NPH3 - PFAM28P - GREMLIN Contacts

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NPH3 - NPH3 family

PFAM:	PF03000	Sequences: DWWFEDLSELSIDLFKRVITAMKSKGVKPEVIGEALMHYAKKWLPSASDESEQRVLLETIVSLLPSEKGSVSCSFLLGLLRAAIILGASPSCREELERRIGLQLDQATLDDLLIPSSETLYDVDLVQRILEHFLSQDEQEEESSSPSLSSLLKVAKLVDGYLAEIAPDPNLKLSKFIALAEALPDSARPSHDGLYRAIDIYLKAHPGLSESERKRLCRLMDCQKLSLEAC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	230 (228)
Sequences:	1137 (592)
Seq/√Len:	39.2
META:	0.052

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_F	35_A	4.973	1.00
124_D	175_K	4.714	1.00
97_E	128_R	4.618	1.00
125_L	129_I	4.086	1.00
184_P	187_A	3.240	1.00
119_T	170_N	3.206	1.00
209_S	212_E	3.101	1.00
155_A	226_S	3.060	1.00
205_H	217_C	2.970	1.00
159_D	194_L	2.568	1.00
67_E	70_S	2.528	1.00
40_A	75_F	2.402	1.00
159_D	188_R	2.318	1.00
87_G	93_R	2.289	1.00
105_D	133_F	2.264	1.00
22_M	78_G	2.184	0.99
89_S	175_K	2.179	0.99
77_L	158_V	2.176	0.99
26_G	99_R	2.116	0.99
159_D	184_P	1.962	0.99
123_V	194_L	1.915	0.98
44_L	216_L	1.801	0.98
57_L	86_L	1.771	0.97
184_P	188_R	1.752	0.97
113_L	121_Y	1.708	0.97
198_I	220_M	1.707	0.97
97_E	129_I	1.700	0.97
216_L	220_M	1.666	0.96
127_Q	170_N	1.654	0.96
5_E	19_I	1.653	0.96
156_K	194_L	1.650	0.96
205_H	225_L	1.629	0.96
204_A	214_K	1.601	0.95
139_Q	142_E	1.600	0.95
15_F	19_I	1.585	0.95
32_I	61_V	1.582	0.95
4_F	34_E	1.567	0.95
134_L	158_V	1.559	0.94
3_W	188_R	1.555	0.94
107_A	115_P	1.542	0.94
224_K	228_E	1.530	0.94
33_G	71_V	1.515	0.93
204_A	209_S	1.513	0.93
87_G	94_E	1.507	0.93
106_Q	213_R	1.477	0.93
6_D	155_A	1.463	0.92
185_D	200_I	1.453	0.92
103_Q	226_S	1.444	0.92
186_S	198_I	1.440	0.92
108_T	156_K	1.428	0.91
157_L	168_D	1.410	0.91
134_L	179_L	1.385	0.90
18_V	41_K	1.361	0.89
18_V	30_E	1.360	0.89
187_A	224_K	1.356	0.89
22_M	110_D	1.347	0.89
23_K	194_L	1.341	0.88
65_P	75_F	1.340	0.88
78_G	81_R	1.334	0.88
203_K	206_P	1.329	0.88
109_L	208_L	1.316	0.87
155_A	211_S	1.310	0.87
93_R	114_I	1.302	0.87
87_G	159_D	1.302	0.87
130_L	179_L	1.270	0.86
17_R	169_P	1.261	0.85
94_E	134_L	1.257	0.85
150_S	198_I	1.256	0.85
58_E	128_R	1.249	0.85
15_F	36_L	1.248	0.85
65_P	99_R	1.246	0.84
81_R	92_C	1.240	0.84
72_S	125_L	1.240	0.84
163_A	193_G	1.229	0.84
56_L	79_L	1.216	0.83
16_K	19_I	1.216	0.83
71_V	130_L	1.212	0.83
55_V	108_T	1.208	0.83
167_P	172_K	1.202	0.82
6_D	147_S	1.197	0.82
198_I	219_L	1.184	0.81
40_A	45_P	1.176	0.81
109_L	157_L	1.166	0.80
190_S	226_S	1.146	0.79
218_R	222_C	1.140	0.79
15_F	200_I	1.132	0.78
129_I	190_S	1.131	0.78
10_L	18_V	1.125	0.78
72_S	230_C	1.119	0.77
133_F	171_L	1.112	0.77
5_E	221_D	1.111	0.77
210_E	214_K	1.103	0.76
220_M	229_A	1.093	0.76
93_R	122_D	1.086	0.75
126_V	129_I	1.083	0.75
40_A	60_I	1.078	0.75
61_V	92_C	1.055	0.73
49_D	150_S	1.050	0.73
59_T	112_L	1.047	0.72
164_E	199_D	1.045	0.72
43_W	101_G	1.042	0.72
26_G	109_L	1.038	0.72
15_F	206_P	1.037	0.72
40_A	44_L	1.034	0.71
53_Q	191_H	1.033	0.71
62_S	95_E	1.031	0.71
101_G	132_H	1.031	0.71
7_L	165_I	1.030	0.71
60_I	174_S	1.021	0.71
31_V	114_I	1.019	0.70
81_R	143_S	1.018	0.70
128_R	171_L	1.012	0.70
24_S	67_E	1.004	0.69
58_E	99_R	1.004	0.69
46_S	49_D	0.999	0.69
92_C	115_P	0.997	0.69
36_L	212_E	0.993	0.68
163_A	200_I	0.991	0.68
7_L	176_F	0.985	0.68
12_I	228_E	0.983	0.68
119_T	220_M	0.981	0.67
177_I	181_E	0.975	0.67
149_S	155_A	0.968	0.66
18_V	229_A	0.967	0.66
210_E	223_Q	0.965	0.66
122_D	126_V	0.956	0.65
122_D	165_I	0.948	0.65
53_Q	58_E	0.947	0.65
1_D	16_K	0.946	0.65
120_L	208_L	0.945	0.64
115_P	194_L	0.944	0.64
125_L	165_I	0.938	0.64
99_R	129_I	0.936	0.64
41_K	158_V	0.933	0.63
128_R	164_E	0.917	0.62
35_A	38_H	0.913	0.62
83_A	201_Y	0.906	0.61
165_I	224_K	0.905	0.61
158_V	228_E	0.904	0.61
60_I	93_R	0.902	0.61
103_Q	121_Y	0.893	0.60
100_I	110_D	0.892	0.60
113_L	165_I	0.889	0.60
114_I	193_G	0.888	0.60
112_L	130_L	0.881	0.59
58_E	62_S	0.881	0.59
164_E	193_G	0.880	0.59
28_K	103_Q	0.880	0.59
193_G	196_R	0.878	0.59
78_G	230_C	0.874	0.58
7_L	191_H	0.873	0.58
211_S	222_C	0.872	0.58
36_L	63_L	0.866	0.58
211_S	227_L	0.851	0.56
111_D	160_G	0.850	0.56
8_S	38_H	0.847	0.56
33_G	214_K	0.844	0.56
153_K	216_L	0.843	0.56
31_V	122_D	0.840	0.55
71_V	182_A	0.839	0.55
123_V	157_L	0.839	0.55
110_D	161_Y	0.839	0.55
33_G	63_L	0.835	0.55
138_E	141_E	0.832	0.55
107_A	157_L	0.829	0.54
15_F	65_P	0.829	0.54
73_C	125_L	0.826	0.54
151_L	155_A	0.825	0.54
140_E	143_S	0.822	0.54
23_K	79_L	0.819	0.53
168_D	201_Y	0.816	0.53
159_D	191_H	0.815	0.53
4_F	82_A	0.814	0.53
22_M	172_K	0.810	0.53
99_R	203_K	0.809	0.53
188_R	194_L	0.809	0.53
161_Y	188_R	0.807	0.52
149_S	182_A	0.806	0.52
105_D	206_P	0.805	0.52
15_F	203_K	0.805	0.52
101_G	164_E	0.796	0.51
112_L	116_S	0.796	0.51
153_K	186_S	0.794	0.51
64_L	120_L	0.794	0.51
101_G	121_Y	0.792	0.51
69_G	182_A	0.792	0.51
27_V	94_E	0.789	0.51
129_I	152_L	0.786	0.50
95_E	214_K	0.781	0.50
88_A	152_L	0.780	0.50
64_L	79_L	0.776	0.50
69_G	103_Q	0.770	0.49
1_D	107_A	0.762	0.48
32_I	153_K	0.759	0.48
193_G	199_D	0.757	0.48
196_R	199_D	0.750	0.47
81_R	199_D	0.750	0.47
11_S	97_E	0.747	0.47
54_R	103_Q	0.746	0.47
38_H	183_L	0.744	0.47
7_L	14_L	0.742	0.46
34_E	213_R	0.741	0.46
192_D	197_A	0.735	0.46
32_I	56_L	0.735	0.46
171_L	199_D	0.734	0.46
204_A	213_R	0.733	0.46
3_W	184_P	0.726	0.45
2_W	35_A	0.725	0.45
15_F	40_A	0.722	0.45
209_S	230_C	0.721	0.45
78_G	183_L	0.719	0.44
56_L	114_I	0.717	0.44
84_I	182_A	0.717	0.44
26_G	32_I	0.717	0.44
154_V	171_L	0.717	0.44
107_A	114_I	0.714	0.44
133_F	174_S	0.713	0.44
133_F	197_A	0.713	0.44
109_L	184_P	0.710	0.44
71_V	222_C	0.709	0.43
43_W	88_A	0.703	0.43
111_D	162_L	0.696	0.42
163_A	229_A	0.696	0.42
98_R	175_K	0.693	0.42
204_A	225_L	0.692	0.42
54_R	88_A	0.690	0.42
144_S	179_L	0.689	0.42
79_L	210_E	0.683	0.41
3_W	175_K	0.683	0.41
27_V	209_S	0.682	0.41
66_S	158_V	0.681	0.41
58_E	187_A	0.680	0.41
199_D	220_M	0.671	0.40
43_W	220_M	0.669	0.40
19_I	130_L	0.669	0.40
18_V	109_L	0.664	0.40
81_R	164_E	0.661	0.39
81_R	86_L	0.658	0.39
30_E	130_L	0.655	0.39
139_Q	143_S	0.654	0.39
39_Y	107_A	0.650	0.38
53_Q	128_R	0.648	0.38
124_D	164_E	0.647	0.38
164_E	171_L	0.646	0.38
56_L	93_R	0.643	0.38
59_T	175_K	0.643	0.38
60_I	211_S	0.643	0.38
82_A	155_A	0.642	0.38
7_L	128_R	0.642	0.38
32_I	147_S	0.642	0.38
194_L	209_S	0.642	0.38
152_L	189_P	0.642	0.38
188_R	191_H	0.639	0.37
88_A	170_N	0.637	0.37
128_R	163_A	0.635	0.37
36_L	39_Y	0.634	0.37
71_V	227_L	0.631	0.37
25_K	220_M	0.629	0.37
61_V	93_R	0.624	0.36
39_Y	56_L	0.620	0.36
57_L	218_R	0.617	0.36
69_G	78_G	0.610	0.35
61_V	94_E	0.609	0.35
15_F	34_E	0.608	0.35
4_F	38_H	0.608	0.35
61_V	95_E	0.605	0.35
171_L	208_L	0.604	0.34
77_L	167_P	0.604	0.34
36_L	121_Y	0.604	0.34
211_S	226_S	0.603	0.34
156_K	230_C	0.599	0.34
67_E	116_S	0.597	0.34
2_W	72_S	0.595	0.34
115_P	179_L	0.591	0.33
37_M	97_E	0.589	0.33
127_Q	134_L	0.587	0.33
160_G	216_L	0.584	0.33
112_L	208_L	0.579	0.32
180_A	219_L	0.576	0.32
6_D	77_L	0.574	0.32
93_R	110_D	0.574	0.32
45_P	170_N	0.574	0.32
28_K	36_L	0.573	0.32
62_S	89_S	0.573	0.32
138_E	142_E	0.572	0.32
180_A	192_D	0.572	0.32
14_L	211_S	0.571	0.32
8_S	25_K	0.569	0.32
7_L	18_V	0.569	0.32
156_K	170_N	0.568	0.32
62_S	153_K	0.567	0.31
4_F	31_V	0.565	0.31
24_S	158_V	0.564	0.31
211_S	219_L	0.564	0.31
53_Q	97_E	0.560	0.31
162_L	198_I	0.557	0.31
25_K	123_V	0.557	0.31
37_M	210_E	0.556	0.31
73_C	77_L	0.554	0.30
67_E	121_Y	0.553	0.30
3_W	159_D	0.551	0.30
46_S	185_D	0.551	0.30
180_A	213_R	0.549	0.30
67_E	150_S	0.546	0.30
16_K	213_R	0.546	0.30
40_A	65_P	0.544	0.30
35_A	186_S	0.543	0.30
34_E	38_H	0.538	0.29
155_A	218_R	0.537	0.29
100_I	126_V	0.536	0.29
2_W	126_V	0.535	0.29
205_H	224_K	0.534	0.29
123_V	165_I	0.534	0.29
217_C	225_L	0.530	0.29
202_L	229_A	0.530	0.29
89_S	103_Q	0.529	0.29
207_G	214_K	0.529	0.29
3_W	10_L	0.525	0.28
50_E	83_A	0.524	0.28
34_E	42_K	0.524	0.28
165_I	175_K	0.524	0.28
30_E	56_L	0.523	0.28
41_K	74_S	0.520	0.28
205_H	226_S	0.518	0.28
98_R	131_E	0.518	0.28
64_L	166_A	0.516	0.28
83_A	88_A	0.515	0.28
31_V	37_M	0.515	0.28
197_A	202_L	0.514	0.27
11_S	210_E	0.513	0.27
24_S	125_L	0.510	0.27
85_I	216_L	0.510	0.27
192_D	195_Y	0.509	0.27
87_G	125_L	0.508	0.27
7_L	190_S	0.507	0.27
208_L	216_L	0.505	0.27
73_C	101_G	0.505	0.27
210_E	221_D	0.504	0.27
40_A	222_C	0.504	0.27
30_E	134_L	0.503	0.27
125_L	214_K	0.500	0.26
127_Q	131_E	0.500	0.26

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
3i3nA	2	0.4391	51.1	0.956	Contact Map
3hveA	1	0.3174	39.4	0.959	Contact Map
1j5sA	3	0.8565	32.7	0.961	Contact Map
2q01A	3	0.8826	29	0.962	Contact Map
3iacA	3	0.9043	18.8	0.965	Contact Map
4hxiA	1	0.1826	17.4	0.966	Contact Map
3v9rB	1	0.2913	14.1	0.967	Contact Map
4h4dA	1	0.2957	13.6	0.967	Contact Map
3dnfA	2	0.1957	10.9	0.969	Contact Map
3h0lB	1	0.1957	10.7	0.969	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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