DUF4158 - PFAM28P - GREMLIN Contacts

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DUF4158 - Domain of unknown function (DUF4158)

PFAM:	PF13700	Sequences: ILTDAERTALPRLPRFSEEELARYFTLSDADLALIRRRRGDHNRLGFALQLKYFRALGRFLDDPEEVPAAVVAYVARQLGVADPAALADYAWRGRTRRRHRAEIREYLGFRPFTAADRRALARWLAEAALTTDRPADLFNAAIEWLRERRIELPGYSTLERLVASA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	166 (162)
Sequences:	8867 (6382)
Seq/√Len:	501.4
META:	0.878

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
145_W	149_R	3.605	1.00
34_L	47_F	3.148	1.00
111_R	117_D	2.554	1.00
114_T	117_D	2.539	1.00
94_G	98_R	2.513	1.00
27_L	48_A	2.498	1.00
145_W	148_E	2.369	1.00
95_R	98_R	2.268	1.00
125_L	142_A	2.224	1.00
90_Y	100_H	2.158	1.00
38_R	103_E	2.143	1.00
155_G	158_T	2.084	1.00
49_L	75_V	2.080	1.00
97_R	101_R	2.047	1.00
54_F	110_F	2.036	1.00
52_K	55_R	2.006	1.00
157_S	161_R	1.985	1.00
40_G	43_N	1.931	1.00
105_R	152_E	1.893	1.00
32_L	36_R	1.840	1.00
120_A	149_R	1.839	1.00
125_L	138_L	1.838	1.00
121_L	146_L	1.826	1.00
54_F	152_E	1.805	1.00
121_L	142_A	1.788	1.00
36_R	44_R	1.771	1.00
34_L	107_Y	1.769	1.00
124_W	145_W	1.707	1.00
31_D	55_R	1.686	1.00
143_I	153_L	1.673	1.00
46_G	100_H	1.650	1.00
35_I	48_A	1.553	1.00
24_Y	56_A	1.512	1.00
132_T	137_D	1.511	1.00
31_D	107_Y	1.507	1.00
95_R	99_R	1.499	1.00
69_A	73_A	1.494	1.00
113_F	118_R	1.492	1.00
60_F	101_R	1.492	1.00
141_A	144_E	1.477	1.00
46_G	90_Y	1.475	1.00
18_E	22_A	1.427	1.00
17_S	20_E	1.418	1.00
45_L	72_V	1.408	1.00
27_L	35_I	1.394	1.00
139_F	163_V	1.391	1.00
13_L	53_Y	1.390	1.00
8_T	12_R	1.389	1.00
93_R	99_R	1.381	1.00
54_F	60_F	1.303	1.00
47_F	104_I	1.301	1.00
45_L	76_A	1.289	1.00
113_F	117_D	1.261	1.00
51_L	108_L	1.254	1.00
98_R	101_R	1.247	1.00
122_A	126_A	1.239	1.00
105_R	112_P	1.232	1.00
98_R	102_A	1.224	1.00
30_A	33_A	1.212	1.00
128_A	141_A	1.200	1.00
52_K	75_V	1.185	1.00
29_D	33_A	1.178	1.00
134_R	137_D	1.170	1.00
135_P	163_V	1.169	1.00
136_A	140_N	1.148	1.00
47_F	103_E	1.147	1.00
27_L	52_K	1.141	1.00
34_L	103_E	1.140	1.00
4_D	7_R	1.136	1.00
49_L	72_V	1.134	1.00
143_I	147_R	1.127	1.00
144_E	148_E	1.115	1.00
103_E	106_E	1.096	1.00
119_R	123_R	1.091	1.00
48_A	79_L	1.082	1.00
48_A	75_V	1.078	1.00
47_F	107_Y	1.076	1.00
58_G	147_R	1.070	1.00
4_D	8_T	1.069	1.00
156_Y	160_E	1.062	1.00
25_F	71_V	1.059	1.00
122_A	165_S	1.045	1.00
118_R	158_T	1.036	1.00
110_F	150_R	1.033	1.00
123_R	127_E	1.032	1.00
7_R	160_E	1.023	1.00
139_F	159_L	1.017	1.00
50_Q	100_H	1.015	1.00
26_T	74_Y	1.006	1.00
67_V	71_V	1.004	1.00
38_R	47_F	1.000	1.00
27_L	78_Q	0.994	1.00
142_A	159_L	0.978	1.00
139_F	143_I	0.973	1.00
25_F	56_A	0.971	1.00
118_R	122_A	0.968	1.00
49_L	67_V	0.960	1.00
45_L	75_V	0.951	1.00
50_Q	61_L	0.945	1.00
115_A	118_R	0.936	1.00
31_D	51_L	0.928	1.00
63_D	66_E	0.927	1.00
89_D	92_W	0.925	1.00
146_L	159_L	0.919	1.00
5_A	9_A	0.916	1.00
83_D	86_A	0.908	1.00
102_A	105_R	0.904	1.00
47_F	51_L	0.904	1.00
25_F	52_K	0.898	1.00
160_E	164_A	0.896	1.00
96_T	99_R	0.893	1.00
124_W	141_A	0.887	1.00
16_F	20_E	0.880	1.00
21_L	71_V	0.878	1.00
50_Q	104_I	0.869	1.00
157_S	160_E	0.867	1.00
101_R	105_R	0.865	1.00
70_A	73_A	0.838	1.00
49_L	87_L	0.837	1.00
127_E	130_L	0.829	1.00
5_A	8_T	0.823	1.00
128_A	131_T	0.818	1.00
22_A	26_T	0.808	1.00
19_E	23_R	0.805	1.00
56_A	71_V	0.800	1.00
53_Y	67_V	0.795	1.00
73_A	77_R	0.791	1.00
103_E	107_Y	0.781	1.00
121_L	125_L	0.773	1.00
142_A	146_L	0.768	1.00
120_A	145_W	0.766	1.00
122_A	162_L	0.763	1.00
51_L	104_I	0.762	1.00
53_Y	57_L	0.759	1.00
13_L	21_L	0.748	1.00
138_L	141_A	0.745	1.00
41_D	44_R	0.739	1.00
143_I	156_Y	0.733	1.00
125_L	129_A	0.732	1.00
28_S	31_D	0.731	1.00
141_A	145_W	0.728	1.00
102_A	106_E	0.727	1.00
125_L	163_V	0.723	1.00
95_R	102_A	0.716	1.00
111_R	114_T	0.713	1.00
124_W	142_A	0.707	1.00
54_F	104_I	0.702	1.00
121_L	124_W	0.701	1.00
37_R	107_Y	0.701	1.00
117_D	151_I	0.699	1.00
93_R	96_T	0.698	1.00
86_A	89_D	0.696	1.00
16_F	70_A	0.695	1.00
45_L	81_V	0.691	1.00
43_N	100_H	0.691	1.00
140_N	144_E	0.689	1.00
93_R	98_R	0.687	1.00
8_T	11_P	0.680	1.00
50_Q	101_R	0.679	1.00
87_L	90_Y	0.673	1.00
110_F	147_R	0.672	1.00
18_E	21_L	0.671	1.00
158_T	161_R	0.671	1.00
124_W	128_A	0.670	1.00
138_L	142_A	0.663	1.00
158_T	162_L	0.663	1.00
139_F	160_E	0.662	1.00
113_F	151_I	0.661	1.00
136_A	139_F	0.661	1.00
74_Y	78_Q	0.660	1.00
27_L	31_D	0.658	1.00
113_F	146_L	0.654	1.00
121_L	162_L	0.647	1.00
120_A	124_W	0.647	1.00
25_F	57_L	0.645	1.00
34_L	37_R	0.644	1.00
30_A	107_Y	0.642	1.00
35_I	38_R	0.639	1.00
53_Y	59_R	0.636	1.00
42_H	46_G	0.635	1.00
53_Y	71_V	0.629	1.00
106_E	109_G	0.626	1.00
123_R	126_A	0.624	1.00
137_D	140_N	0.624	1.00
132_T	135_P	0.620	1.00
16_F	21_L	0.616	1.00
27_L	32_L	0.609	0.99
31_D	52_K	0.608	0.99
50_Q	53_Y	0.607	0.99
52_K	56_A	0.604	0.99
81_V	86_A	0.600	0.99
137_D	153_L	0.594	0.99
28_S	108_L	0.593	0.99
35_I	44_R	0.590	0.99
19_E	22_A	0.589	0.99
102_A	112_P	0.588	0.99
116_A	120_A	0.584	0.99
41_D	81_V	0.583	0.99
4_D	9_A	0.581	0.99
94_G	101_R	0.575	0.99
142_A	145_W	0.575	0.99
39_R	43_N	0.575	0.99
137_D	141_A	0.570	0.99
52_K	71_V	0.564	0.99
161_R	165_S	0.563	0.99
53_Y	60_F	0.562	0.99
48_A	78_Q	0.561	0.99
10_L	13_L	0.560	0.99
116_A	119_R	0.559	0.99
75_V	79_L	0.559	0.99
85_A	88_A	0.558	0.99
113_F	158_T	0.556	0.99
46_G	87_L	0.554	0.99
20_E	56_A	0.553	0.99
135_P	164_A	0.552	0.99
153_L	159_L	0.551	0.99
50_Q	54_F	0.551	0.99
13_L	68_P	0.549	0.99
59_R	153_L	0.545	0.99
53_Y	56_A	0.540	0.99
32_L	78_Q	0.537	0.99
113_F	154_P	0.536	0.99
96_T	100_H	0.534	0.99
64_P	97_R	0.533	0.99
110_F	152_E	0.533	0.99
13_L	16_F	0.530	0.99
33_A	37_R	0.528	0.99
119_R	122_A	0.526	0.99
44_R	48_A	0.520	0.98
34_L	38_R	0.519	0.98
10_L	153_L	0.518	0.98
53_Y	61_L	0.518	0.98
88_A	91_A	0.515	0.98
140_N	143_I	0.512	0.98
46_G	50_Q	0.508	0.98
144_E	147_R	0.505	0.98
32_L	35_I	0.505	0.98
85_A	89_D	0.503	0.98
16_F	56_A	0.503	0.98
60_F	104_I	0.502	0.98
83_D	88_A	0.501	0.98
86_A	90_Y	0.500	0.98
133_D	137_D	0.500	0.98

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
4fcyA	4	0.741	10.3	0.931	Contact Map
1xl7A	1	0.8554	5.9	0.938	Contact Map
1dp7P	1	0.3012	5.9	0.938	Contact Map
1xszA	1	0.6747	5.4	0.939	Contact Map
2o4dA	3	0.4157	5.3	0.939	Contact Map
1pdnC	1	0.6024	5.1	0.94	Contact Map
1nm8A	1	0.8614	4.6	0.941	Contact Map
1pm6A	1	0.1687	4.2	0.942	Contact Map
4n78F	1	0.7771	4.1	0.942	Contact Map
3i3nA	2	0.6446	4.1	0.942	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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