DpnII - PFAM28P - GREMLIN Contacts

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DpnII - DpnII restriction endonuclease

PFAM:	PF04556	Sequences: DFEEFLSTLKESIATYDYFVDFEKVYRNVDKIKIELNILNSLIGKKNIEEEFEELLKKYPEVLKVIPILLAVREKEIKVLDDDGNEFLYNFKKKNYFESIEQYVEFMRKTGLFDLFQNKIIKNLVDYVFGVEVGLDSNGRKNRGGHLMENLVESYIKKAGIKKNEYFKEAYASEIKEKWGIDLSVGKSEKRFDFVIKTKKKIYLIETNFYSGGGSKLNETARSYKTLAPELKSIDGFEFVWITDGKGWKSAKNNLEETFDVIDYIYNLNMLENGILEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	278 (276)
Sequences:	1393 (983)
Seq/√Len:	59.2
META:	0.827

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
49_E	108_R	5.864	1.00
47_N	50_E	4.997	1.00
58_K	61_E	4.068	1.00
201_K	238_E	3.760	1.00
55_L	62_V	3.715	1.00
33_K	45_K	3.536	1.00
68_I	128_V	3.499	1.00
45_K	51_E	3.240	1.00
114_D	118_N	2.993	1.00
53_E	104_V	2.958	1.00
41_S	45_K	2.884	1.00
269_N	273_N	2.809	1.00
34_I	38_I	2.771	1.00
38_I	59_Y	2.705	1.00
20_V	133_V	2.702	1.00
204_L	237_F	2.688	1.00
37_N	40_N	2.550	1.00
169_E	191_R	2.549	1.00
33_K	41_S	2.504	1.00
24_K	136_D	2.419	1.00
213_G	250_S	2.309	1.00
5_F	9_L	2.254	1.00
220_T	224_Y	2.240	1.00
146_H	169_E	2.180	1.00
8_T	267_N	2.136	1.00
256_E	260_D	2.121	1.00
153_E	168_K	2.063	1.00
105_E	109_K	2.042	1.00
246_K	249_K	1.985	1.00
229_P	261_V	1.964	1.00
48_I	113_F	1.923	1.00
30_D	33_K	1.914	1.00
41_S	51_E	1.880	1.00
242_I	276_L	1.862	1.00
89_Y	105_E	1.836	1.00
219_E	223_S	1.811	0.99
34_I	37_N	1.805	0.99
49_E	104_V	1.782	0.99
11_E	78_K	1.780	0.99
187_K	256_E	1.780	0.99
53_E	101_E	1.731	0.99
226_T	229_P	1.729	0.99
219_E	222_R	1.703	0.99
153_E	157_K	1.698	0.99
91_F	96_Y	1.690	0.99
148_M	268_L	1.671	0.99
38_I	55_L	1.592	0.99
217_L	251_A	1.592	0.99
29_V	125_V	1.584	0.99
52_F	104_V	1.576	0.99
57_K	97_F	1.570	0.99
107_M	113_F	1.565	0.98
204_L	231_L	1.550	0.98
10_K	272_E	1.546	0.98
271_L	276_L	1.544	0.98
171_Y	191_R	1.527	0.98
39_L	62_V	1.522	0.98
232_K	263_D	1.507	0.98
166_Y	169_E	1.479	0.98
258_T	262_I	1.476	0.98
53_E	100_I	1.475	0.98
165_E	178_K	1.447	0.97
149_E	169_E	1.441	0.97
156_I	161_I	1.440	0.97
20_V	25_V	1.412	0.97
8_T	269_N	1.408	0.97
238_E	264_Y	1.393	0.97
91_F	94_K	1.387	0.97
35_E	64_K	1.385	0.97
173_S	189_E	1.377	0.97
6_L	252_K	1.376	0.97
41_S	59_Y	1.374	0.97
155_Y	271_L	1.372	0.97
79_V	83_D	1.364	0.96
32_I	68_I	1.343	0.96
104_V	108_R	1.336	0.96
162_K	277_E	1.333	0.96
225_K	261_V	1.317	0.96
99_S	102_Q	1.305	0.95
51_E	54_E	1.305	0.95
227_L	231_L	1.304	0.95
190_K	222_R	1.301	0.95
192_F	227_L	1.293	0.95
79_V	105_E	1.269	0.95
57_K	100_I	1.268	0.95
176_K	182_D	1.265	0.94
167_F	170_A	1.263	0.94
26_Y	115_L	1.260	0.94
218_N	222_R	1.249	0.94
218_N	223_S	1.245	0.94
170_A	175_I	1.239	0.94
153_E	166_Y	1.227	0.94
24_K	132_E	1.210	0.93
11_E	246_K	1.186	0.92
79_V	84_G	1.179	0.92
190_K	223_S	1.166	0.92
80_L	86_E	1.156	0.91
14_A	22_F	1.151	0.91
3_E	256_E	1.151	0.91
26_Y	120_I	1.133	0.90
3_E	7_S	1.132	0.90
29_V	32_I	1.130	0.90
196_I	205_I	1.128	0.90
38_I	41_S	1.126	0.90
188_S	253_N	1.121	0.90
54_E	58_K	1.117	0.90
210_Y	241_W	1.111	0.90
27_R	30_D	1.106	0.89
172_A	176_K	1.097	0.89
242_I	271_L	1.094	0.89
35_E	38_I	1.094	0.89
63_L	66_I	1.089	0.89
41_S	55_L	1.089	0.89
176_K	189_E	1.083	0.88
34_I	41_S	1.082	0.88
37_N	125_V	1.076	0.88
36_L	125_V	1.076	0.88
229_P	232_K	1.072	0.88
173_S	177_E	1.052	0.87
66_I	223_S	1.051	0.87
33_K	37_N	1.032	0.86
213_G	251_A	1.011	0.85
89_Y	102_Q	1.007	0.84
146_H	191_R	1.006	0.84
157_K	166_Y	0.992	0.84
253_N	256_E	0.987	0.83
47_N	51_E	0.986	0.83
35_E	58_K	0.983	0.83
190_K	218_N	0.981	0.83
218_N	254_N	0.979	0.83
165_E	179_W	0.973	0.82
63_L	103_Y	0.969	0.82
115_L	123_N	0.969	0.82
154_S	158_K	0.963	0.82
231_L	237_F	0.956	0.81
213_G	217_L	0.953	0.81
26_Y	129_F	0.951	0.81
115_L	121_I	0.949	0.81
30_D	45_K	0.944	0.80
161_I	165_E	0.943	0.80
50_E	54_E	0.938	0.80
231_L	262_I	0.938	0.80
190_K	219_E	0.937	0.80
15_T	147_L	0.934	0.80
170_A	195_V	0.934	0.80
52_F	56_L	0.932	0.80
186_G	190_K	0.931	0.79
73_R	132_E	0.927	0.79
228_A	232_K	0.925	0.79
259_F	265_I	0.920	0.79
15_T	150_N	0.916	0.78
166_Y	170_A	0.912	0.78
184_S	192_F	0.911	0.78
195_V	204_L	0.910	0.78
146_H	168_K	0.910	0.78
27_R	31_K	0.903	0.77
36_L	128_V	0.895	0.77
17_D	23_E	0.893	0.77
226_T	230_E	0.891	0.76
52_F	103_Y	0.884	0.76
171_Y	174_E	0.883	0.76
161_I	167_F	0.881	0.76
163_K	167_F	0.877	0.75
146_H	150_N	0.875	0.75
56_L	62_V	0.871	0.75
113_F	117_Q	0.871	0.75
104_V	113_F	0.871	0.75
212_G	250_S	0.870	0.75
240_V	276_L	0.865	0.74
225_K	258_T	0.863	0.74
97_F	100_I	0.862	0.74
81_D	84_G	0.857	0.74
270_M	273_N	0.846	0.73
39_L	55_L	0.838	0.72
218_N	251_A	0.831	0.71
14_A	147_L	0.829	0.71
100_I	104_V	0.827	0.71
221_A	241_W	0.827	0.71
220_T	225_K	0.825	0.71
186_G	230_E	0.825	0.71
56_L	100_I	0.822	0.70
243_T	248_W	0.820	0.70
181_I	237_F	0.816	0.70
80_L	105_E	0.816	0.70
249_K	252_K	0.814	0.70
156_I	196_I	0.812	0.69
6_L	9_L	0.810	0.69
205_I	242_I	0.803	0.69
4_E	7_S	0.803	0.69
192_F	204_L	0.800	0.68
150_N	168_K	0.800	0.68
66_I	100_I	0.799	0.68
29_V	133_V	0.798	0.68
167_F	172_A	0.797	0.68
217_L	221_A	0.796	0.68
93_K	96_Y	0.794	0.68
35_E	61_E	0.791	0.67
258_T	265_I	0.790	0.67
154_S	157_K	0.787	0.67
21_D	139_G	0.787	0.67
7_S	27_R	0.786	0.67
37_N	41_S	0.783	0.67
14_A	18_Y	0.782	0.67
32_I	55_L	0.776	0.66
181_I	202_I	0.773	0.66
189_E	253_N	0.773	0.66
34_I	58_K	0.772	0.66
17_D	154_S	0.771	0.65
218_N	221_A	0.768	0.65
107_M	112_L	0.768	0.65
102_Q	105_E	0.767	0.65
49_E	53_E	0.767	0.65
56_L	89_Y	0.757	0.64
90_N	95_N	0.756	0.64
192_F	231_L	0.755	0.64
172_A	188_S	0.754	0.64
222_R	257_E	0.752	0.63
189_E	226_T	0.750	0.63
210_Y	221_A	0.750	0.63
71_A	133_V	0.749	0.63
9_L	252_K	0.749	0.63
40_N	123_N	0.748	0.63
49_E	113_F	0.747	0.63
48_I	71_A	0.746	0.63
269_N	272_E	0.745	0.63
210_Y	224_Y	0.740	0.62
137_S	172_A	0.740	0.62
217_L	220_T	0.738	0.62
5_F	13_I	0.737	0.62
185_V	233_S	0.737	0.62
233_S	238_E	0.734	0.62
146_H	149_E	0.734	0.62
36_L	69_L	0.734	0.62
25_V	133_V	0.729	0.61
249_K	253_N	0.726	0.61
32_I	125_V	0.725	0.61
130_G	141_K	0.724	0.61
23_E	27_R	0.721	0.60
70_L	110_T	0.720	0.60
238_E	263_D	0.720	0.60
14_A	19_F	0.719	0.60
98_E	102_Q	0.718	0.60
95_N	98_E	0.718	0.60
30_D	51_E	0.717	0.60
130_G	145_G	0.711	0.59
167_F	171_Y	0.705	0.58
227_L	238_E	0.704	0.58
225_K	229_P	0.700	0.58
101_E	104_V	0.697	0.58
143_R	248_W	0.697	0.58
39_L	65_V	0.696	0.58
267_N	276_L	0.694	0.57
130_G	206_E	0.692	0.57
73_R	133_V	0.691	0.57
29_V	38_I	0.691	0.57
108_R	117_Q	0.689	0.57
31_K	129_F	0.688	0.57
68_I	72_V	0.688	0.57
40_N	125_V	0.685	0.56
67_P	106_F	0.683	0.56
43_I	259_F	0.681	0.56
196_I	274_G	0.680	0.56
166_Y	172_A	0.677	0.55
172_A	189_E	0.674	0.55
70_L	157_K	0.672	0.55
33_K	122_K	0.670	0.55
46_K	118_N	0.670	0.55
137_S	146_H	0.667	0.54
155_Y	158_K	0.666	0.54
133_V	136_D	0.666	0.54
52_F	113_F	0.665	0.54
12_S	18_Y	0.664	0.54
19_F	151_L	0.664	0.54
153_E	156_I	0.664	0.54
108_R	113_F	0.663	0.54
220_T	223_S	0.662	0.54
188_S	220_T	0.660	0.54
4_E	8_T	0.659	0.53
90_N	94_K	0.658	0.53
7_S	11_E	0.655	0.53
208_N	243_T	0.654	0.53
229_P	240_V	0.652	0.53
135_L	144_G	0.642	0.52
33_K	125_V	0.642	0.52
66_I	103_Y	0.639	0.51
140_R	143_R	0.637	0.51
25_V	139_G	0.634	0.51
141_K	216_K	0.633	0.51
223_S	254_N	0.628	0.50
66_I	107_M	0.627	0.50
262_I	265_I	0.625	0.50
228_A	262_I	0.625	0.50
155_Y	159_A	0.624	0.50
115_L	120_I	0.623	0.49
83_D	105_E	0.623	0.49
81_D	85_N	0.620	0.49
48_I	104_V	0.619	0.49
134_G	141_K	0.619	0.49
191_R	220_T	0.618	0.49
13_I	147_L	0.616	0.49
221_A	224_Y	0.614	0.48
266_Y	270_M	0.614	0.48
203_Y	240_V	0.613	0.48
56_L	224_Y	0.610	0.48
116_F	124_L	0.609	0.48
156_I	160_G	0.608	0.48
174_E	178_K	0.605	0.47
141_K	206_E	0.605	0.47
202_I	237_F	0.605	0.47
115_L	147_L	0.604	0.47
23_E	53_E	0.603	0.47
87_F	102_Q	0.603	0.47
42_L	51_E	0.602	0.47
254_N	270_M	0.600	0.47
98_E	168_K	0.600	0.47
206_E	216_K	0.597	0.47
50_E	57_K	0.589	0.46
31_K	64_K	0.588	0.46
219_E	224_Y	0.586	0.45
160_G	190_K	0.585	0.45
112_L	116_F	0.584	0.45
18_Y	144_G	0.582	0.45
231_L	234_I	0.581	0.45
115_L	129_F	0.578	0.44
17_D	150_N	0.578	0.44
186_G	261_V	0.577	0.44
170_A	179_W	0.577	0.44
222_R	227_L	0.573	0.44
61_E	64_K	0.571	0.44
156_I	166_Y	0.571	0.44
20_V	122_K	0.570	0.44
34_I	62_V	0.568	0.43
144_G	147_L	0.567	0.43
157_K	165_E	0.567	0.43
10_K	13_I	0.566	0.43
201_K	264_Y	0.565	0.43
88_L	96_Y	0.565	0.43
40_N	43_I	0.560	0.42
174_E	177_E	0.560	0.42
12_S	39_L	0.559	0.42
174_E	181_I	0.557	0.42
136_D	139_G	0.556	0.42
14_A	211_S	0.556	0.42
175_I	179_W	0.556	0.42
91_F	95_N	0.554	0.42
160_G	270_M	0.551	0.41
61_E	93_K	0.550	0.41
40_N	124_L	0.550	0.41
127_Y	133_V	0.550	0.41
46_K	50_E	0.550	0.41
225_K	230_E	0.549	0.41
33_K	51_E	0.549	0.41
160_G	218_N	0.548	0.41
43_I	116_F	0.548	0.41
18_Y	139_G	0.545	0.41
251_A	254_N	0.545	0.41
148_M	203_Y	0.543	0.41
35_E	59_Y	0.542	0.41
21_D	108_R	0.541	0.40
37_N	44_G	0.541	0.40
72_V	77_I	0.541	0.40
177_E	246_K	0.534	0.40
93_K	273_N	0.534	0.40
169_E	172_A	0.534	0.40
50_E	53_E	0.531	0.39
67_P	115_L	0.530	0.39
161_I	198_T	0.529	0.39
136_D	143_R	0.528	0.39
75_K	93_K	0.528	0.39
77_I	81_D	0.527	0.39
14_A	144_G	0.526	0.39
179_W	197_K	0.526	0.39
21_D	137_S	0.526	0.39
20_V	124_L	0.524	0.39
141_K	208_N	0.524	0.39
45_K	55_L	0.523	0.38
19_F	224_Y	0.522	0.38
127_Y	132_E	0.521	0.38
222_R	254_N	0.519	0.38
89_Y	135_L	0.519	0.38
211_S	247_G	0.519	0.38
130_G	216_K	0.519	0.38
220_T	258_T	0.518	0.38
85_N	98_E	0.516	0.38
14_A	20_V	0.516	0.38
48_I	117_Q	0.515	0.38
16_Y	81_D	0.515	0.38
71_A	74_E	0.514	0.38
128_V	258_T	0.514	0.38
82_D	88_L	0.514	0.38
17_D	233_S	0.513	0.37
170_A	178_K	0.512	0.37
167_F	178_K	0.512	0.37
144_G	217_L	0.512	0.37
238_E	265_I	0.511	0.37
2_F	259_F	0.510	0.37
226_T	238_E	0.510	0.37
79_V	89_Y	0.510	0.37
83_D	88_L	0.507	0.37
31_K	158_K	0.507	0.37
201_K	227_L	0.506	0.37
8_T	11_E	0.506	0.37
130_G	134_G	0.505	0.37
165_E	197_K	0.505	0.37
173_S	253_N	0.504	0.37
43_I	48_I	0.503	0.36
114_D	232_K	0.503	0.36
219_E	254_N	0.502	0.36
22_F	160_G	0.502	0.36
95_N	100_I	0.502	0.36
103_Y	113_F	0.502	0.36
36_L	65_V	0.501	0.36
89_Y	96_Y	0.501	0.36
91_F	103_Y	0.500	0.36

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
2gb7A	2	0.8058	81.5	0.95	Contact Map
3bm3A	2	0.7302	64.7	0.956	Contact Map
1na6A	2	0.7878	34.5	0.964	Contact Map
1y88A	5	0.4209	30.5	0.965	Contact Map
4qs4A	3	0.5827	12.1	0.971	Contact Map
3oyyA	1	0.3309	9.9	0.972	Contact Map
1gefA	2	0.3849	9.5	0.972	Contact Map
3h1tA	1	0.4496	9.3	0.972	Contact Map
3hrlA	1	0.3273	9.1	0.972	Contact Map
1uebA	1	0.3237	8.8	0.972	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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