NICK - BACSU - GREMLIN Contacts

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NICK - Putative DNA relaxase NicK

UniProt:	P96635	Sequences: MDELKQPPHANRGVVIVKEKNEAVESPLVSMVDYIRVSFKTHDVDRIIEEVLHLSKDFMTEKQSGFYGYVGTYELDYIKVFYSAPDDNRGVLIEMSGQGCRQFESFLECRKKTWYDFFQDCMQQGGSFTRFDLAIDDKKTYFSIPELLKKAQKGECISRFRKSDFNGSFDLSDGITGGTTIYFGSKKSEAYLCFYEKNYEQAEKYNIPLEELGDWNRYELRLKNERAQVAIDALLKTKDLTLIAMQIINNYVRFVDADENITREHWKTSLFWSDFIGDVGRLPLYVKPQKDFYQKSRNWLRNSCAPTMKMVLEADEHLGKTDLSDMIAEAELADKHKKMLDVYMADVADMVV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	352 (321)
Sequences:	298 (220)
Seq/√Len:	12.3

BACSU - NICK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
193_C	221_R	5.755	1.00
150_K	155_E	5.623	1.00
101_R	104_E	4.421	1.00
296_S	307_T	3.901	0.99
136_D	215_W	3.375	0.98
194_F	218_Y	3.293	0.98
196_E	216_N	3.181	0.97
100_C	114_W	3.178	0.97
226_R	251_Y	3.089	0.97
311_V	314_A	3.025	0.96
137_D	141_Y	2.644	0.92
334_D	337_K	2.636	0.92
142_F	275_F	2.565	0.91
104_E	114_W	2.532	0.90
35_I	118_F	2.523	0.90
101_R	114_W	2.489	0.89
73_Y	95_M	2.451	0.89
137_D	254_F	2.370	0.87
137_D	275_F	2.369	0.87
180_T	193_C	2.343	0.86
73_Y	91_V	2.335	0.86
96_S	193_C	2.221	0.83
300_L	326_M	2.208	0.83
97_G	100_C	2.132	0.80
36_R	92_L	2.123	0.80
313_E	316_E	2.104	0.79
38_S	215_W	2.100	0.79
32_V	35_I	2.089	0.79
34_Y	193_C	2.044	0.77
163_S	169_F	1.981	0.75
315_D	320_K	1.945	0.73
78_I	101_R	1.881	0.71
35_I	54_L	1.880	0.71
137_D	272_W	1.875	0.71
113_T	116_D	1.869	0.70
201_Q	223_K	1.860	0.70
34_Y	248_I	1.839	0.69
34_Y	94_E	1.826	0.68
198_N	215_W	1.779	0.66
157_I	253_R	1.761	0.66
192_L	248_I	1.728	0.64
323_L	326_M	1.721	0.64
156_C	250_N	1.692	0.62
100_C	104_E	1.690	0.62
133_L	161_R	1.680	0.62
117_F	181_I	1.655	0.61
190_A	220_L	1.641	0.60
40_K	129_T	1.629	0.59
195_Y	219_E	1.622	0.59
195_Y	217_R	1.622	0.59
178_G	299_W	1.621	0.59
97_G	104_E	1.613	0.58
304_C	308_M	1.609	0.58
150_K	299_W	1.602	0.58
57_D	338_K	1.569	0.56
46_R	50_E	1.568	0.56
172_S	340_L	1.558	0.56
310_M	340_L	1.534	0.55
155_E	266_W	1.529	0.54
192_L	220_L	1.515	0.54
150_K	275_F	1.511	0.53
49_E	131_F	1.508	0.53
40_K	127_S	1.503	0.53
132_D	195_Y	1.493	0.52
34_Y	92_L	1.465	0.51
77_Y	98_Q	1.446	0.50
292_F	308_M	1.433	0.49
29_V	118_F	1.417	0.49
107_L	204_K	1.414	0.48
132_D	217_R	1.412	0.48
132_D	219_E	1.412	0.48
197_K	217_R	1.407	0.48
197_K	219_E	1.407	0.48
136_D	214_D	1.407	0.48
201_Q	288_P	1.401	0.48
90_G	200_E	1.394	0.47
101_R	272_W	1.381	0.47
137_D	144_I	1.370	0.46
34_Y	221_R	1.358	0.46
127_S	136_D	1.354	0.45
168_S	208_P	1.353	0.45
78_I	97_G	1.350	0.45
102_Q	106_F	1.344	0.45
38_S	129_T	1.338	0.45
169_F	192_L	1.336	0.44
300_L	307_T	1.327	0.44
37_V	93_I	1.323	0.44
306_P	336_H	1.322	0.44
94_E	193_C	1.320	0.44
305_A	327_I	1.307	0.43
282_L	315_D	1.297	0.43
131_F	230_A	1.294	0.42
218_Y	248_I	1.286	0.42
216_N	299_W	1.286	0.42
97_G	101_R	1.278	0.42
193_C	248_I	1.277	0.42
132_D	197_K	1.277	0.42
230_A	247_I	1.265	0.41
32_V	222_L	1.250	0.40
70_V	99_G	1.245	0.40
136_D	195_Y	1.233	0.39
28_L	135_I	1.222	0.39
300_L	311_V	1.207	0.38
202_A	218_Y	1.199	0.38
194_F	202_A	1.191	0.37
137_D	299_W	1.190	0.37
189_E	226_R	1.182	0.37
184_G	195_Y	1.178	0.37
172_S	311_V	1.175	0.37
321_T	335_K	1.168	0.36
99_G	245_M	1.167	0.36
34_Y	272_W	1.164	0.36
186_K	191_Y	1.163	0.36
77_Y	102_Q	1.160	0.36
130_R	195_Y	1.160	0.36
80_V	93_I	1.148	0.35
144_I	254_F	1.144	0.35
128_F	154_G	1.125	0.34
115_Y	175_I	1.123	0.34
69_Y	197_K	1.121	0.34
191_Y	220_L	1.118	0.34
294_Q	334_D	1.117	0.34
107_L	216_N	1.109	0.34
134_A	222_L	1.104	0.33
34_Y	295_K	1.101	0.33
47_I	51_V	1.099	0.33
48_I	54_L	1.098	0.33
184_G	217_R	1.096	0.33
184_G	219_E	1.096	0.33
98_Q	201_Q	1.096	0.33
231_I	234_L	1.093	0.33
147_L	196_E	1.092	0.33
335_K	344_M	1.091	0.33
136_D	219_E	1.091	0.33
136_D	217_R	1.091	0.33
29_V	75_L	1.090	0.33
116_D	288_P	1.090	0.33
59_M	240_L	1.078	0.32
130_R	217_R	1.076	0.32
130_R	219_E	1.076	0.32
84_A	209_L	1.075	0.32
54_L	266_W	1.066	0.32
76_D	166_N	1.061	0.31
192_L	245_M	1.055	0.31
97_G	134_A	1.047	0.31
133_L	260_N	1.042	0.31
118_F	303_S	1.036	0.30
93_I	173_D	1.034	0.30
38_S	92_L	1.033	0.30
189_E	225_E	1.030	0.30
153_K	257_A	1.020	0.30
103_F	290_K	1.018	0.30
305_A	330_A	1.017	0.30
258_D	280_G	1.016	0.29
147_L	341_D	1.014	0.29
253_R	284_L	1.006	0.29
118_F	252_V	0.999	0.29
33_D	195_Y	0.996	0.29
137_D	252_V	0.994	0.29
196_E	199_Y	0.992	0.28
245_M	275_F	0.992	0.28
53_H	205_Y	0.990	0.28
151_A	183_F	0.990	0.28
146_E	271_F	0.988	0.28
272_W	299_W	0.983	0.28
182_Y	299_W	0.979	0.28
117_F	201_Q	0.978	0.28
100_C	284_L	0.968	0.28
236_K	328_A	0.968	0.28
133_L	226_R	0.966	0.27
99_G	199_Y	0.965	0.27
34_Y	192_L	0.964	0.27
161_R	304_C	0.964	0.27
180_T	223_K	0.961	0.27
131_F	306_P	0.961	0.27
191_Y	221_R	0.961	0.27
46_R	61_E	0.960	0.27
65_G	154_G	0.959	0.27
184_G	197_K	0.959	0.27
66_F	81_F	0.958	0.27
80_V	189_E	0.953	0.27
133_L	206_N	0.952	0.27
104_E	272_W	0.951	0.27
132_D	184_G	0.947	0.27
157_I	255_V	0.946	0.27
48_I	56_K	0.945	0.27
231_I	235_L	0.943	0.26
103_F	152_Q	0.943	0.26
130_R	197_K	0.941	0.26
293_Y	311_V	0.938	0.26
304_C	307_T	0.938	0.26
32_V	54_L	0.935	0.26
136_D	197_K	0.932	0.26
210_E	270_L	0.931	0.26
169_F	322_D	0.930	0.26
222_L	247_I	0.929	0.26
336_H	340_L	0.922	0.26
36_R	145_P	0.922	0.26
54_L	106_F	0.914	0.25
190_A	251_Y	0.910	0.25
125_G	284_L	0.909	0.25
33_D	217_R	0.904	0.25
33_D	219_E	0.904	0.25
226_R	285_Y	0.896	0.25
156_C	171_L	0.890	0.24
287_K	341_D	0.889	0.24
132_D	136_D	0.884	0.24
32_V	86_D	0.882	0.24
179_T	196_E	0.878	0.24
125_G	187_K	0.877	0.24
89_R	177_G	0.872	0.24
196_E	215_W	0.868	0.24
81_F	194_F	0.868	0.24
30_S	298_N	0.862	0.23
36_R	277_G	0.861	0.23
38_S	291_D	0.861	0.23
30_S	136_D	0.858	0.23
199_Y	210_E	0.857	0.23
202_A	213_G	0.856	0.23
154_G	174_G	0.853	0.23
68_G	90_G	0.852	0.23
331_E	340_L	0.851	0.23
191_Y	314_A	0.844	0.23
167_G	315_D	0.842	0.23
69_Y	195_Y	0.842	0.23
157_I	223_K	0.842	0.23
48_I	222_L	0.841	0.23
313_E	341_D	0.840	0.23
114_W	272_W	0.838	0.23
82_Y	136_D	0.831	0.22
333_A	336_H	0.831	0.22
97_G	272_W	0.826	0.22
102_Q	289_Q	0.824	0.22
135_I	294_Q	0.822	0.22
314_A	344_M	0.819	0.22
257_A	266_W	0.817	0.22
252_V	282_L	0.804	0.21
39_F	99_G	0.802	0.21
171_L	249_N	0.801	0.21
160_F	275_F	0.797	0.21
161_R	323_L	0.797	0.21
292_F	328_A	0.797	0.21
106_F	154_G	0.797	0.21
94_E	221_R	0.795	0.21
178_G	308_M	0.793	0.21
157_I	284_L	0.793	0.21
42_H	246_Q	0.791	0.21
143_S	149_K	0.791	0.21
113_T	231_I	0.789	0.21
176_T	340_L	0.789	0.21
237_T	293_Y	0.788	0.21
68_G	251_Y	0.787	0.21
96_S	142_F	0.786	0.21
298_N	329_E	0.784	0.21
149_K	325_D	0.781	0.21
186_K	223_K	0.774	0.20
272_W	275_F	0.773	0.20
90_G	201_Q	0.770	0.20
80_V	149_K	0.768	0.20
102_Q	213_G	0.764	0.20
194_F	213_G	0.764	0.20
33_D	197_K	0.764	0.20
171_L	308_M	0.762	0.20
296_S	339_M	0.758	0.20
78_I	221_R	0.757	0.20
38_S	228_Q	0.757	0.20
129_T	136_D	0.756	0.20
33_D	132_D	0.756	0.20
52_L	200_E	0.756	0.20
39_F	67_Y	0.756	0.20
39_F	326_M	0.755	0.20
107_L	121_C	0.752	0.20
32_V	146_E	0.747	0.19
221_R	266_W	0.746	0.19
36_R	223_K	0.744	0.19
28_L	244_A	0.741	0.19
61_E	71_G	0.740	0.19
150_K	216_N	0.740	0.19
129_T	193_C	0.740	0.19
122_M	335_K	0.740	0.19
153_K	280_G	0.739	0.19
312_L	327_I	0.737	0.19
97_G	299_W	0.736	0.19
69_Y	219_E	0.736	0.19
69_Y	217_R	0.736	0.19
209_L	244_A	0.736	0.19
54_L	79_K	0.735	0.19
259_E	345_A	0.734	0.19
129_T	224_N	0.734	0.19
149_K	236_K	0.733	0.19
107_L	188_S	0.732	0.19
34_Y	96_S	0.731	0.19
154_G	321_T	0.730	0.19
32_V	226_R	0.726	0.19
25_E	327_I	0.725	0.19
82_Y	129_T	0.724	0.19
191_Y	295_K	0.724	0.19
229_V	284_L	0.724	0.19
112_K	302_N	0.720	0.19
79_K	121_C	0.719	0.19
112_K	120_D	0.718	0.19
131_F	313_E	0.717	0.19
103_F	118_F	0.716	0.19
136_D	212_L	0.716	0.19
39_F	93_I	0.714	0.18
102_Q	199_Y	0.711	0.18
29_V	49_E	0.707	0.18
255_V	266_W	0.704	0.18
202_A	216_N	0.703	0.18
99_G	107_L	0.702	0.18
244_A	300_L	0.701	0.18
221_R	248_I	0.701	0.18
173_D	334_D	0.700	0.18
38_S	261_I	0.700	0.18
266_W	275_F	0.700	0.18
87_D	98_Q	0.698	0.18
206_N	328_A	0.696	0.18
141_Y	198_N	0.695	0.18
152_Q	167_G	0.693	0.18
230_A	234_L	0.693	0.18
77_Y	300_L	0.687	0.18
178_G	272_W	0.685	0.18
195_Y	200_E	0.676	0.17
59_M	340_L	0.675	0.17
138_K	340_L	0.674	0.17
78_I	282_L	0.672	0.17
252_V	314_A	0.672	0.17
178_G	247_I	0.672	0.17
34_Y	291_D	0.671	0.17
187_K	286_V	0.671	0.17
309_K	330_A	0.664	0.17
107_L	201_Q	0.662	0.17
69_Y	340_L	0.660	0.17
160_F	294_Q	0.658	0.17
179_T	293_Y	0.658	0.17
228_Q	232_D	0.654	0.17
160_F	251_Y	0.653	0.17
37_V	53_H	0.648	0.17
37_V	121_C	0.647	0.16
149_K	239_D	0.646	0.16
118_F	158_S	0.644	0.16
98_Q	327_I	0.642	0.16
186_K	254_F	0.642	0.16
254_F	275_F	0.641	0.16
333_A	342_V	0.640	0.16
100_C	272_W	0.638	0.16
299_W	304_C	0.634	0.16
100_C	134_A	0.633	0.16
90_G	94_E	0.633	0.16
77_Y	322_D	0.632	0.16
54_L	75_L	0.632	0.16
121_C	126_G	0.631	0.16
80_V	337_K	0.630	0.16
50_E	341_D	0.630	0.16
320_K	335_K	0.629	0.16
93_I	238_K	0.629	0.16
162_K	177_G	0.627	0.16
161_R	224_N	0.624	0.16
231_I	259_E	0.623	0.16
293_Y	322_D	0.622	0.16
258_D	277_G	0.622	0.16
111_K	206_N	0.621	0.16
340_L	344_M	0.620	0.16
51_V	80_V	0.620	0.16
65_G	244_A	0.618	0.16
300_L	323_L	0.618	0.16
176_T	190_A	0.615	0.16
321_T	325_D	0.613	0.16
334_D	340_L	0.609	0.15
53_H	110_R	0.609	0.15
97_G	195_Y	0.608	0.15
270_L	328_A	0.607	0.15
93_I	314_A	0.606	0.15
292_F	311_V	0.603	0.15
66_F	335_K	0.602	0.15
75_L	232_D	0.601	0.15
138_K	244_A	0.601	0.15
136_D	274_D	0.600	0.15
174_G	218_Y	0.600	0.15
67_Y	168_S	0.600	0.15
136_D	139_K	0.597	0.15
221_R	315_D	0.596	0.15
137_D	266_W	0.596	0.15
184_G	200_E	0.596	0.15
104_E	200_E	0.595	0.15
112_K	198_N	0.595	0.15
49_E	312_L	0.593	0.15
143_S	192_L	0.592	0.15
32_V	50_E	0.590	0.15
150_K	271_F	0.584	0.15
177_G	199_Y	0.584	0.15
78_I	104_E	0.582	0.15
137_D	150_K	0.582	0.15
69_Y	88_N	0.580	0.15
200_E	219_E	0.579	0.15
200_E	217_R	0.579	0.15
130_R	184_G	0.578	0.15
101_R	284_L	0.577	0.15
161_R	256_D	0.575	0.15
135_I	155_E	0.574	0.15
319_G	344_M	0.574	0.15
40_K	126_G	0.573	0.15
99_G	266_W	0.573	0.15
334_D	341_D	0.570	0.14
48_I	261_I	0.568	0.14
218_Y	299_W	0.566	0.14
83_S	122_M	0.565	0.14
115_Y	294_Q	0.564	0.14
76_D	199_Y	0.564	0.14
124_Q	284_L	0.564	0.14
137_D	179_T	0.563	0.14
161_R	191_Y	0.563	0.14
156_C	310_M	0.562	0.14
282_L	337_K	0.562	0.14
106_F	281_R	0.561	0.14
142_F	183_F	0.561	0.14
26_S	273_S	0.560	0.14
99_G	204_K	0.560	0.14
137_D	188_S	0.559	0.14
196_E	244_A	0.559	0.14
328_A	344_M	0.559	0.14
69_Y	132_D	0.557	0.14
45_D	49_E	0.557	0.14
194_F	216_N	0.556	0.14
104_E	134_A	0.555	0.14
44_V	56_K	0.555	0.14
131_F	209_L	0.555	0.14
194_F	198_N	0.554	0.14
160_F	307_T	0.553	0.14
234_L	252_V	0.553	0.14
230_A	248_I	0.550	0.14
193_C	223_K	0.548	0.14
41_T	230_A	0.546	0.14
97_G	220_L	0.545	0.14
173_D	317_H	0.544	0.14
171_L	196_E	0.543	0.14
311_V	321_T	0.542	0.14
187_K	279_V	0.541	0.14
221_R	300_L	0.538	0.14
185_S	305_A	0.538	0.14
58_F	204_K	0.537	0.14
165_F	183_F	0.536	0.14
133_L	240_L	0.535	0.14
244_A	321_T	0.535	0.14
42_H	183_F	0.534	0.14
154_G	310_M	0.534	0.14
113_T	230_A	0.533	0.14
101_R	200_E	0.532	0.14
85_P	337_K	0.532	0.14
144_I	147_L	0.531	0.13
179_T	186_K	0.529	0.13
51_V	165_F	0.529	0.13
136_D	305_A	0.527	0.13
80_V	90_G	0.526	0.13
121_C	162_K	0.522	0.13
146_E	149_K	0.520	0.13
33_D	38_S	0.519	0.13
47_I	52_L	0.517	0.13
259_E	308_M	0.517	0.13
30_S	135_I	0.517	0.13
151_A	171_L	0.516	0.13
55_S	239_D	0.514	0.13
255_V	331_E	0.513	0.13
177_G	276_I	0.512	0.13
173_D	270_L	0.511	0.13
78_I	100_C	0.511	0.13
254_F	276_I	0.510	0.13
64_S	223_K	0.509	0.13
99_G	162_K	0.509	0.13
319_G	346_D	0.507	0.13
183_F	294_Q	0.507	0.13
289_Q	306_P	0.506	0.13
142_F	269_S	0.506	0.13
311_V	325_D	0.506	0.13
97_G	219_E	0.505	0.13
97_G	217_R	0.505	0.13
142_F	218_Y	0.504	0.13
125_G	337_K	0.504	0.13
150_K	256_D	0.504	0.13
92_L	291_D	0.502	0.13
30_S	232_D	0.501	0.13
80_V	159_R	0.500	0.13

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
4cijA	2	0.7244	100	0.37	Contact Map
4cwcA	2	0.7301	100	0.7	Contact Map
4nj6A	3	0.2557	6.4	0.975	Contact Map
2hyeC	1	0.196	6	0.976	Contact Map
2g31A	1	0.1705	5.1	0.976	Contact Map
2do7A	1	0.2131	4.4	0.977	Contact Map
1k8kF	1	0.3494	4.2	0.977	Contact Map
1ldjA	1	0.2017	3.5	0.978	Contact Map
4yvqA	2	0.1477	3.4	0.978	Contact Map
3dplC	1	0.2017	3.3	0.978	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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