RE_HpaII - PFAM28P - GREMLIN Contacts

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RE_HpaII - HpaII restriction endonuclease

PFAM:	PF09561	Sequences: NKGEWSELYAFLKLLADGKLYAADENLNKIEDLFYPILKIIREESDGTLEYSIDDDDNIIIINGNGEEELRIPISEFKEKAEKLLEKIKSSSGGTFSIPEIEEFLNSIGCTKLKAKSSDKSDITIVIHDLRTGITPELGFSIKSQLGSPSTLLNASKTTNFIYKITGLKLSDEEINEINSIDTRSKIKDRIKAIKELGGKLEFVKVENETFENNLILIDSLLPEILAEMLLLFYSSGISKIKDLVEKLEEENPLNYDLSNNHPFYEYKIKRFLTAVALGMTPSKVWDGKYDATGGYIVVKEDGEVLCYHIYNRNEFEDYLFNNTKLETPSTSRHKFGKIYKENGEYYFKLNLQIRF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	356 (355)
Sequences:	951 (760)
Seq/√Len:	40.3
META:	0.876

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
164_K	345_E	7.668	1.00
24_D	28_N	4.094	1.00
165_I	339_I	3.714	1.00
145_Q	150_S	3.553	1.00
194_I	199_G	3.533	1.00
229_M	326_L	3.496	1.00
162_I	207_E	3.443	1.00
328_T	336_F	3.328	1.00
157_K	335_K	3.309	1.00
207_E	349_K	3.180	1.00
172_D	341_K	3.055	1.00
164_K	202_E	3.047	1.00
193_A	196_E	2.944	1.00
104_F	108_I	2.926	1.00
205_K	212_E	2.882	1.00
271_R	317_E	2.675	1.00
155_A	334_H	2.631	1.00
183_T	189_D	2.576	1.00
339_I	346_Y	2.548	1.00
245_V	321_F	2.534	1.00
244_L	326_L	2.530	1.00
153_L	276_V	2.525	1.00
221_L	224_E	2.481	1.00
186_K	189_D	2.470	1.00
187_I	331_T	2.359	1.00
162_I	349_K	2.356	1.00
77_F	104_F	2.353	1.00
181_I	186_K	2.321	1.00
187_I	190_R	2.304	1.00
21_Y	29_K	2.296	1.00
233_F	328_T	2.283	1.00
193_A	197_L	2.193	0.99
161_F	230_L	2.176	0.99
166_T	202_E	2.159	0.99
330_S	333_R	2.151	0.99
158_T	283_S	2.148	0.99
229_M	244_L	2.087	0.99
160_N	349_K	2.038	0.99
23_A	308_Y	2.012	0.99
162_I	340_Y	1.980	0.99
39_K	50_E	1.963	0.99
341_K	344_G	1.938	0.99
240_K	243_D	1.911	0.99
175_I	346_Y	1.911	0.99
156_S	329_P	1.884	0.98
13_K	17_D	1.878	0.98
171_S	174_E	1.857	0.98
77_F	108_I	1.818	0.98
253_P	265_Y	1.804	0.98
87_K	100_E	1.784	0.98
327_E	352_L	1.773	0.98
341_K	346_Y	1.761	0.97
229_M	269_I	1.751	0.97
1_N	4_E	1.748	0.97
252_N	265_Y	1.743	0.97
188_K	328_T	1.733	0.97
300_K	304_E	1.714	0.97
165_I	199_G	1.712	0.97
14_L	40_I	1.696	0.97
242_K	322_N	1.677	0.97
153_L	282_P	1.665	0.96
105_L	110_C	1.661	0.96
178_I	190_R	1.659	0.96
267_Y	271_R	1.658	0.96
29_K	304_E	1.655	0.96
203_F	212_E	1.653	0.96
326_L	352_L	1.623	0.96
269_I	326_L	1.623	0.96
168_L	199_G	1.613	0.96
160_N	351_N	1.599	0.95
224_E	228_E	1.561	0.95
158_T	208_N	1.560	0.95
14_L	37_I	1.558	0.95
232_L	247_K	1.541	0.94
241_I	321_F	1.540	0.94
3_G	7_E	1.527	0.94
20_L	297_I	1.523	0.94
19_K	34_F	1.516	0.94
4_E	7_E	1.513	0.94
164_K	204_V	1.485	0.93
23_A	297_I	1.456	0.93
153_L	211_F	1.456	0.93
278_L	292_A	1.443	0.92
158_T	329_P	1.428	0.92
183_T	186_K	1.419	0.92
170_L	179_N	1.416	0.92
174_E	197_L	1.407	0.91
222_L	272_F	1.401	0.91
80_K	101_I	1.395	0.91
271_R	275_A	1.393	0.91
161_F	352_L	1.389	0.91
155_A	327_E	1.386	0.91
83_K	100_E	1.381	0.90
124_T	137_E	1.378	0.90
6_S	144_S	1.370	0.90
248_L	265_Y	1.368	0.90
85_L	146_L	1.361	0.90
76_E	107_S	1.348	0.89
1_N	7_E	1.333	0.89
274_T	316_F	1.312	0.88
1_N	5_W	1.301	0.88
241_I	269_I	1.282	0.87
335_K	338_K	1.275	0.87
252_N	257_D	1.266	0.86
209_E	257_D	1.250	0.85
313_R	317_E	1.231	0.85
10_A	299_V	1.219	0.84
164_K	347_Y	1.217	0.84
175_I	339_I	1.216	0.84
343_N	347_Y	1.210	0.84
342_E	349_K	1.208	0.83
187_I	191_I	1.207	0.83
219_D	268_K	1.206	0.83
149_P	325_K	1.202	0.83
178_I	193_A	1.201	0.83
121_S	139_G	1.194	0.83
178_I	194_I	1.192	0.83
3_G	6_S	1.192	0.83
233_F	236_S	1.174	0.82
92_S	304_E	1.170	0.81
56_D	71_R	1.167	0.81
133_G	136_P	1.165	0.81
36_P	128_H	1.160	0.81
155_A	159_T	1.154	0.80
162_I	205_K	1.153	0.80
102_E	106_N	1.152	0.80
25_E	318_D	1.151	0.80
153_L	354_I	1.151	0.80
220_S	264_F	1.149	0.80
201_L	348_F	1.136	0.79
170_L	174_E	1.134	0.79
114_K	120_K	1.132	0.79
59_I	63_N	1.132	0.79
172_D	179_N	1.126	0.79
280_M	307_C	1.124	0.79
153_L	159_T	1.124	0.79
179_N	183_T	1.122	0.79
336_F	351_N	1.119	0.78
12_L	108_I	1.112	0.78
234_Y	328_T	1.111	0.78
195_K	235_S	1.092	0.77
141_S	294_G	1.086	0.76
242_K	246_E	1.085	0.76
182_D	186_K	1.085	0.76
60_I	63_N	1.082	0.76
228_E	251_E	1.071	0.75
342_E	347_Y	1.060	0.74
77_F	81_A	1.049	0.74
6_S	147_G	1.048	0.74
13_K	82_E	1.042	0.73
181_I	189_D	1.039	0.73
159_T	282_P	1.039	0.73
230_L	352_L	1.038	0.73
340_Y	349_K	1.037	0.73
161_F	206_V	1.034	0.73
29_K	306_L	1.032	0.72
25_E	315_E	1.032	0.72
15_L	53_I	1.031	0.72
165_I	305_V	1.030	0.72
247_K	250_E	1.029	0.72
11_F	117_S	1.024	0.72
132_T	136_P	1.023	0.72
88_I	91_S	1.015	0.71
1_N	6_S	1.013	0.71
183_T	194_I	1.012	0.71
217_L	267_Y	1.010	0.71
11_F	297_I	1.003	0.70
165_I	240_K	0.998	0.70
277_A	292_A	0.997	0.70
53_I	59_I	0.993	0.69
209_E	339_I	0.990	0.69
201_L	231_L	0.990	0.69
44_E	115_A	0.987	0.69
312_N	315_E	0.986	0.69
195_K	201_L	0.983	0.69
228_E	231_L	0.983	0.69
184_R	189_D	0.981	0.69
61_I	68_E	0.980	0.68
328_T	334_H	0.973	0.68
121_S	124_T	0.971	0.68
101_I	105_L	0.968	0.67
308_Y	316_F	0.965	0.67
226_L	230_L	0.960	0.67
16_A	81_A	0.957	0.67
23_A	312_N	0.952	0.66
22_A	312_N	0.951	0.66
289_K	314_N	0.950	0.66
238_I	243_D	0.946	0.66
298_V	321_F	0.941	0.65
188_K	233_F	0.938	0.65
115_A	305_V	0.936	0.65
186_K	331_T	0.933	0.65
324_T	356_F	0.931	0.64
232_L	251_E	0.930	0.64
321_F	326_L	0.929	0.64
206_V	212_E	0.917	0.63
290_Y	313_R	0.915	0.63
213_N	264_F	0.914	0.63
233_F	334_H	0.910	0.63
15_L	18_G	0.909	0.63
241_I	246_E	0.903	0.62
245_V	269_I	0.901	0.62
2_K	88_I	0.896	0.61
23_A	34_F	0.894	0.61
81_A	104_F	0.893	0.61
139_G	270_K	0.885	0.60
267_Y	314_N	0.879	0.60
208_N	283_S	0.878	0.60
179_N	186_K	0.875	0.60
12_L	101_I	0.874	0.59
287_D	291_D	0.870	0.59
202_E	345_E	0.868	0.59
228_E	232_L	0.867	0.59
237_G	354_I	0.867	0.59
212_E	216_I	0.866	0.59
215_L	226_L	0.860	0.58
332_S	335_K	0.857	0.58
21_Y	34_F	0.857	0.58
203_F	206_V	0.854	0.58
298_V	310_I	0.852	0.58
232_L	248_L	0.851	0.57
352_L	355_R	0.848	0.57
160_N	207_E	0.848	0.57
185_S	189_D	0.844	0.57
8_L	113_L	0.844	0.57
201_L	339_I	0.839	0.56
171_S	179_N	0.839	0.56
8_L	12_L	0.838	0.56
153_L	199_G	0.838	0.56
353_Q	356_F	0.836	0.56
256_Y	271_R	0.836	0.56
101_I	104_F	0.835	0.56
11_F	23_A	0.834	0.56
145_Q	149_P	0.830	0.56
166_T	200_K	0.830	0.56
177_E	193_A	0.829	0.55
205_K	342_E	0.823	0.55
11_F	145_Q	0.823	0.55
22_A	327_E	0.822	0.55
328_T	337_G	0.821	0.55
23_A	138_L	0.818	0.54
15_L	51_Y	0.817	0.54
22_A	34_F	0.816	0.54
178_I	181_I	0.815	0.54
51_Y	54_D	0.814	0.54
277_A	307_C	0.803	0.53
167_G	199_G	0.802	0.53
233_F	238_I	0.799	0.53
114_K	150_S	0.798	0.53
78_K	82_E	0.796	0.52
281_T	284_K	0.796	0.52
179_N	189_D	0.793	0.52
190_R	194_I	0.791	0.52
183_T	190_R	0.789	0.52
233_F	239_S	0.786	0.52
217_L	264_F	0.784	0.51
174_E	177_E	0.784	0.51
40_I	125_I	0.783	0.51
86_E	90_S	0.782	0.51
85_L	89_K	0.782	0.51
290_Y	310_I	0.780	0.51
177_E	181_I	0.779	0.51
234_Y	336_F	0.778	0.51
290_Y	312_N	0.776	0.51
82_E	86_E	0.775	0.50
165_I	192_K	0.774	0.50
252_N	264_F	0.771	0.50
206_V	226_L	0.770	0.50
37_I	125_I	0.769	0.50
252_N	256_Y	0.765	0.50
152_L	278_L	0.765	0.50
204_V	347_Y	0.764	0.49
274_T	290_Y	0.762	0.49
42_R	115_A	0.756	0.49
12_L	30_I	0.756	0.49
156_S	334_H	0.755	0.49
176_N	180_S	0.755	0.49
181_I	190_R	0.753	0.48
37_I	104_F	0.752	0.48
140_F	307_C	0.751	0.48
152_L	356_F	0.750	0.48
314_N	318_D	0.748	0.48
145_Q	316_F	0.747	0.48
23_A	306_L	0.745	0.48
129_D	311_Y	0.745	0.48
225_I	269_I	0.742	0.47
270_K	321_F	0.741	0.47
12_L	105_L	0.741	0.47
143_K	154_N	0.739	0.47
218_I	272_F	0.738	0.47
277_A	280_M	0.738	0.47
329_P	353_Q	0.737	0.47
103_E	163_Y	0.735	0.47
190_R	331_T	0.733	0.47
120_K	281_T	0.731	0.46
152_L	296_Y	0.729	0.46
179_N	190_R	0.729	0.46
160_N	336_F	0.728	0.46
267_Y	317_E	0.726	0.46
32_D	88_I	0.724	0.46
92_S	106_N	0.723	0.46
324_T	354_I	0.720	0.45
107_S	246_E	0.720	0.45
147_G	150_S	0.718	0.45
14_L	18_G	0.718	0.45
340_Y	347_Y	0.717	0.45
128_H	132_T	0.714	0.45
198_G	201_L	0.711	0.45
267_Y	288_G	0.709	0.44
222_L	268_K	0.708	0.44
206_V	230_L	0.705	0.44
28_N	250_E	0.705	0.44
268_K	282_P	0.703	0.44
62_I	65_N	0.703	0.44
173_E	176_N	0.702	0.44
217_L	253_P	0.701	0.44
155_A	329_P	0.700	0.44
146_L	199_G	0.700	0.44
266_E	321_F	0.696	0.43
163_Y	227_A	0.690	0.43
60_I	66_G	0.690	0.43
87_K	90_S	0.689	0.43
108_I	113_L	0.685	0.42
300_K	309_H	0.685	0.42
152_L	277_A	0.684	0.42
65_N	69_E	0.683	0.42
140_F	295_G	0.682	0.42
270_K	318_D	0.680	0.42
3_G	154_N	0.679	0.42
232_L	244_L	0.678	0.42
267_Y	277_A	0.676	0.41
140_F	309_H	0.675	0.41
35_Y	311_Y	0.674	0.41
191_I	194_I	0.672	0.41
192_K	196_E	0.670	0.41
81_A	301_E	0.665	0.40
84_L	293_T	0.664	0.40
10_A	248_L	0.663	0.40
335_K	349_K	0.658	0.40
126_V	137_E	0.656	0.40
223_P	269_I	0.652	0.39
162_I	204_V	0.651	0.39
141_S	277_A	0.651	0.39
333_R	355_R	0.650	0.39
72_I	165_I	0.650	0.39
22_A	308_Y	0.649	0.39
59_I	62_I	0.649	0.39
24_D	203_F	0.646	0.39
35_Y	108_I	0.646	0.39
66_G	69_E	0.646	0.39
297_I	356_F	0.644	0.39
292_A	296_Y	0.643	0.39
11_F	282_P	0.643	0.39
56_D	163_Y	0.643	0.39
277_A	296_Y	0.642	0.38
84_L	217_L	0.642	0.38
81_A	254_L	0.637	0.38
107_S	205_K	0.637	0.38
112_K	318_D	0.636	0.38
19_K	23_A	0.635	0.38
253_P	256_Y	0.634	0.38
51_Y	227_A	0.632	0.38
212_E	257_D	0.632	0.38
217_L	317_E	0.629	0.37
296_Y	356_F	0.628	0.37
240_K	339_I	0.626	0.37
114_K	117_S	0.626	0.37
10_A	14_L	0.623	0.37
99_P	272_F	0.622	0.37
282_P	313_R	0.621	0.37
211_F	215_L	0.620	0.37
213_N	261_N	0.619	0.36
175_I	179_N	0.618	0.36
243_D	348_F	0.618	0.36
190_R	347_Y	0.617	0.36
156_S	281_T	0.617	0.36
213_N	216_I	0.617	0.36
110_C	194_I	0.617	0.36
86_E	111_T	0.615	0.36
218_I	325_K	0.615	0.36
225_I	296_Y	0.614	0.36
37_I	77_F	0.614	0.36
278_L	307_C	0.614	0.36
28_N	300_K	0.613	0.36
318_D	322_N	0.613	0.36
185_S	190_R	0.613	0.36
76_E	235_S	0.612	0.36
342_E	345_E	0.612	0.36
139_G	152_L	0.612	0.36
165_I	225_I	0.611	0.36
5_W	9_Y	0.611	0.36
84_L	101_I	0.604	0.35
300_K	306_L	0.602	0.35
113_L	127_I	0.601	0.35
188_K	236_S	0.600	0.35
322_N	338_K	0.599	0.35
314_N	317_E	0.597	0.35
23_A	140_F	0.596	0.35
125_I	158_T	0.595	0.34
167_G	179_N	0.592	0.34
272_F	354_I	0.592	0.34
120_K	319_Y	0.592	0.34
22_A	30_I	0.591	0.34
98_I	211_F	0.587	0.34
298_V	309_H	0.587	0.34
249_E	266_E	0.586	0.34
76_E	79_E	0.586	0.34
39_K	126_V	0.584	0.34
41_I	48_T	0.584	0.34
41_I	137_E	0.584	0.34
279_G	286_W	0.583	0.33
275_A	290_Y	0.583	0.33
73_P	125_I	0.583	0.33
1_N	9_Y	0.581	0.33
98_I	192_K	0.580	0.33
85_L	145_Q	0.579	0.33
83_K	87_K	0.579	0.33
35_Y	127_I	0.577	0.33
59_I	64_G	0.577	0.33
153_L	333_R	0.576	0.33
159_T	328_T	0.576	0.33
326_L	354_I	0.576	0.33
113_L	274_T	0.575	0.33
130_L	134_I	0.573	0.33
200_K	209_E	0.573	0.33
185_S	238_I	0.572	0.33
156_S	283_S	0.572	0.33
128_H	314_N	0.571	0.32
10_A	18_G	0.570	0.32
89_K	165_I	0.570	0.32
278_L	309_H	0.569	0.32
110_C	126_V	0.568	0.32
42_R	51_Y	0.568	0.32
187_I	282_P	0.566	0.32
254_L	265_Y	0.565	0.32
350_L	354_I	0.565	0.32
262_H	285_V	0.564	0.32
296_Y	311_Y	0.564	0.32
270_K	278_L	0.563	0.32
293_T	310_I	0.563	0.32
275_A	287_D	0.560	0.32
136_P	317_E	0.560	0.32
256_Y	275_A	0.560	0.32
29_K	302_D	0.559	0.32
192_K	235_S	0.558	0.31
257_D	262_H	0.556	0.31
36_P	104_F	0.555	0.31
115_A	273_L	0.554	0.31
151_T	154_N	0.553	0.31
167_G	341_K	0.552	0.31
187_I	328_T	0.552	0.31
194_I	348_F	0.552	0.31
282_P	292_A	0.551	0.31
16_A	342_E	0.551	0.31
281_T	291_D	0.551	0.31
97_S	247_K	0.550	0.31
328_T	331_T	0.550	0.31
297_I	317_E	0.550	0.31
336_F	349_K	0.549	0.31
254_L	317_E	0.549	0.31
155_A	281_T	0.549	0.31
97_S	197_L	0.549	0.31
258_L	261_N	0.547	0.31
253_P	275_A	0.547	0.31
18_G	74_I	0.546	0.31
70_L	79_E	0.545	0.30
164_K	171_S	0.545	0.30
33_L	136_P	0.544	0.30
191_I	327_E	0.543	0.30
172_D	176_N	0.543	0.30
217_L	271_R	0.542	0.30
92_S	95_T	0.542	0.30
334_H	338_K	0.541	0.30
139_G	356_F	0.541	0.30
249_E	321_F	0.539	0.30
35_Y	305_V	0.539	0.30
246_E	250_E	0.539	0.30
174_E	178_I	0.538	0.30
12_L	77_F	0.538	0.30
213_N	217_L	0.537	0.30
61_I	67_E	0.536	0.30
160_N	334_H	0.535	0.30
249_E	263_P	0.535	0.30
73_P	77_F	0.535	0.30
4_E	85_L	0.534	0.30
163_Y	273_L	0.533	0.29
267_Y	292_A	0.533	0.29
223_P	300_K	0.532	0.29
134_I	290_Y	0.532	0.29
168_L	197_L	0.532	0.29
159_T	278_L	0.529	0.29
348_F	351_N	0.529	0.29
69_E	173_E	0.526	0.29
40_I	95_T	0.524	0.29
8_L	101_I	0.524	0.29
105_L	115_A	0.523	0.29
3_G	9_Y	0.518	0.28
274_T	313_R	0.518	0.28
3_G	141_S	0.517	0.28
194_I	201_L	0.516	0.28
204_V	246_E	0.516	0.28
213_N	285_V	0.516	0.28
150_S	316_F	0.515	0.28
216_I	252_N	0.514	0.28
92_S	266_E	0.513	0.28
60_I	64_G	0.513	0.28
68_E	71_R	0.512	0.28
196_E	251_E	0.511	0.28
154_N	286_W	0.510	0.28
87_K	237_G	0.510	0.28
66_G	86_E	0.510	0.28
140_F	316_F	0.510	0.28
127_I	244_L	0.509	0.28
14_L	290_Y	0.508	0.28
40_I	88_I	0.508	0.28
123_I	146_L	0.508	0.28
173_E	343_N	0.508	0.28
304_E	310_I	0.507	0.28
157_K	334_H	0.507	0.28
159_T	352_L	0.507	0.28
204_V	339_I	0.506	0.27
9_Y	51_Y	0.504	0.27
178_I	183_T	0.503	0.27
172_D	175_I	0.503	0.27
108_I	354_I	0.502	0.27
36_P	132_T	0.502	0.27
256_Y	317_E	0.501	0.27
203_F	286_W	0.501	0.27
123_I	297_I	0.501	0.27
200_K	231_L	0.500	0.27
340_Y	345_E	0.500	0.27
175_I	178_I	0.500	0.27

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
4bwpA	2	0.2331	39.3	0.972	Contact Map
4czxB	2	0.2247	30.1	0.974	Contact Map
4xr7L	2	0.2416	26.3	0.974	Contact Map
4bwxA	2	0.2219	19.2	0.976	Contact Map
4d0kB	2	0.2303	17.1	0.977	Contact Map
4cyiA	3	0.2331	10.6	0.979	Contact Map
4e3yA	1	0.2978	7.7	0.98	Contact Map
1y9qA	1	0.3848	7.4	0.98	Contact Map
3mcbB	1	0.1348	6.8	0.98	Contact Map
1sa3A	1	0.6685	6.3	0.981	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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