHHHHHHHC
Confidence 34455688999999999999999886643
No 147
>PF05869 Dam: DNA N-6-adenine-methyltransferase (Dam); InterPro: IPR008593 This family consists of several bacterial and phage DNA N-6-adenine-methyltransferase (Dam) like sequences [].; GO: 0003677 DNA binding, 0009007 site-specific DNA-methyltransferase (adenine-specific) activity, 0032775 DNA methylation on adenine
Probab=28.49 E-value=56 Score=35.83 Aligned_cols=131 Identities=21% Similarity=0.340 Sum_probs=67.1
Q ss_pred cchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHHHhhhCCccccccccccCCCCCccccccccccccCCCCCC
Q 000595 707 FTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKKLDETGKNCLYKNYDILPAKNDFNFEKRDWMTVEPKELAP 786 (1401)
Q Consensus 707 ftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~kl~~~gk~c~~kn~dl~~~kn~f~Fe~~dw~~v~~~elp~ 786 (1401)
-|-.+-+..+...++|| .||.||-..+ ..|. +-|.. .. |.=..||-.. |.
T Consensus 15 ~TP~~lf~~l~~~fg~f------~LD~aa~~~N-------------a~~~-~y~T~--~~---DgL~~~W~~~----~~- 64 (181)
T PF05869_consen 15 QTPPELFDALNREFGPF------DLDPAASDEN-------------AKCP-RYYTE--ED---DGLAQDWSAE----LM- 64 (181)
T ss_pred cCCHHHHHHHHHHhCCc------cccccCCCCC-------------hhhh-hhcCc--cc---cHhhhhhhhc----cc-
Confidence 46667777777777874 5788875432 1231 12221 12 3334556432 11
Q ss_pred CCeeeeeeCCCccchhhhHHHHHHhhhccC---CcEEEEecCCccccccccCCCceeeeccc---cccCC-cceecCCCc
Q 000595 787 GSRLIMGLNPPFGVKAGLANKFINKALEFN---PKLLILIVPPETERLDRKESAYELVWEDD---QFLSG-KSFYLPGSV 859 (1401)
Q Consensus 787 G~~LimgLnPPfg~~a~lAnkFi~kal~f~---Pkliili~P~~t~rld~k~~~Y~liwed~---~~l~g-ksFylPGsv 859 (1401)
|. | =+||||+.. ...||.||.+.. =..|+||+|-.+.. .=|+.+++.. .+|.| -+|+.|.
T Consensus 65 g~--v-f~NPPYs~~---i~~wv~Ka~~e~~~g~~~VvLL~~~~~st-----~W~~~~~~~a~~I~fi~GRl~F~~p~-- 131 (181)
T PF05869_consen 65 GR--V-FCNPPYSRG---IGPWVEKAIEEYERGNQTVVLLPPADTST-----WWFEDALENADEIRFIRGRLKFINPV-- 131 (181)
T ss_pred ce--E-EecCchhhh---HHHHHHHHHHHHHhCCcEEEEEeccCCCc-----cHHHHHHhcCCEEEEecCceeeccCC--
Confidence 22 2 459999942 667777776532 14566777665541 1333332211 23334 2677772
Q ss_pred ccchhhhcccccCCCCeeeeecc
Q 000595 860 DENDKQMDQWNMTAPPLYLWSRH 882 (1401)
Q Consensus 860 d~ndk~~eqwn~~pP~l~lWsr~ 882 (1401)
.++.-.+.|..|-.|.+|.-.
T Consensus 132 --~g~~~~~~~~~gs~l~if~p~ 152 (181)
T PF05869_consen 132 --TGKEGKNGNPKGSMLVIFRPT 152 (181)
T ss_pred --CCccCCCCCCCceEEEEECCC
Confidence 223323455556666676543
No 148
>TIGR00675 dcm DNA-methyltransferase (dcm). All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.32 E-value=64 Score=37.46 Aligned_cols=91 Identities=20% Similarity=0.369 Sum_probs=55.3
Q ss_pred EEeccCCcchHHHHHHHHHhhhCCccccccccccCC-----CCCc--cccccccccccCCCCCCCCeeeeeeCC--Ccc-
Q 000595 730 IVDFCCGANDFSCLMKKKLDETGKNCLYKNYDILPA-----KNDF--NFEKRDWMTVEPKELAPGSRLIMGLNP--PFG- 799 (1401)
Q Consensus 730 ivdfccg~n~fs~lmk~kl~~~gk~c~~kn~dl~~~-----kn~f--~Fe~~dw~~v~~~elp~G~~LimgLnP--Pfg- 799 (1401)
||||+||+--++.=++ ..|-.+.+ -+|+-+. +.+| .+...|=-++.+.++|.=+-|+.| =| +|-
T Consensus 1 vidLF~G~GG~~~Gl~----~aG~~~~~-a~e~~~~a~~ty~~N~~~~~~~~Di~~~~~~~~~~~dvl~gg-~PCq~fS~ 74 (315)
T TIGR00675 1 FIDLFAGIGGIRLGFE----QAGFKCVF-ASEIDKYAQKTYEANFGNKVPFGDITKISPSDIPDFDILLGG-FPCQPFSI 74 (315)
T ss_pred CEEEecCccHHHHHHH----HcCCeEEE-EEeCCHHHHHHHHHhCCCCCCccChhhhhhhhCCCcCEEEec-CCCcccch
Confidence 6899999999986664 44644432 1111000 0000 223356666777778876655555 33 343
Q ss_pred ---------chhhhHHHHHHhhhccCCcEEEEecCC
Q 000595 800 ---------VKAGLANKFINKALEFNPKLLILIVPP 826 (1401)
Q Consensus 800 ---------~~a~lAnkFi~kal~f~Pkliili~P~ 826 (1401)
.++.|.-.|++-+-.++|+++|+==-+
T Consensus 75 ag~~~~~~d~r~~L~~~~~r~i~~~~P~~~v~ENV~ 110 (315)
T TIGR00675 75 AGKRKGFEDTRGTLFFEIVRILKEKKPKFFLLENVK 110 (315)
T ss_pred hcccCCCCCchhhHHHHHHHHHhhcCCCEEEeeccH
Confidence 356788889999999999998874333
No 149
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.32 E-value=12 Score=46.22 Aligned_cols=29 Identities=24% Similarity=0.854 Sum_probs=23.2
Q ss_pred CCCCCCcccccccccccchHHHHHHHhHhhccCCceeCCCCcccc
Q 000595 314 TCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAGESFTCPLHKCCI 358 (1401)
Q Consensus 314 sCGRFYHpkCLa~l~~pvde~~ateLekkIaaGksFrCPlH~C~v 358 (1401)
-|.+.||..|+..+. ++.+..||.|+|+.
T Consensus 605 PC~HifH~~CL~~WM----------------d~ykl~CPvCR~pL 633 (636)
T KOG0828|consen 605 PCHHIFHRQCLLQWM----------------DTYKLICPVCRCPL 633 (636)
T ss_pred chHHHHHHHHHHHHH----------------hhhcccCCccCCCC
Confidence 799999999999874 23458899988863
No 150
>COG1307 DegV Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.20 E-value=2.4e+02 Score=32.84 Aligned_cols=98 Identities=22% Similarity=0.275 Sum_probs=67.7
Q ss_pred HhhHHHHHHHHhhhcCCCChHHHhhhcChhhHhHHHHHhhccccccc---------------------------cccccc
Q 000595 646 TLGKAIRTALKKLDVDGSSIEDAKAVCEPEVLSQIFKWKNKLKVYLA---------------------------PFLHGM 698 (1401)
Q Consensus 646 t~gkAvr~AL~kLe~~g~siedAkAvc~p~vl~ql~~wk~kL~vyla---------------------------P~l~G~ 698 (1401)
.+|-.|..|.++++ +|.+.+ ++++.|..++++.+.|++ |.|.-.
T Consensus 123 ~~g~~v~~a~~l~~-~G~s~~--------ei~~~l~~~~~~t~~~~~v~~L~~L~kgGRIs~~~a~lg~lL~ikPIl~~~ 193 (282)
T COG1307 123 GLGFLVLEAAELAK-AGKSFE--------EILKKLEEIREKTKAYFVVDDLDNLVKGGRISKAAAFLGNLLKIKPILSFE 193 (282)
T ss_pred HHHHHHHHHHHHHH-cCCCHH--------HHHHHHHHHHhhcEEEEEECchhHHHhCCCcchhHHHHHhhhcceEEEEEe
Confidence 34558888889988 999966 467777788877777754 444433
Q ss_pred --cccccCcccchhhhHHHHHHhhcccccCCCc--EEeccCCcchHHHHHHHHHhhhC
Q 000595 699 --RYTSFGRHFTKVDKLQAIVDKLHWYVNDGDM--IVDFCCGANDFSCLMKKKLDETG 752 (1401)
Q Consensus 699 --ryts~grhftk~ekl~~i~~~Lh~yv~~gd~--ivdfccg~n~fs~lmk~kl~~~g 752 (1401)
++..+++-+|..-.++.+++.+.=.+.++.. ++-.--..++--..++++|.+.+
T Consensus 194 ~G~~~~~~K~R~~kka~~~l~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~~~ 251 (282)
T COG1307 194 DGELVLLGKVRGQKKAIKKLIELLKKEVKDGAGYRVAVLHGDAPEAAEQLKEKLLNKF 251 (282)
T ss_pred CCEEEEEeecccHHHHHHHHHHHHHHHhccCCceEEEEEeCCchhHHHHHHHHHHhhc
Confidence 6779999999999999999999888864333 33333333343455556566543
No 151
>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=25.64 E-value=17 Score=33.97 Aligned_cols=15 Identities=53% Similarity=1.333 Sum_probs=13.8
Q ss_pred CCCCCCccccccccc
Q 000595 314 TCGHFYHPHCVSKLL 328 (1401)
Q Consensus 314 sCGRFYHpkCLa~l~ 328 (1401)
.|+..||..||..++
T Consensus 49 ~C~H~FH~~Ci~~Wl 63 (73)
T PF12678_consen 49 PCGHIFHFHCISQWL 63 (73)
T ss_dssp TTSEEEEHHHHHHHH
T ss_pred ccCCCEEHHHHHHHH
Confidence 699999999999886
No 152
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=25.63 E-value=87 Score=37.86 Aligned_cols=25 Identities=20% Similarity=0.420 Sum_probs=21.8
Q ss_pred ccCCCcEEeccCCcchHHHHHHHHH
Q 000595 724 VNDGDMIVDFCCGANDFSCLMKKKL 748 (1401)
Q Consensus 724 v~~gd~ivdfccg~n~fs~lmk~kl 748 (1401)
+++|++|+|+|||.-.++..|-+++
T Consensus 248 ~~~g~~VLDlgaG~G~~t~~la~~~ 272 (444)
T PRK14902 248 PKGGDTVLDACAAPGGKTTHIAELL 272 (444)
T ss_pred CCCCCEEEEeCCCCCHHHHHHHHHh
Confidence 4789999999999999998887654
No 153
>cd02440 AdoMet_MTases S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
Probab=25.56 E-value=75 Score=27.55 Aligned_cols=89 Identities=17% Similarity=0.346 Sum_probs=44.3
Q ss_pred cEEeccCCcchHHHHHHHHHhhhCCccccccccc-------cC------CCCCccccccccccccCCCCCCCCeeeeeeC
Q 000595 729 MIVDFCCGANDFSCLMKKKLDETGKNCLYKNYDI-------LP------AKNDFNFEKRDWMTVEPKELAPGSRLIMGLN 795 (1401)
Q Consensus 729 ~ivdfccg~n~fs~lmk~kl~~~gk~c~~kn~dl-------~~------~kn~f~Fe~~dw~~v~~~elp~G~~LimgLn 795 (1401)
+|+|+.||...++..|-+ ..+ +.+--.|+ .+ ......|...|+...... .+.+=.+|+- |
T Consensus 1 ~ildig~G~G~~~~~~~~---~~~--~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~d~i~~-~ 73 (107)
T cd02440 1 RVLDLGCGTGALALALAS---GPG--ARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPE-ADESFDVIIS-D 73 (107)
T ss_pred CeEEEcCCccHHHHHHhc---CCC--CEEEEEeCCHHHHHHHHHHHhcccccceEEEEcChhhhccc-cCCceEEEEE-c
Confidence 589999999998887754 111 11111111 11 112344555555554431 1222235544 7
Q ss_pred CCccchhhhHHHHHHhhhc-cCCcEEEEec
Q 000595 796 PPFGVKAGLANKFINKALE-FNPKLLILIV 824 (1401)
Q Consensus 796 PPfg~~a~lAnkFi~kal~-f~Pkliili~ 824 (1401)
+||..-......++..++. .+|.=++++.
T Consensus 74 ~~~~~~~~~~~~~l~~~~~~l~~~g~~~~~ 103 (107)
T cd02440 74 PPLHHLVEDLARFLEEARRLLKPGGVLVLT 103 (107)
T ss_pred cceeehhhHHHHHHHHHHHHcCCCCEEEEE
Confidence 8877623345555555443 3565555544
No 154
>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=25.31 E-value=45 Score=41.14 Aligned_cols=43 Identities=28% Similarity=0.767 Sum_probs=33.4
Q ss_pred CcccccccccccccccccCCCCCCCCCCCCeeeecCCCCCCCCCcccccccc
Q 000595 276 LNFFCKNCEYKQHQCFACGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKL 327 (1401)
Q Consensus 276 ~sW~C~nCe~gQHqCFVCGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l 327 (1401)
..=+|..|. |.+|.+.... ..+--.+.|. .|+.+-|..|--..
T Consensus 122 ~~gFC~~C~-----C~iC~kfD~~--~n~~~Wi~Cd--~CgH~cH~dCALr~ 164 (446)
T PF07227_consen 122 EPGFCRRCM-----CCICSKFDDN--KNTCSWIGCD--VCGHWCHLDCALRH 164 (446)
T ss_pred CCCccccCC-----ccccCCcccC--CCCeeEEecc--CCCceehhhhhccc
Confidence 455789995 9999987432 3455789998 89999999998754
No 155
>PRK04266 fibrillarin; Provisional
Probab=25.14 E-value=81 Score=35.23 Aligned_cols=36 Identities=11% Similarity=0.219 Sum_probs=27.2
Q ss_pred HHHHHHhh-cccccCCCcEEeccCCcchHHHHHHHHH
Q 000595 713 LQAIVDKL-HWYVNDGDMIVDFCCGANDFSCLMKKKL 748 (1401)
Q Consensus 713 l~~i~~~L-h~yv~~gd~ivdfccg~n~fs~lmk~kl 748 (1401)
...|...+ .--+.+|++|+|++||..-|+..|.+..
T Consensus 58 ~~~ll~~~~~l~i~~g~~VlD~G~G~G~~~~~la~~v 94 (226)
T PRK04266 58 AAAILKGLKNFPIKKGSKVLYLGAASGTTVSHVSDIV 94 (226)
T ss_pred HHHHHhhHhhCCCCCCCEEEEEccCCCHHHHHHHHhc
Confidence 44455544 2357899999999999999999886644
No 156
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=24.92 E-value=96 Score=33.18 Aligned_cols=39 Identities=28% Similarity=0.454 Sum_probs=30.1
Q ss_pred cchhhhHHHHHHhhcccccCCCcEEeccCCcchHHHHHHHH
Q 000595 707 FTKVDKLQAIVDKLHWYVNDGDMIVDFCCGANDFSCLMKKK 747 (1401)
Q Consensus 707 ftk~ekl~~i~~~Lh~yv~~gd~ivdfccg~n~fs~lmk~k 747 (1401)
+|+.|.-.-++.+|. +.+|++|+|++||.-.|+..+-+.
T Consensus 23 ~t~~~~r~~~l~~l~--~~~~~~vlDlG~GtG~~s~~~a~~ 61 (198)
T PRK00377 23 MTKEEIRALALSKLR--LRKGDMILDIGCGTGSVTVEASLL 61 (198)
T ss_pred CCHHHHHHHHHHHcC--CCCcCEEEEeCCcCCHHHHHHHHH
Confidence 777766444456664 679999999999999999877543
No 157
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=24.52 E-value=31 Score=45.16 Aligned_cols=93 Identities=20% Similarity=0.440 Sum_probs=0.0
Q ss_pred cccccCCccccccCC----CCceeeccccccccccCccccCcccccccCCCChhhhhccCcccccccccccc------cc
Q 000595 221 EEDELFDSVCSFCDN----GGDLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYKQH------QC 290 (1401)
Q Consensus 221 e~dDl~DdVCaIC~d----GGeLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~gQH------qC 290 (1401)
++-......|.||-. ...+..|. .|...||+.|+...... .+......|.|+.|.+.+. .|
T Consensus 185 ~~l~~~~yeCmIC~e~I~~t~~~WSC~-sCYhVFHl~CI~~WArs--------~ek~~~~~WrCP~Cqsv~~~~~~~y~C 255 (950)
T KOG1952|consen 185 EQLSNRKYECMICTERIKRTAPVWSCK-SCYHVFHLNCIKKWARS--------SEKTGQDGWRCPACQSVSKTVPKTYLC 255 (950)
T ss_pred HHHhcCceEEEEeeeeccccCCceecc-hhhhhhhHHHHHHHHHH--------hhhccCccccCCcccchhccCCcccce
Q ss_pred cccCCCCCCCCCCCCeeeecCCCCCCCCCccccc
Q 000595 291 FACGKLGSSDKETGAEVFPCVSATCGHFYHPHCV 324 (1401)
Q Consensus 291 FVCGklGSSDk~SGaEVfrCsvasCGRFYHpkCL 324 (1401)
| ||+....+-..+.--.-|. ..|++.--..|.
T Consensus 256 ~-CGk~~nP~~~~~~~PHSCG-E~C~k~~~~~C~ 287 (950)
T KOG1952|consen 256 F-CGKVKNPEFSRNELPHSCG-EVCGKPRPGGCP 287 (950)
T ss_pred e-cCcccCCCCCCCCCCcccc-ccccCCCCCCCC
No 158
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=24.46 E-value=34 Score=39.61 Aligned_cols=138 Identities=17% Similarity=0.338 Sum_probs=0.0
Q ss_pred cCCccccccCC--CCceeeccccccccccCccccCcccccccCCCChhhhhccCcccccccccc-------cccccccCC
Q 000595 225 LFDSVCSFCDN--GGDLLCCEGRCLRSFHATIDAGEESHCASLGLTKDEVEAMLNFFCKNCEYK-------QHQCFACGK 295 (1401)
Q Consensus 225 l~DdVCaIC~d--GGeLLCCDG~C~RSFH~~CldGeeS~CltLGLTeaEvq~~~sW~C~nCe~g-------QHqCFVCGk 295 (1401)
++...|..|+. -|..+.=.. .++|+.|..-.. |....-+.--+...++-+|..|..+ ...|..|+.
T Consensus 71 LfaPcC~kC~EFiiGrVikamn---nSwHp~CF~Cd~--Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~ 145 (332)
T KOG2272|consen 71 LFAPCCGKCGEFIIGRVIKAMN---NSWHPACFRCDL--CNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHA 145 (332)
T ss_pred hhchhhcccccchhhHHHHhhc---cccCcccchhHH--HHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhh
Q ss_pred CCCCCCCCCCeeeecCCCCCCCCCcccccccccccchHHHHHHHhHhhccCCceeCCCCc-------ccccCCCCCCC--
Q 000595 296 LGSSDKETGAEVFPCVSATCGHFYHPHCVSKLLLRDDEVAADQLAKSIIAGESFTCPLHK-------CCICKQGENKA-- 366 (1401)
Q Consensus 296 lGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~~pvde~~ateLekkIaaGksFrCPlH~-------C~vCkqseDkn-- 366 (1401)
.-+ .+.+.=. ..--..||-+|..-...-..+.. ......+|+.|. |..|++.=+..
T Consensus 146 ~iD------~~~l~fr-~d~yH~yHFkCt~C~keL~sdaR--------evk~eLyClrChD~mgipiCgaC~rpIeervi 210 (332)
T KOG2272|consen 146 HID------EQPLTFR-GDPYHPYHFKCTTCGKELTSDAR--------EVKGELYCLRCHDKMGIPICGACRRPIEERVI 210 (332)
T ss_pred hcc------ccccccc-CCCCCccceecccccccccchhh--------hhccceeccccccccCCcccccccCchHHHHH
Q ss_pred -----CCCCceeecccCCccc
Q 000595 367 -----DSDLQFAVCRRCPKAY 382 (1401)
Q Consensus 367 -----~segKLI~CdRCPkAY 382 (1401)
-....-.+|..|.+-|
T Consensus 211 ~amgKhWHveHFvCa~CekPF 231 (332)
T KOG2272|consen 211 FAMGKHWHVEHFVCAKCEKPF 231 (332)
T ss_pred HHhccccchhheeehhcCCcc
No 159
>COG2890 HemK Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]
Probab=24.13 E-value=66 Score=36.98 Aligned_cols=65 Identities=17% Similarity=0.163 Sum_probs=37.6
Q ss_pred cEEeccCCcchHHHHHHHHHhh---hCCccc-------cccccccCCCCCccccccccccccCCCCCCCCeeeeeeCCCc
Q 000595 729 MIVDFCCGANDFSCLMKKKLDE---TGKNCL-------YKNYDILPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLNPPF 798 (1401)
Q Consensus 729 ~ivdfccg~n~fs~lmk~kl~~---~gk~c~-------~kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLnPPf 798 (1401)
+|+|+|||+---.--+..+.-. ++-+++ =+|-....- .++.|...||+.--.+ .=.||+- ||||
T Consensus 113 ~ilDlGTGSG~iai~la~~~~~~~V~a~Dis~~Al~~A~~Na~~~~l-~~~~~~~~dlf~~~~~----~fDlIVs-NPPY 186 (280)
T COG2890 113 RILDLGTGSGAIAIALAKEGPDAEVIAVDISPDALALARENAERNGL-VRVLVVQSDLFEPLRG----KFDLIVS-NPPY 186 (280)
T ss_pred cEEEecCChHHHHHHHHhhCcCCeEEEEECCHHHHHHHHHHHHHcCC-ccEEEEeeecccccCC----ceeEEEe-CCCC
Confidence 7999999999888777665532 222222 223333332 3355555588764332 2235555 9998
Q ss_pred c
Q 000595 799 G 799 (1401)
Q Consensus 799 g 799 (1401)
=
T Consensus 187 i 187 (280)
T COG2890 187 I 187 (280)
T ss_pred C
Confidence 5
No 160
>PRK06202 hypothetical protein; Provisional
Probab=23.58 E-value=75 Score=34.56 Aligned_cols=38 Identities=16% Similarity=0.237 Sum_probs=26.9
Q ss_pred cCCCcEEeccCCcchHHHHHHHHHhhhCCccccccccc
Q 000595 725 NDGDMIVDFCCGANDFSCLMKKKLDETGKNCLYKNYDI 762 (1401)
Q Consensus 725 ~~gd~ivdfccg~n~fs~lmk~kl~~~gk~c~~kn~dl 762 (1401)
..+.+|+|++||.-+++..|.+.+.+.|....+--.|+
T Consensus 59 ~~~~~iLDlGcG~G~~~~~L~~~~~~~g~~~~v~gvD~ 96 (232)
T PRK06202 59 DRPLTLLDIGCGGGDLAIDLARWARRDGLRLEVTAIDP 96 (232)
T ss_pred CCCcEEEEeccCCCHHHHHHHHHHHhCCCCcEEEEEcC
Confidence 57789999999999999888765554454444444443
No 161
>KOG4217 consensus Nuclear receptors of the nerve growth factor-induced protein B type [Transcription]
Probab=23.52 E-value=22 Score=43.89 Aligned_cols=26 Identities=31% Similarity=0.875 Sum_probs=19.8
Q ss_pred CccccccCCCC-----ceeeccccccccccCc
Q 000595 227 DSVCSFCDNGG-----DLLCCEGRCLRSFHAT 253 (1401)
Q Consensus 227 DdVCaIC~dGG-----eLLCCDG~C~RSFH~~ 253 (1401)
+..|++|++.. ..-.|+| |...|--+
T Consensus 269 e~~CAVCgDnAaCqHYGvRTCEG-CKGFFKRT 299 (605)
T KOG4217|consen 269 EGLCAVCGDNAACQHYGVRTCEG-CKGFFKRT 299 (605)
T ss_pred cceeeecCChHHhhhcCcccccc-chHHHHHH
Confidence 78999999853 3567996 88877654
No 162
>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=23.38 E-value=36 Score=33.55 Aligned_cols=14 Identities=57% Similarity=1.018 Sum_probs=12.8
Q ss_pred CCCChHHHhhhcCh
Q 000595 661 DGSSIEDAKAVCEP 674 (1401)
Q Consensus 661 ~g~siedAkAvc~p 674 (1401)
.|||++||||+|+.
T Consensus 42 kGCsidD~k~iC~~ 55 (92)
T PF05413_consen 42 KGCSIDDLKAICEK 55 (92)
T ss_pred CCCCHHHHHHHHhh
Confidence 79999999999973
No 163
>PLN02271 serine hydroxymethyltransferase
Probab=23.05 E-value=49 Score=42.13 Aligned_cols=17 Identities=53% Similarity=0.868 Sum_probs=12.8
Q ss_pred CCCCCCCeeeeeeCCCcc
Q 000595 782 KELAPGSRLIMGLNPPFG 799 (1401)
Q Consensus 782 ~elp~G~~LimgLnPPfg 799 (1401)
.=|.+|+ -||||+.++|
T Consensus 233 ALl~PGD-~IL~ldl~~G 249 (586)
T PLN02271 233 GLLLPGD-RIMGLDSPSG 249 (586)
T ss_pred HhcCCCC-EEEEecCCCC
Confidence 4467787 5788888887
No 164
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=22.93 E-value=46 Score=36.68 Aligned_cols=40 Identities=23% Similarity=0.593 Sum_probs=27.7
Q ss_pred eCCCC-----cccccCCCCCCC-CCCCceeecccCCccccccCCCC
Q 000595 350 TCPLH-----KCCICKQGENKA-DSDLQFAVCRRCPKAYHRKCLPR 389 (1401)
Q Consensus 350 rCPlH-----~C~vCkqseDkn-~segKLI~CdRCPkAYH~kCLPP 389 (1401)
.|++| .|..|..++--= ......++|..|-..||..|...
T Consensus 144 ~C~lC~~kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~ 189 (202)
T PF13901_consen 144 SCELCQQKGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK 189 (202)
T ss_pred HhHHHHhCCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC
Confidence 46554 489997763210 11225789999999999999875
No 165
>COG0461 PyrE Orotate phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=22.62 E-value=24 Score=39.37 Aligned_cols=35 Identities=23% Similarity=0.389 Sum_probs=29.6
Q ss_pred hhhhHhHhhHHHHHHHHhhhcCCCChHHHhhhcCh
Q 000595 640 AVDKAITLGKAIRTALKKLDVDGSSIEDAKAVCEP 674 (1401)
Q Consensus 640 ~~~k~it~gkAvr~AL~kLe~~g~siedAkAvc~p 674 (1401)
+||+.||+|++|+.|.+.|+.+|+.+..+=++-+-
T Consensus 117 vVEDViTTG~Si~eai~~l~~~G~~V~gv~~ivDR 151 (201)
T COG0461 117 VVEDVITTGGSILEAVEALREAGAEVVGVAVIVDR 151 (201)
T ss_pred EEEecccCCHhHHHHHHHHHHcCCeEEEEEEEEec
Confidence 48999999999999999998899988776555543
No 166
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=22.47 E-value=47 Score=32.90 Aligned_cols=33 Identities=30% Similarity=0.594 Sum_probs=22.2
Q ss_pred cccccCCCCCCCCCCCCeeeecCCCCCCCCCcccccccccc
Q 000595 289 QCFACGKLGSSDKETGAEVFPCVSATCGHFYHPHCVSKLLL 329 (1401)
Q Consensus 289 qCFVCGklGSSDk~SGaEVfrCsvasCGRFYHpkCLa~l~~ 329 (1401)
.|-.|..+|.. -.+..+ .|+..||..||..++.
T Consensus 34 ~Cp~Ck~Pgd~-----Cplv~g---~C~H~FH~hCI~kWl~ 66 (85)
T PF12861_consen 34 CCPDCKFPGDD-----CPLVWG---KCSHNFHMHCILKWLS 66 (85)
T ss_pred CCCCccCCCCC-----Cceeec---cCccHHHHHHHHHHHc
Confidence 35556555531 234444 5999999999999874
No 167
>PRK10458 DNA cytosine methylase; Provisional
Probab=22.42 E-value=3.4e+02 Score=33.93 Aligned_cols=121 Identities=21% Similarity=0.395 Sum_probs=68.3
Q ss_pred cEEeccCCcchHHHHHHHHHhhhCCcccc-------------ccccccCCCCCccccccccccccC--------------
Q 000595 729 MIVDFCCGANDFSCLMKKKLDETGKNCLY-------------KNYDILPAKNDFNFEKRDWMTVEP-------------- 781 (1401)
Q Consensus 729 ~ivdfccg~n~fs~lmk~kl~~~gk~c~~-------------kn~dl~~~kn~f~Fe~~dw~~v~~-------------- 781 (1401)
++|||+||.--|+.=++ ..|..|.+ .||--.+....| ..|=-+|..
T Consensus 90 ~~iDLFsGiGGl~lGfe----~aG~~~v~a~Eid~~A~~TY~~N~~~~p~~~~~---~~DI~~i~~~~~~~~~~~~~~~~ 162 (467)
T PRK10458 90 RFIDLFAGIGGIRRGFE----AIGGQCVFTSEWNKHAVRTYKANWYCDPATHRF---NEDIRDITLSHKEGVSDEEAAEH 162 (467)
T ss_pred eEEEeCcCccHHHHHHH----HcCCEEEEEEechHHHHHHHHHHcCCCCcccee---ccChhhCccccccccchhhhhhh
Confidence 69999999999998775 45777754 233100100111 122223332
Q ss_pred --CCCCCCCeeeeeeCC--Cccch-------------------hhhHHHHHHhhhccCCcEEEEecCCcccccccc----
Q 000595 782 --KELAPGSRLIMGLNP--PFGVK-------------------AGLANKFINKALEFNPKLLILIVPPETERLDRK---- 834 (1401)
Q Consensus 782 --~elp~G~~LimgLnP--Pfg~~-------------------a~lAnkFi~kal~f~Pkliili~P~~t~rld~k---- 834 (1401)
.++|.=+-|+.| =| ||-+. +.|.-.|+.-+-.++|+++||===+.....|+.
T Consensus 163 ~~~~~p~~DvL~gG-pPCQ~FS~AG~~k~~~~gr~~g~~~d~rg~Lf~~~~rii~~~kPk~fvlENV~gl~s~~~g~~f~ 241 (467)
T PRK10458 163 IRQHIPDHDVLLAG-FPCQPFSLAGVSKKNSLGRAHGFECETQGTLFFDVARIIDAKRPAIFVLENVKNLKSHDKGKTFR 241 (467)
T ss_pred hhccCCCCCEEEEc-CCCCccchhcccccccccccccccCCccccHHHHHHHHHHHhCCCEEEEeCcHhhhcccccHHHH
Confidence 245555655555 45 67532 336677777777899999887432222222221
Q ss_pred -------CCCceeeec------cccccCCcceecCCC
Q 000595 835 -------ESAYELVWE------DDQFLSGKSFYLPGS 858 (1401)
Q Consensus 835 -------~~~Y~liwe------d~~~l~gksFylPGs 858 (1401)
.-+|.+.|- +-.+|.+.-| +|=.
T Consensus 242 ~i~~~L~~lGY~v~~~~~~g~~~~~vlna~~f-VPQ~ 277 (467)
T PRK10458 242 IIMQTLDELGYDVADAEDNGPDDPKIIDGKHF-LPQH 277 (467)
T ss_pred HHHHHHHHcCCeEEeccccCcccceEeehhhC-CCcc
Confidence 358998763 3356666655 7754
No 168
>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]
Probab=22.20 E-value=60 Score=39.00 Aligned_cols=40 Identities=25% Similarity=0.537 Sum_probs=31.7
Q ss_pred CCcccCcCcc--ccccchhhhhhcCCCCCCCCCCCCCCCCCCCC-CCCCCCCCc
Q 000595 1275 LGYRPSMSTD--RELTMWPLARIYGQDFPAPTPGYGQMGSVPSN-LYGNLGSSA 1325 (1401)
Q Consensus 1275 ~~~~~~~~~~--~~~~~~~~~~~yg~~~~~~~~~~~~m~s~~s~-~y~~~gs~~ 1325 (1401)
=||||.+.++ -..++|++++.| .-|++.|++ .||.+|.+.
T Consensus 33 ekyrP~~l~dv~~~~ei~st~~~~-----------~~~~~lPh~L~YgPPGtGk 75 (360)
T KOG0990|consen 33 EKYRPPFLGIVIKQEPIWSTENRY-----------SGMPGLPHLLFYGPPGTGK 75 (360)
T ss_pred cCCCCchhhhHhcCCchhhHHHHh-----------ccCCCCCcccccCCCCCCC
Confidence 3899999998 677899999887 556667764 588888876
No 169
>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=21.92 E-value=53 Score=31.23 Aligned_cols=28 Identities=18% Similarity=0.382 Sum_probs=19.1
Q ss_pred CccccccCCC--CceeeccccccccccCccc
Q 000595 227 DSVCSFCDNG--GDLLCCEGRCLRSFHATID 255 (1401)
Q Consensus 227 DdVCaIC~dG--GeLLCCDG~C~RSFH~~Cl 255 (1401)
+..|.+|++. ...+.-- +|...||..|.
T Consensus 78 ~~~C~vC~k~l~~~~f~~~-p~~~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVF-PCGHVVHYSCI 107 (109)
T ss_pred CCCccCcCCcCCCceEEEe-CCCeEEecccc
Confidence 3679999982 3322222 67899999974
No 170
>KOG2187 consensus tRNA uracil-5-methyltransferase and related tRNA-modifying enzymes [Translation, ribosomal structure and biogenesis]
Probab=21.85 E-value=1.9e+02 Score=36.65 Aligned_cols=126 Identities=20% Similarity=0.405 Sum_probs=77.7
Q ss_pred cccccccccccccc-ccCcccchh----hhHHHHHHhhcccccCC-CcEEeccCCcchHHHHHHHHHh------------
Q 000595 688 KVYLAPFLHGMRYT-SFGRHFTKV----DKLQAIVDKLHWYVNDG-DMIVDFCCGANDFSCLMKKKLD------------ 749 (1401)
Q Consensus 688 ~vylaP~l~G~ryt-s~grhftk~----ekl~~i~~~Lh~yv~~g-d~ivdfccg~n~fs~lmk~kl~------------ 749 (1401)
+.|+-=-|.|.|++ |=|-+|-.- |+|-.+|.- |--.++ -++||.|||..-|+--+.+.-.
T Consensus 341 ~~~I~E~l~~ltF~iSp~AFFQ~Nt~~aevLys~i~e--~~~l~~~k~llDv~CGTG~iglala~~~~~ViGvEi~~~aV 418 (534)
T KOG2187|consen 341 DPYITESLLGLTFRISPGAFFQTNTSAAEVLYSTIGE--WAGLPADKTLLDVCCGTGTIGLALARGVKRVIGVEISPDAV 418 (534)
T ss_pred ccEEEeecCCeEEEECCchhhccCcHHHHHHHHHHHH--HhCCCCCcEEEEEeecCCceehhhhccccceeeeecChhhc
Confidence 34555556677776 778888543 333333322 433444 4589999999999866544321
Q ss_pred -hhCCc---cccccccccCCCCCccccccccccccCCCCCCCCeeeeeeCCCccchhhhHHHHHHhhhccC-CcEEEEec
Q 000595 750 -ETGKN---CLYKNYDILPAKNDFNFEKRDWMTVEPKELAPGSRLIMGLNPPFGVKAGLANKFINKALEFN-PKLLILIV 824 (1401)
Q Consensus 750 -~~gk~---c~~kn~dl~~~kn~f~Fe~~dw~~v~~~elp~G~~LimgLnPPfg~~a~lAnkFi~kal~f~-Pkliili~ 824 (1401)
...+. =.--|=++|+.+.- |=|+.--+-...+.+|||-++||= +-|=-|||.-.+.++ |+.||.|+
T Consensus 419 ~dA~~nA~~NgisNa~Fi~gqaE------~~~~sl~~~~~~~~~~v~iiDPpR---~Glh~~~ik~l~~~~~~~rlvyvS 489 (534)
T KOG2187|consen 419 EDAEKNAQINGISNATFIVGQAE------DLFPSLLTPCCDSETLVAIIDPPR---KGLHMKVIKALRAYKNPRRLVYVS 489 (534)
T ss_pred chhhhcchhcCccceeeeecchh------hccchhcccCCCCCceEEEECCCc---ccccHHHHHHHHhccCccceEEEE
Confidence 11111 11346666664221 222222332234666999999995 779999999999999 99998886
No 171
>TIGR01091 upp uracil phosphoribosyltransferase. that includes uracil phosphoribosyltransferase, uridine kinases, and other, uncharacterized proteins.
Probab=21.76 E-value=44 Score=36.67 Aligned_cols=52 Identities=25% Similarity=0.364 Sum_probs=43.1
Q ss_pred hhhHhHhhHHHHHHHHhhhcCC-CChHHHhhhcChhhHhHHHHHhhccccccc
Q 000595 641 VDKAITLGKAIRTALKKLDVDG-SSIEDAKAVCEPEVLSQIFKWKNKLKVYLA 692 (1401)
Q Consensus 641 ~~k~it~gkAvr~AL~kLe~~g-~siedAkAvc~p~vl~ql~~wk~kL~vyla 692 (1401)
+|..|.+|..+..|++.|...| .+|.=|=.++.|+-|.+|....-++++|.|
T Consensus 128 vDd~laTG~Tl~~ai~~L~~~G~~~I~v~~ll~~~~gl~~l~~~~p~v~i~~~ 180 (207)
T TIGR01091 128 LDPMLATGGTMIAALDLLKKRGAKKIKVLSIVAAPEGIEAVEKAHPDVDIYTA 180 (207)
T ss_pred ECCCccchHHHHHHHHHHHHcCCCEEEEEEEecCHHHHHHHHHHCCCCEEEEE
Confidence 8999999999999999986455 234445567899999999999899999988
No 172
>KOG3092 consensus Casein kinase II, beta subunit [Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Transcription]
Probab=21.64 E-value=84 Score=35.46 Aligned_cols=31 Identities=29% Similarity=0.699 Sum_probs=21.9
Q ss_pred cCCccccc--cCCCCCccccccccccccccccccccCCCceeEeccCC
Q 000595 377 RCPKAYHR--KCLPRKIAFEDKLEEGIITRAWEGLLPNHRILIYCLKH 422 (1401)
Q Consensus 377 RCPkAYH~--kCLPPpIsfe~~~~EgIp~RAW~cLLpncRiLIyCpkH 422 (1401)
+||+.|+. .|||.++. +++.. ..+.||||++
T Consensus 108 ~CPRV~C~~q~~LPvGLs-------Dipg~--------~~VklYCP~C 140 (216)
T KOG3092|consen 108 RCPRVYCCGQPVLPVGLS-------DIPGK--------STVKLYCPSC 140 (216)
T ss_pred cCCcccccCCcccccccc-------CCCCc--------ceEEEeCCCc
Confidence 57777776 58998885 34321 2468999999
No 173
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=20.88 E-value=87 Score=32.71 Aligned_cols=38 Identities=29% Similarity=0.432 Sum_probs=29.6
Q ss_pred ccccccchhhhHhHhhH-----HHHHHHHhhhcCCCChHHHhhhcChhhHhHHHHH
Q 000595 633 HAYASKSAVDKAITLGK-----AIRTALKKLDVDGSSIEDAKAVCEPEVLSQIFKW 683 (1401)
Q Consensus 633 ~~~~~~~~~~k~it~gk-----Avr~AL~kLe~~g~siedAkAvc~p~vl~ql~~w 683 (1401)
.+.-++.++||.||++| |=|.|+..|. +.++++.||..
T Consensus 40 KAKelr~~vEkLITlaK~~~l~~RR~a~~~l~-------------d~~~v~kLF~~ 82 (116)
T COG0203 40 KAKELRRVVEKLITLAKKGDLANRRLAFARLR-------------DKDAVKKLFDE 82 (116)
T ss_pred HHHHHHHHHHHHHHHhhcccHHHHHHHHHHcc-------------cHHHHHHHHHH
Confidence 45667889999999999 6677777766 44688888866
No 174
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=20.82 E-value=97 Score=37.59 Aligned_cols=26 Identities=19% Similarity=0.471 Sum_probs=21.8
Q ss_pred ccCCCcEEeccCCcchHHHHHHHHHh
Q 000595 724 VNDGDMIVDFCCGANDFSCLMKKKLD 749 (1401)
Q Consensus 724 v~~gd~ivdfccg~n~fs~lmk~kl~ 749 (1401)
.++|++|+|+|||...++..|-+.+.
T Consensus 248 ~~~g~~VLDlgaG~G~kt~~la~~~~ 273 (445)
T PRK14904 248 PQPGSTVLDLCAAPGGKSTFMAELMQ 273 (445)
T ss_pred CCCCCEEEEECCCCCHHHHHHHHHhC
Confidence 47899999999999999988866543
No 175
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=20.46 E-value=71 Score=38.56 Aligned_cols=25 Identities=16% Similarity=0.407 Sum_probs=21.5
Q ss_pred ccCCCcEEeccCCcchHHHHHHHHH
Q 000595 724 VNDGDMIVDFCCGANDFSCLMKKKL 748 (1401)
Q Consensus 724 v~~gd~ivdfccg~n~fs~lmk~kl 748 (1401)
+++|++|+|+|||...++..|-+.+
T Consensus 250 ~~~g~~VLDl~ag~G~kt~~la~~~ 274 (434)
T PRK14901 250 PQPGEVILDACAAPGGKTTHIAELM 274 (434)
T ss_pred CCCcCEEEEeCCCCchhHHHHHHHh
Confidence 5789999999999999998886643
No 176
>PF10237 N6-adenineMlase: Probable N6-adenine methyltransferase; InterPro: IPR019369 This family of proteins, which are of approximately 200 residues in length, contain a highly conserved Glu-Phe-Trp (QFW) motif close to the N terminus and an Asp/Asn-Pro-Pro-Tyr/Phe motif in the centre. This latter motif is characteristic of N-6 adenine-specific DNA methylases and could be involved in substrate binding or in the catalytic activity (, ).
Probab=20.39 E-value=1e+02 Score=33.37 Aligned_cols=47 Identities=28% Similarity=0.424 Sum_probs=26.6
Q ss_pred CCCCCCCCeeeeeeCCCccchhhhHHHHHHhhhc-cCC-cEEEEecCCccc
Q 000595 781 PKELAPGSRLIMGLNPPFGVKAGLANKFINKALE-FNP-KLLILIVPPETE 829 (1401)
Q Consensus 781 ~~elp~G~~LimgLnPPfg~~a~lAnkFi~kal~-f~P-kliili~P~~t~ 829 (1401)
|.+| +|+..+|-.+||| +.-.++.|+..-+-- .+| -=||++.+.+.+
T Consensus 80 ~~~l-~~~~d~vv~DPPF-l~~ec~~k~a~ti~~L~k~~~kii~~Tg~~~~ 128 (162)
T PF10237_consen 80 PEEL-KGKFDVVVIDPPF-LSEECLTKTAETIRLLLKPGGKIILCTGEEME 128 (162)
T ss_pred hhhc-CCCceEEEECCCC-CCHHHHHHHHHHHHHHhCccceEEEecHHHHH
Confidence 3444 7899999999999 544455444332211 122 234566665543
No 177
>COG2264 PrmA Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]
Probab=20.30 E-value=1.3e+02 Score=35.74 Aligned_cols=61 Identities=28% Similarity=0.558 Sum_probs=47.2
Q ss_pred HHhhcccccccccccccccc-----------------------cc--CcccchhhhHHHHHHhhcccccCCCcEEeccCC
Q 000595 682 KWKNKLKVYLAPFLHGMRYT-----------------------SF--GRHFTKVDKLQAIVDKLHWYVNDGDMIVDFCCG 736 (1401)
Q Consensus 682 ~wk~kL~vylaP~l~G~ryt-----------------------s~--grhftk~ekl~~i~~~Lh~yv~~gd~ivdfccg 736 (1401)
.|.+.-+=|+-|+.-|.|.+ .| |-|=|..-+|+.+=+ |+++|.+|+||=||
T Consensus 97 DW~~~wk~~~~P~rig~~f~I~Psw~~~~~~~~~~~i~lDPGlAFGTG~HpTT~lcL~~Le~----~~~~g~~vlDvGcG 172 (300)
T COG2264 97 DWEREWKKYFHPVRIGERFVIVPSWREYPEPSDELNIELDPGLAFGTGTHPTTSLCLEALEK----LLKKGKTVLDVGCG 172 (300)
T ss_pred HHHHHHHhcCCcEEeeeeEEECCCCccCCCCCCceEEEEccccccCCCCChhHHHHHHHHHH----hhcCCCEEEEecCC
Confidence 45555556777988888765 24 567788888877655 45599999999999
Q ss_pred cchHHHHHHH
Q 000595 737 ANDFSCLMKK 746 (1401)
Q Consensus 737 ~n~fs~lmk~ 746 (1401)
+-.++--+.+
T Consensus 173 SGILaIAa~k 182 (300)
T COG2264 173 SGILAIAAAK 182 (300)
T ss_pred hhHHHHHHHH
Confidence 9999998876
No 178
>PF02645 DegV: Uncharacterised protein, DegV family COG1307; InterPro: IPR003797 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 other than to most homologs from other species. This suggests both recent paralogy and diversity of function.; PDB: 2DT8_A 3LUP_A 3NYI_B 3PL5_A 1PZX_B 1MGP_A 1VPV_B 3FYS_A 3EGL_C 3JR7_A ....
Probab=20.18 E-value=2.7e+02 Score=31.76 Aligned_cols=95 Identities=18% Similarity=0.310 Sum_probs=60.2
Q ss_pred hHHHHHHHHhhhcCCCChHHHhhhcChhhHhHHHHHhhccccccccc-----ccccc-----------------------
Q 000595 648 GKAIRTALKKLDVDGSSIEDAKAVCEPEVLSQIFKWKNKLKVYLAPF-----LHGMR----------------------- 699 (1401)
Q Consensus 648 gkAvr~AL~kLe~~g~siedAkAvc~p~vl~ql~~wk~kL~vylaP~-----l~G~r----------------------- 699 (1401)
|-.|..|+++++ +|.+++ +++.+|...+++.++|+.|- ..|-|
T Consensus 124 g~lv~~a~~l~~-~G~s~~--------ei~~~l~~~~~~~~~~f~~~~L~~L~kgGRis~~~a~ig~lL~IkPIl~~~~G 194 (280)
T PF02645_consen 124 GLLVLEAAKLIE-QGKSFE--------EIVEKLEELRERTRTYFVVDDLKYLRKGGRISKAAAFIGNLLNIKPILSFDDG 194 (280)
T ss_dssp HHHHHHHHHHHH-TT--HH--------HHHHHHHHHHHTEEEEEEES-SHHHHHCTSSGHHHHHHHHCTTEEEEEEEETT
T ss_pred hHHHHHHHHHHH-cCCCHH--------HHHHHHHHHHhhceEEEEechHHHHHHCCCcCchhhhhhhhhcCcEEEEEECC
Confidence 447888899999 899988 46777777777887776542 22333
Q ss_pred -ccccCcccchhhhHHHHHHhhcccccC-CCc-EEeccCCcchHHHHHHHHHhhh
Q 000595 700 -YTSFGRHFTKVDKLQAIVDKLHWYVND-GDM-IVDFCCGANDFSCLMKKKLDET 751 (1401)
Q Consensus 700 -yts~grhftk~ekl~~i~~~Lh~yv~~-gd~-ivdfccg~n~fs~lmk~kl~~~ 751 (1401)
...+|+..|....++++++.+--+... .+. |.=..+|+.+--.-|+++|.+.
T Consensus 195 ~i~~~~k~Rg~kka~~~l~~~~~~~~~~~~~~~i~i~~~~~~e~a~~l~~~l~~~ 249 (280)
T PF02645_consen 195 EIEPVGKVRGRKKAIKKLIEIIKEEIKDPKNYRIAISHAGNEEEAEELKEELKEE 249 (280)
T ss_dssp EEEEEEEESSHHHHHHHHHHHHHHHHCTGCGEEEEEEESS-HHHHHHHHHHHHHH
T ss_pred EEEEEeeeccHHHHHHHHHHHhhhhhhcCCceeEEEEEcCCHHHHHHHHHHHHHh
Confidence 447788888888888888877323332 223 3334455556666777777763
Done!