DUF647 - PFAM28P - GREMLIN Contacts

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DUF647 - Vitamin B6 photo-protection and homoeostasis

PFAM:	PF04884	Sequences: WRRRRSLRSFLRDVFLPAGYPDSVSPDYLPYQIWDSLQAFASSIAGVLATQALLEGVGVGDASASPTAAALNWVLKDGLGRLGRILFASRFGSSFDSDPKRWRLFADILNDLAMGLELLTPLFPSLFLPLACLANVLKAICGVAAGATRAALTQHFARRGNLADVSAKDGSQETVVSLLGLLLGILLASLVGSSTAVWAAFLLLTALHLYANYRAVRSVVLRTLNRQRASILLSEFLETG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	240 (233)
Sequences:	721 (485)
Seq/√Len:	31.8
META:	0.312

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
117_E	138_K	4.700	1.00
210_Y	214_R	4.162	1.00
40_F	183_L	4.004	1.00
73_W	78_G	3.779	1.00
117_E	134_A	3.543	1.00
224_L	232_L	2.785	1.00
127_F	131_A	2.744	1.00
98_D	101_R	2.620	1.00
113_A	134_A	2.587	1.00
41_A	207_L	2.546	1.00
111_D	208_H	2.453	0.99
23_S	159_R	2.404	0.99
74_V	184_G	2.321	0.99
126_L	129_P	2.315	0.99
113_A	137_L	2.259	0.99
208_H	212_N	2.210	0.99
169_D	173_E	2.199	0.99
35_D	38_Q	2.192	0.99
107_D	212_N	2.120	0.98
128_L	131_A	2.034	0.98
50_T	80_G	2.006	0.98
70_A	152_L	1.978	0.97
21_P	24_V	1.966	0.97
96_D	161_N	1.953	0.97
47_V	138_K	1.940	0.97
57_V	66_P	1.859	0.96
19_G	23_S	1.859	0.96
156_F	180_G	1.849	0.96
120_T	127_F	1.848	0.96
158_R	222_R	1.819	0.96
153_T	164_D	1.802	0.95
60_G	66_P	1.728	0.94
73_W	77_D	1.715	0.94
142_G	146_G	1.715	0.94
152_L	219_V	1.703	0.94
38_Q	107_D	1.688	0.93
143_V	166_S	1.686	0.93
34_W	214_R	1.666	0.93
229_A	233_L	1.662	0.93
230_S	234_S	1.658	0.93
49_A	53_L	1.592	0.91
32_Q	169_D	1.586	0.91
178_L	184_G	1.568	0.91
94_S	98_D	1.547	0.90
179_L	182_L	1.541	0.90
59_V	65_S	1.491	0.88
180_G	184_G	1.474	0.88
81_R	177_S	1.474	0.88
79_L	114_M	1.461	0.87
10_F	13_D	1.441	0.87
42_S	110_N	1.438	0.86
34_W	165_V	1.438	0.86
149_R	165_V	1.436	0.86
107_D	142_G	1.435	0.86
156_F	184_G	1.428	0.86
16_L	21_P	1.425	0.86
207_L	211_A	1.382	0.84
81_R	84_R	1.382	0.84
135_N	138_K	1.365	0.83
34_W	37_L	1.352	0.83
39_A	173_E	1.309	0.81
24_V	28_Y	1.308	0.81
70_A	73_W	1.306	0.80
39_A	42_S	1.306	0.80
49_A	200_A	1.284	0.79
22_D	159_R	1.241	0.77
43_S	169_D	1.238	0.77
151_A	164_D	1.236	0.77
153_T	169_D	1.232	0.76
32_Q	36_S	1.227	0.76
174_T	177_S	1.221	0.76
128_L	135_N	1.220	0.76
153_T	170_G	1.215	0.75
122_L	214_R	1.213	0.75
36_S	176_V	1.211	0.75
186_L	193_S	1.209	0.75
203_L	207_L	1.205	0.75
87_F	177_S	1.204	0.75
111_D	121_P	1.199	0.74
83_G	96_D	1.198	0.74
73_W	80_G	1.194	0.74
47_V	70_A	1.187	0.74
157_A	161_N	1.183	0.73
141_C	145_A	1.175	0.73
186_L	203_L	1.174	0.73
74_V	80_G	1.173	0.73
84_R	170_G	1.170	0.73
39_A	43_S	1.151	0.71
101_R	104_L	1.137	0.70
32_Q	35_D	1.131	0.70
160_G	223_T	1.126	0.70
84_R	177_S	1.118	0.69
112_L	209_L	1.109	0.68
35_D	39_A	1.105	0.68
181_L	184_G	1.101	0.68
87_F	143_V	1.099	0.68
76_K	96_D	1.098	0.68
120_T	197_V	1.094	0.67
86_L	104_L	1.090	0.67
69_A	100_K	1.088	0.67
150_A	221_L	1.087	0.67
227_Q	231_I	1.086	0.67
84_R	109_L	1.076	0.66
7_L	124_P	1.074	0.66
118_L	201_F	1.071	0.66
149_R	166_S	1.057	0.65
42_S	141_C	1.055	0.64
118_L	198_W	1.014	0.61
159_R	237_L	1.012	0.61
192_G	197_V	1.010	0.61
169_D	175_V	0.997	0.60
147_A	233_L	0.996	0.60
50_T	73_W	0.989	0.59
62_A	108_I	0.989	0.59
120_T	135_N	0.989	0.59
110_N	155_H	0.988	0.59
79_L	223_T	0.985	0.59
30_P	33_I	0.982	0.59
52_A	154_Q	0.981	0.59
16_L	23_S	0.977	0.58
116_L	199_A	0.972	0.58
35_D	110_N	0.968	0.58
147_A	172_Q	0.965	0.57
76_K	135_N	0.959	0.57
106_A	208_H	0.956	0.57
221_L	232_L	0.955	0.57
35_D	148_T	0.954	0.57
183_L	196_A	0.953	0.57
106_A	121_P	0.949	0.56
91_F	163_A	0.945	0.56
73_W	83_G	0.944	0.56
198_W	205_T	0.937	0.55
15_F	28_Y	0.935	0.55
20_Y	195_T	0.928	0.54
86_L	89_S	0.927	0.54
17_P	28_Y	0.922	0.54
26_P	204_L	0.921	0.54
112_L	219_V	0.921	0.54
73_W	135_N	0.919	0.54
231_I	234_S	0.908	0.53
111_D	145_A	0.907	0.53
30_P	133_L	0.904	0.53
27_D	30_P	0.901	0.52
50_T	54_L	0.900	0.52
49_A	118_L	0.894	0.52
16_L	19_G	0.889	0.51
135_N	221_L	0.888	0.51
156_F	181_L	0.886	0.51
42_S	176_V	0.874	0.50
113_A	116_L	0.874	0.50
80_G	135_N	0.871	0.50
63_S	86_L	0.868	0.50
41_A	124_P	0.865	0.49
11_L	14_V	0.863	0.49
69_A	103_R	0.861	0.49
73_W	164_D	0.859	0.49
26_P	162_L	0.852	0.48
119_L	209_L	0.852	0.48
111_D	212_N	0.852	0.48
23_S	210_Y	0.848	0.48
27_D	155_H	0.847	0.48
35_D	169_D	0.846	0.48
37_L	211_A	0.843	0.48
98_D	119_L	0.843	0.48
56_G	68_A	0.842	0.47
65_S	212_N	0.840	0.47
38_Q	142_G	0.838	0.47
30_P	112_L	0.831	0.47
6_S	9_S	0.830	0.46
86_L	206_A	0.826	0.46
146_G	170_G	0.822	0.46
95_F	164_D	0.820	0.46
150_A	171_S	0.819	0.46
89_S	102_W	0.817	0.45
15_F	175_V	0.816	0.45
73_W	161_N	0.816	0.45
27_D	152_L	0.814	0.45
22_D	26_P	0.811	0.45
49_A	181_L	0.811	0.45
73_W	163_A	0.809	0.45
40_F	179_L	0.809	0.45
139_A	155_H	0.805	0.44
161_N	164_D	0.802	0.44
15_F	164_D	0.801	0.44
26_P	30_P	0.801	0.44
53_L	131_A	0.797	0.44
188_A	192_G	0.793	0.43
28_Y	172_Q	0.784	0.43
212_N	225_N	0.783	0.43
31_Y	167_A	0.782	0.43
76_K	197_V	0.780	0.42
47_V	184_G	0.778	0.42
201_F	205_T	0.776	0.42
31_Y	149_R	0.776	0.42
148_T	201_F	0.776	0.42
90_R	232_L	0.768	0.42
202_L	206_A	0.768	0.42
81_R	174_T	0.767	0.41
133_L	163_A	0.766	0.41
46_G	114_M	0.756	0.41
179_L	203_L	0.753	0.40
139_A	142_G	0.752	0.40
72_N	76_K	0.752	0.40
35_D	42_S	0.750	0.40
22_D	130_L	0.750	0.40
115_G	201_F	0.747	0.40
7_L	29_L	0.746	0.40
120_T	148_T	0.743	0.40
34_W	162_L	0.741	0.39
234_S	238_E	0.741	0.39
64_A	106_A	0.737	0.39
9_S	229_A	0.736	0.39
68_A	78_G	0.734	0.39
73_W	76_K	0.732	0.39
83_G	176_V	0.730	0.39
63_S	186_L	0.728	0.38
207_L	220_V	0.728	0.38
160_G	199_A	0.724	0.38
98_D	227_Q	0.724	0.38
6_S	11_L	0.723	0.38
162_L	222_R	0.719	0.38
12_R	203_L	0.718	0.38
130_L	165_V	0.702	0.36
106_A	212_N	0.701	0.36
179_L	183_L	0.701	0.36
108_I	182_L	0.701	0.36
56_G	83_G	0.699	0.36
98_D	118_L	0.699	0.36
97_S	160_G	0.697	0.36
35_D	48_L	0.695	0.36
83_G	139_A	0.695	0.36
67_T	180_G	0.693	0.36
98_D	226_R	0.693	0.36
129_P	229_A	0.692	0.36
229_A	236_F	0.691	0.36
153_T	162_L	0.691	0.36
63_S	95_F	0.690	0.35
196_A	203_L	0.690	0.35
78_G	99_P	0.689	0.35
8_R	12_R	0.682	0.35
61_D	165_V	0.671	0.34
102_W	105_F	0.668	0.34
143_V	152_L	0.668	0.34
41_A	113_A	0.664	0.34
133_L	137_L	0.664	0.34
79_L	186_L	0.663	0.33
8_R	11_L	0.659	0.33
61_D	207_L	0.649	0.32
57_V	80_G	0.649	0.32
110_N	208_H	0.647	0.32
102_W	163_A	0.642	0.32
61_D	160_G	0.636	0.32
114_M	181_L	0.634	0.31
143_V	146_G	0.634	0.31
87_F	198_W	0.632	0.31
83_G	87_F	0.631	0.31
125_S	129_P	0.631	0.31
26_P	220_V	0.628	0.31
67_T	71_L	0.625	0.31
80_G	96_D	0.620	0.30
19_G	22_D	0.620	0.30
63_S	206_A	0.619	0.30
145_A	169_D	0.619	0.30
149_R	153_T	0.614	0.30
186_L	221_L	0.614	0.30
50_T	84_R	0.613	0.30
110_N	141_C	0.613	0.30
84_R	166_S	0.613	0.30
138_K	168_K	0.613	0.30
171_S	184_G	0.610	0.30
70_A	74_V	0.608	0.30
99_P	137_L	0.607	0.30
133_L	235_E	0.605	0.29
99_P	184_G	0.602	0.29
106_A	145_A	0.601	0.29
81_R	142_G	0.599	0.29
125_S	133_L	0.598	0.29
155_H	173_E	0.598	0.29
84_R	146_G	0.597	0.29
50_T	92_G	0.597	0.29
42_S	46_G	0.596	0.29
149_R	171_S	0.595	0.29
53_L	108_I	0.593	0.29
112_L	119_L	0.592	0.29
70_A	188_A	0.591	0.28
8_R	13_D	0.591	0.28
141_C	149_R	0.590	0.28
38_Q	42_S	0.589	0.28
62_A	77_D	0.586	0.28
180_G	204_L	0.585	0.28
47_V	74_V	0.585	0.28
67_T	70_A	0.584	0.28
34_W	210_Y	0.582	0.28
214_R	217_R	0.578	0.28
35_D	142_G	0.578	0.28
78_G	123_F	0.577	0.28
96_D	127_F	0.577	0.28
112_L	115_G	0.575	0.27
110_N	173_E	0.574	0.27
148_T	178_L	0.573	0.27
11_L	159_R	0.573	0.27
142_G	173_E	0.572	0.27
31_Y	177_S	0.566	0.27
103_R	145_A	0.564	0.27
132_C	231_I	0.563	0.27
84_R	148_T	0.563	0.27
116_L	133_L	0.563	0.27
47_V	181_L	0.561	0.26
8_R	22_D	0.561	0.26
161_N	215_A	0.561	0.26
69_A	92_G	0.559	0.26
170_G	177_S	0.559	0.26
189_S	218_S	0.555	0.26
73_W	118_L	0.552	0.26
47_V	54_L	0.551	0.26
156_F	169_D	0.549	0.26
53_L	209_L	0.548	0.26
158_R	236_F	0.547	0.26
44_I	79_L	0.546	0.26
14_V	99_P	0.542	0.25
92_G	120_T	0.541	0.25
183_L	218_S	0.539	0.25
66_P	93_S	0.535	0.25
114_M	201_F	0.534	0.25
106_A	110_N	0.533	0.25
76_K	127_F	0.529	0.25
119_L	234_S	0.528	0.24
137_L	178_L	0.527	0.24
27_D	208_H	0.527	0.24
131_A	188_A	0.526	0.24
107_D	146_G	0.525	0.24
100_K	103_R	0.523	0.24
186_L	235_E	0.523	0.24
39_A	106_A	0.522	0.24
69_A	117_E	0.522	0.24
92_G	100_K	0.520	0.24
31_Y	43_S	0.519	0.24
8_R	30_P	0.516	0.24
13_D	22_D	0.514	0.24
87_F	147_A	0.514	0.24
37_L	195_T	0.512	0.23
134_A	174_T	0.512	0.23
60_G	64_A	0.512	0.23
183_L	221_L	0.511	0.23
115_G	191_V	0.508	0.23
127_F	181_L	0.507	0.23
225_N	228_R	0.507	0.23
108_I	209_L	0.503	0.23
147_A	237_L	0.500	0.23
103_R	228_R	0.500	0.23

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
3wdoA	1	0.8625	25	0.96	Contact Map
2cfqA	1	0.8583	23.7	0.96	Contact Map
4m64A	1	0.8917	21.5	0.961	Contact Map
4c8dA	1	0.2208	16.3	0.963	Contact Map
1pw4A	1	0.8875	13.5	0.964	Contact Map
2gfpA	2	0.8292	12.6	0.965	Contact Map
4zw9A	1	0.8708	10.1	0.966	Contact Map
4j05A	3	0.8792	7.9	0.968	Contact Map
4u4vA	1	0.8875	6.1	0.97	Contact Map
3na2A	2	0.225	3.4	0.973	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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