RE_LlaJI - PFAM28P - GREMLIN Contacts

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RE_LlaJI - LlaJI restriction endonuclease

PFAM:	PF09563	Sequences: FVGIKIDKDNILVYFPKGYNLPDDDLREDIRKLIKLLLKVLAKYSKKEDSIEELLFLNEAESSVDFPLAAYLELINDYLENGLYTEREKIYKTNGSGKINWKKTIKKSTPIISNGSPIYLDFVTRKKTPNEDNLITRIHKYCVYESFKKLGWLFGLFMPEKPLIDEELDDLGDKEYIISILNKELNNTFNDRKKRLLKSLIAYLEYLDEKDSDNQIFYFGTNSFEYVWEKMIDKVFNGIEDKNKYFPKPKWKLDGGKEKEKSTLRPDTIMIYNDKFYILDAKYYKYGLTPKNLPGSSDINKQITYGEALKKFIKFKEKGKNKKVYNAFIMPYNKKDNKFKIIGNVNFENIGEAVGDWKNGKNYERIQGILIDTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	374 (345)
Sequences:	578 (495)
Seq/√Len:	26.7
META:	0.735

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
142_C	200_L	4.782	1.00
33_L	37_L	4.054	1.00
233_D	268_T	3.857	1.00
178_I	201_I	3.840	1.00
300_N	304_T	3.733	1.00
279_L	327_A	3.523	1.00
182_N	201_I	3.376	1.00
299_I	328_F	3.345	1.00
181_L	197_L	3.287	1.00
181_L	201_I	3.271	1.00
99_I	122_F	3.003	1.00
77_D	192_R	2.984	1.00
29_D	33_L	2.841	1.00
174_K	204_L	2.696	0.99
86_E	184_E	2.597	0.99
296_S	300_N	2.556	0.99
185_L	194_K	2.384	0.99
77_D	139_H	2.375	0.99
264_L	300_N	2.332	0.98
142_C	203_Y	2.329	0.98
111_I	120_L	2.303	0.98
296_S	304_T	2.301	0.98
185_L	198_K	2.295	0.98
83_L	140_K	2.284	0.98
145_E	203_Y	2.220	0.98
66_F	69_A	2.200	0.98
232_I	268_T	2.196	0.98
296_S	299_I	2.194	0.98
184_E	197_L	2.189	0.98
251_W	279_L	2.185	0.98
178_I	205_E	2.149	0.97
344_N	348_E	2.095	0.97
110_P	119_Y	2.089	0.97
289_T	292_N	2.062	0.96
73_E	195_R	2.058	0.96
279_L	329_I	2.042	0.96
232_I	281_A	2.029	0.96
15_F	19_Y	2.017	0.96
191_D	194_K	2.014	0.96
221_T	251_W	2.010	0.96
33_L	36_L	1.974	0.95
112_I	117_P	1.937	0.95
34_I	37_L	1.921	0.95
277_Y	327_A	1.884	0.94
120_L	196_L	1.875	0.94
146_S	203_Y	1.874	0.94
343_G	348_E	1.837	0.93
201_I	205_E	1.833	0.93
196_L	228_W	1.802	0.93
27_R	30_I	1.764	0.92
1_F	14_Y	1.762	0.92
27_R	33_L	1.762	0.92
302_Q	305_Y	1.752	0.92
89_K	125_R	1.741	0.91
241_D	244_K	1.733	0.91
100_N	125_R	1.701	0.90
143_V	163_L	1.700	0.90
223_S	226_Y	1.688	0.90
340_K	345_V	1.682	0.90
91_Y	123_V	1.669	0.89
343_G	349_N	1.661	0.89
192_R	196_L	1.634	0.88
86_E	193_K	1.624	0.88
249_P	261_K	1.617	0.88
309_L	312_F	1.593	0.87
345_V	350_I	1.591	0.87
139_H	228_W	1.590	0.87
83_L	196_L	1.574	0.86
102_K	106_K	1.566	0.86
264_L	308_A	1.565	0.86
294_P	328_F	1.554	0.86
30_I	33_L	1.542	0.85
295_G	298_D	1.535	0.85
301_K	305_Y	1.529	0.85
103_K	107_K	1.519	0.84
267_D	281_A	1.506	0.84
56_F	59_E	1.498	0.83
343_G	350_I	1.484	0.83
345_V	348_E	1.480	0.83
37_L	224_F	1.475	0.82
285_K	292_N	1.460	0.82
190_N	193_K	1.455	0.82
224_F	228_W	1.443	0.81
282_K	302_Q	1.425	0.80
139_H	197_L	1.423	0.80
264_L	304_T	1.418	0.80
3_G	16_P	1.412	0.80
104_T	229_E	1.408	0.79
326_N	331_P	1.397	0.79
182_N	205_E	1.394	0.79
147_F	159_P	1.393	0.79
41_L	96_S	1.392	0.79
343_G	346_N	1.391	0.79
163_L	273_N	1.378	0.78
239_I	242_K	1.375	0.78
232_I	329_I	1.368	0.77
251_W	266_P	1.368	0.77
108_S	123_V	1.364	0.77
138_I	152_W	1.345	0.76
249_P	283_Y	1.345	0.76
40_V	44_Y	1.338	0.76
12_L	17_K	1.325	0.75
264_L	299_I	1.319	0.75
270_M	277_Y	1.298	0.73
246_F	265_R	1.298	0.73
73_E	77_D	1.281	0.72
284_Y	302_Q	1.272	0.72
134_L	180_I	1.257	0.71
233_D	237_N	1.252	0.71
282_K	301_K	1.251	0.71
266_P	281_A	1.242	0.70
123_V	181_L	1.242	0.70
107_K	123_V	1.239	0.70
278_I	299_I	1.238	0.70
93_T	123_V	1.236	0.70
267_D	294_P	1.232	0.69
280_D	302_Q	1.208	0.68
82_G	189_F	1.202	0.67
343_G	347_F	1.202	0.67
29_D	32_K	1.198	0.67
219_F	269_I	1.198	0.67
134_L	177_I	1.196	0.67
328_F	331_P	1.193	0.67
71_Y	146_S	1.189	0.67
220_G	294_P	1.180	0.66
65_D	78_Y	1.172	0.65
295_G	304_T	1.171	0.65
95_G	124_T	1.170	0.65
299_I	303_I	1.157	0.64
84_Y	184_E	1.143	0.63
226_Y	298_D	1.139	0.63
27_R	181_L	1.135	0.63
253_L	259_K	1.124	0.62
33_L	38_L	1.113	0.61
41_L	221_T	1.112	0.61
11_I	78_Y	1.110	0.61
341_I	344_N	1.107	0.61
10_N	13_V	1.103	0.61
105_I	120_L	1.098	0.60
273_N	290_P	1.098	0.60
251_W	286_Y	1.094	0.60
184_E	188_T	1.088	0.60
130_N	221_T	1.079	0.59
134_L	138_I	1.074	0.59
190_N	279_L	1.070	0.58
41_L	115_G	1.066	0.58
173_D	176_Y	1.066	0.58
22_P	143_V	1.064	0.58
40_V	224_F	1.057	0.57
86_E	196_L	1.052	0.57
71_Y	203_Y	1.049	0.57
264_L	296_S	1.045	0.56
73_E	199_S	1.040	0.56
41_L	227_V	1.033	0.56
341_I	348_E	1.030	0.55
198_K	271_I	1.030	0.55
139_H	235_V	1.022	0.55
2_V	299_I	1.018	0.54
139_H	294_P	1.017	0.54
76_N	96_S	1.014	0.54
251_W	294_P	1.009	0.54
249_P	308_A	1.008	0.54
59_E	208_D	1.006	0.54
274_D	322_K	1.005	0.54
307_E	330_M	1.004	0.53
118_I	178_I	1.001	0.53
15_F	196_L	1.000	0.53
65_D	127_K	0.999	0.53
138_I	181_L	0.998	0.53
181_L	196_L	0.997	0.53
138_I	328_F	0.993	0.53
77_D	81_N	0.991	0.52
49_D	52_E	0.983	0.52
340_K	344_N	0.980	0.52
92_K	95_G	0.975	0.51
300_N	307_E	0.973	0.51
77_D	205_E	0.971	0.51
143_V	227_V	0.970	0.51
225_E	296_S	0.970	0.51
346_N	349_N	0.968	0.51
15_F	236_F	0.966	0.51
196_L	224_F	0.965	0.51
106_K	132_D	0.964	0.50
106_K	120_L	0.957	0.50
280_D	301_K	0.952	0.50
224_F	281_A	0.947	0.49
74_L	187_N	0.947	0.49
101_W	104_T	0.946	0.49
337_N	340_K	0.945	0.49
119_Y	189_F	0.944	0.49
25_D	214_N	0.943	0.49
188_T	197_L	0.941	0.49
114_N	181_L	0.940	0.49
114_N	134_L	0.933	0.48
37_L	40_V	0.927	0.48
335_K	340_K	0.919	0.47
160_E	257_K	0.915	0.47
49_D	78_Y	0.913	0.47
72_L	194_K	0.905	0.46
103_K	183_K	0.905	0.46
339_F	344_N	0.903	0.46
57_L	65_D	0.900	0.46
280_D	284_Y	0.894	0.45
139_H	146_S	0.893	0.45
195_R	198_K	0.890	0.45
83_L	136_T	0.887	0.45
344_N	347_F	0.885	0.45
264_L	327_A	0.877	0.44
227_V	233_D	0.873	0.44
190_N	204_L	0.872	0.44
300_N	303_I	0.872	0.44
284_Y	301_K	0.867	0.43
89_K	201_I	0.867	0.43
41_L	44_Y	0.859	0.43
249_P	295_G	0.858	0.43
74_L	79_L	0.858	0.43
196_L	283_Y	0.857	0.42
104_T	305_Y	0.857	0.42
4_I	102_K	0.854	0.42
17_K	285_K	0.854	0.42
113_S	116_S	0.852	0.42
15_F	18_G	0.850	0.42
340_K	343_G	0.848	0.42
232_I	264_L	0.845	0.42
327_A	332_Y	0.845	0.42
265_R	300_N	0.844	0.42
40_V	43_K	0.843	0.41
249_P	296_S	0.843	0.41
242_K	264_L	0.840	0.41
278_I	309_L	0.840	0.41
177_I	204_L	0.834	0.41
218_Y	238_G	0.833	0.41
101_W	305_Y	0.827	0.40
77_D	294_P	0.827	0.40
1_F	146_S	0.826	0.40
264_L	328_F	0.825	0.40
249_P	300_N	0.825	0.40
17_K	189_F	0.825	0.40
340_K	348_E	0.824	0.40
30_I	35_K	0.823	0.40
72_L	76_N	0.820	0.40
29_D	37_L	0.819	0.40
268_T	298_D	0.818	0.40
138_I	251_W	0.817	0.40
31_R	37_L	0.817	0.40
31_R	35_K	0.816	0.40
62_S	209_E	0.815	0.39
232_I	333_N	0.813	0.39
281_A	306_G	0.810	0.39
293_L	303_I	0.810	0.39
345_V	349_N	0.810	0.39
220_G	328_F	0.804	0.39
70_A	300_N	0.803	0.39
26_L	160_E	0.802	0.39
82_G	331_P	0.800	0.38
281_A	294_P	0.800	0.38
124_T	225_E	0.799	0.38
176_Y	180_I	0.799	0.38
18_G	139_H	0.791	0.38
67_P	70_A	0.789	0.38
109_T	118_I	0.786	0.37
93_T	281_A	0.785	0.37
341_I	345_V	0.785	0.37
186_N	213_D	0.781	0.37
341_I	346_N	0.777	0.37
231_M	286_Y	0.773	0.36
82_G	228_W	0.767	0.36
15_F	21_L	0.766	0.36
107_K	111_I	0.765	0.36
99_I	105_I	0.761	0.36
98_K	102_K	0.758	0.35
55_L	61_E	0.758	0.35
13_V	118_I	0.756	0.35
339_F	343_G	0.756	0.35
286_Y	293_L	0.747	0.35
32_K	189_F	0.747	0.35
140_K	143_V	0.746	0.35
81_N	121_D	0.746	0.35
339_F	345_V	0.745	0.35
209_E	322_K	0.743	0.34
5_K	14_Y	0.743	0.34
53_E	58_N	0.739	0.34
86_E	133_N	0.739	0.34
27_R	31_R	0.737	0.34
70_A	145_E	0.736	0.34
108_S	197_L	0.734	0.34
78_Y	109_T	0.733	0.34
141_Y	146_S	0.733	0.34
236_F	279_L	0.732	0.34
148_K	161_K	0.732	0.34
138_I	217_F	0.727	0.33
193_K	264_L	0.721	0.33
18_G	138_I	0.719	0.33
80_E	259_K	0.718	0.33
148_K	241_D	0.714	0.32
201_I	204_L	0.710	0.32
117_P	178_I	0.706	0.32
184_E	196_L	0.705	0.32
173_D	177_I	0.704	0.32
135_I	184_E	0.703	0.32
76_N	179_S	0.699	0.32
90_I	269_I	0.699	0.32
82_G	101_W	0.699	0.32
137_R	172_G	0.697	0.31
47_K	110_P	0.696	0.31
246_F	249_P	0.693	0.31
227_V	306_G	0.693	0.31
94_N	215_Q	0.689	0.31
196_L	199_S	0.686	0.31
111_I	240_E	0.685	0.31
188_T	266_P	0.685	0.31
42_A	75_I	0.684	0.31
81_N	200_L	0.684	0.31
220_G	267_D	0.683	0.30
205_E	210_K	0.682	0.30
220_G	326_N	0.679	0.30
267_D	328_F	0.677	0.30
221_T	264_L	0.676	0.30
34_I	143_V	0.675	0.30
75_I	79_L	0.674	0.30
100_N	273_N	0.672	0.30
143_V	147_F	0.671	0.30
336_D	340_K	0.671	0.30
251_W	281_A	0.670	0.30
139_H	184_E	0.669	0.30
128_T	174_K	0.667	0.29
194_K	199_S	0.666	0.29
26_L	29_D	0.666	0.29
124_T	145_E	0.665	0.29
294_P	298_D	0.665	0.29
212_S	291_K	0.664	0.29
115_G	158_M	0.663	0.29
149_K	281_A	0.661	0.29
139_H	192_R	0.660	0.29
68_L	335_K	0.660	0.29
136_T	228_W	0.660	0.29
175_E	187_N	0.659	0.29
119_Y	137_R	0.658	0.29
221_T	283_Y	0.657	0.29
122_F	202_A	0.654	0.29
15_F	270_M	0.653	0.29
88_E	143_V	0.653	0.29
282_K	294_P	0.652	0.29
111_I	175_E	0.652	0.29
41_L	179_S	0.651	0.28
219_F	266_P	0.648	0.28
280_D	305_Y	0.647	0.28
186_N	248_K	0.646	0.28
2_V	221_T	0.646	0.28
142_C	146_S	0.646	0.28
13_V	69_A	0.645	0.28
142_C	154_F	0.644	0.28
233_D	281_A	0.644	0.28
346_N	350_I	0.643	0.28
122_F	231_M	0.641	0.28
41_L	132_D	0.640	0.28
341_I	347_F	0.640	0.28
267_D	282_K	0.639	0.28
246_F	330_M	0.639	0.28
34_I	210_K	0.637	0.28
103_K	123_V	0.636	0.28
269_I	276_F	0.633	0.27
84_Y	296_S	0.632	0.27
294_P	299_I	0.631	0.27
103_K	114_N	0.630	0.27
221_T	232_I	0.628	0.27
24_D	35_K	0.628	0.27
123_V	143_V	0.628	0.27
76_N	337_N	0.627	0.27
68_L	209_E	0.627	0.27
143_V	170_D	0.627	0.27
79_L	191_D	0.626	0.27
9_D	323_K	0.626	0.27
337_N	348_E	0.625	0.27
173_D	273_N	0.624	0.27
128_T	212_S	0.623	0.27
249_P	303_I	0.621	0.27
5_K	41_L	0.619	0.27
76_N	125_R	0.617	0.26
100_N	185_L	0.614	0.26
277_Y	325_Y	0.613	0.26
117_P	192_R	0.612	0.26
197_L	201_I	0.611	0.26
78_Y	122_F	0.610	0.26
70_A	142_C	0.610	0.26
237_N	309_L	0.609	0.26
43_K	161_K	0.608	0.26
66_F	142_C	0.606	0.26
154_F	293_L	0.606	0.26
4_I	126_K	0.605	0.26
98_K	138_I	0.605	0.26
336_D	345_V	0.604	0.26
94_N	175_E	0.604	0.26
142_C	293_L	0.604	0.26
294_P	302_Q	0.603	0.26
150_L	153_L	0.601	0.26
221_T	227_V	0.600	0.25
116_S	148_K	0.599	0.25
232_I	239_I	0.599	0.25
228_W	298_D	0.598	0.25
233_D	245_Y	0.598	0.25
294_P	301_K	0.596	0.25
46_K	112_I	0.595	0.25
99_I	189_F	0.594	0.25
189_F	193_K	0.593	0.25
232_I	246_F	0.592	0.25
247_P	264_L	0.590	0.25
249_P	330_M	0.590	0.25
1_F	220_G	0.590	0.25
151_G	281_A	0.589	0.25
41_L	207_L	0.587	0.25
238_G	270_M	0.587	0.25
264_L	294_P	0.586	0.25
296_S	303_I	0.585	0.25
5_K	303_I	0.585	0.25
136_T	197_L	0.585	0.25
135_I	188_T	0.585	0.25
305_Y	331_P	0.585	0.25
80_E	133_N	0.584	0.25
157_F	161_K	0.582	0.24
75_I	160_E	0.581	0.24
337_N	343_G	0.581	0.24
61_E	65_D	0.581	0.24
199_S	268_T	0.579	0.24
179_S	193_K	0.578	0.24
27_R	35_K	0.577	0.24
340_K	346_N	0.576	0.24
70_A	199_S	0.575	0.24
176_Y	254_D	0.574	0.24
84_Y	220_G	0.574	0.24
13_V	349_N	0.574	0.24
338_K	348_E	0.572	0.24
83_L	236_F	0.571	0.24
43_K	68_L	0.571	0.24
110_P	179_S	0.571	0.24
67_P	330_M	0.569	0.24
5_K	285_K	0.569	0.24
26_L	212_S	0.567	0.24
301_K	331_P	0.567	0.24
127_K	143_V	0.566	0.24
263_T	308_A	0.566	0.24
61_E	64_V	0.565	0.24
191_D	306_G	0.559	0.23
93_T	114_N	0.559	0.23
26_L	33_L	0.559	0.23
84_Y	188_T	0.558	0.23
284_Y	294_P	0.558	0.23
151_G	155_G	0.558	0.23
58_N	63_S	0.556	0.23
174_K	212_S	0.555	0.23
194_K	300_N	0.554	0.23
41_L	248_K	0.554	0.23
255_G	290_P	0.553	0.23
9_D	116_S	0.551	0.23
6_I	213_D	0.550	0.23
297_S	300_N	0.550	0.23
200_L	232_I	0.549	0.23
4_I	40_V	0.549	0.23
249_P	304_T	0.549	0.23
2_V	232_I	0.548	0.23
36_L	78_Y	0.547	0.23
267_D	299_I	0.546	0.23
110_P	149_K	0.540	0.22
80_E	202_A	0.540	0.22
120_L	211_D	0.539	0.22
139_H	204_L	0.538	0.22
162_P	189_F	0.537	0.22
121_D	164_I	0.536	0.22
40_V	271_I	0.536	0.22
173_D	204_L	0.535	0.22
15_F	144_Y	0.535	0.22
261_K	276_F	0.535	0.22
152_W	293_L	0.533	0.22
75_I	147_F	0.532	0.22
204_L	281_A	0.532	0.22
98_K	231_M	0.530	0.22
115_G	154_F	0.530	0.22
17_K	232_I	0.530	0.22
83_L	139_H	0.529	0.22
103_K	202_A	0.526	0.22
253_L	256_G	0.526	0.22
231_M	270_M	0.525	0.21
189_F	269_I	0.525	0.21
236_F	266_P	0.524	0.21
240_E	252_K	0.524	0.21
168_L	171_L	0.523	0.21
62_S	65_D	0.523	0.21
300_N	328_F	0.522	0.21
261_K	320_K	0.522	0.21
151_G	154_F	0.522	0.21
126_K	348_E	0.522	0.21
304_T	307_E	0.522	0.21
81_N	192_R	0.521	0.21
24_D	212_S	0.521	0.21
282_K	305_Y	0.521	0.21
77_D	267_D	0.520	0.21
286_Y	290_P	0.519	0.21
269_I	294_P	0.519	0.21
81_N	196_L	0.519	0.21
181_L	185_L	0.518	0.21
74_L	133_N	0.518	0.21
181_L	252_K	0.518	0.21
278_I	282_K	0.516	0.21
107_K	119_Y	0.516	0.21
47_K	219_F	0.516	0.21
104_T	280_D	0.513	0.21
138_I	294_P	0.511	0.21
84_Y	197_L	0.510	0.21
184_E	303_I	0.510	0.21
36_L	40_V	0.509	0.21
189_F	295_G	0.507	0.21
155_G	164_I	0.506	0.21
111_I	121_D	0.506	0.21
121_D	295_G	0.506	0.21
302_Q	331_P	0.506	0.21
2_V	37_L	0.505	0.20
45_S	174_K	0.504	0.20
81_N	112_I	0.500	0.20

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4z9nA	2	0.2861	3.5	0.977	Contact Map
3n4sA	2	0.115	2.9	0.978	Contact Map
4qlbG	1	0.0909	2.9	0.978	Contact Map
2j5lA	1	0	2.8	0.978	Contact Map
4obiA	1	0.0722	2.4	0.979	Contact Map
1y88A	5	0.3422	1.6	0.98	Contact Map
2g7hA	1	0.1497	1.5	0.981	Contact Map
4hs4A	6	0.131	1.5	0.981	Contact Map
2pi2E	1	0.139	1.2	0.982	Contact Map
4khaA	1	0.1711	1.2	0.982	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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