DUF5009 - PFAM28P - GREMLIN Contacts

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DUF5009 - Domain of unknown function (DUF5009)

PFAM:	PF16401	Sequences: RILSIDALRGLTILLMIFVNDLAGKGLPAWMYHAQAPPPDHVFNPDVDGMTFVDLVFPAFLFIVGMSIPFAIGRRLEKGDSKWKILLHILLRTLALLVFGVFMVNAEPYVLSAAPGLSKWLLALLGFILLFLIWNRYPKTWPKKLFLILRIAGILLLILLALIYRYRDGEGFSLTRSWIGILGLIGWALFGSLIYLFTRNNLLLRLGVLAFLLALFLAAKTEGSWVQALWNWSPLPWLYKFYYLKYLFIVIPGTIAGDLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	260 (211)
Sequences:	1202 (997)
Seq/√Len:	68.6
META:	0.892

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
185_I	188_A	3.310	1.00
74_R	78_K	2.929	1.00
153_G	157_L	2.847	1.00
183_G	186_G	2.774	1.00
175_T	178_W	2.766	1.00
129_L	132_L	2.711	1.00
93_T	189_L	2.636	1.00
52_F	56_V	2.627	1.00
174_L	178_W	2.623	1.00
34_A	49_G	2.477	1.00
74_R	77_E	2.426	1.00
176_R	180_G	2.339	1.00
157_L	161_A	2.291	1.00
180_G	183_G	2.262	1.00
181_I	184_L	2.208	1.00
174_L	177_S	2.193	1.00
95_A	99_F	2.137	1.00
150_R	153_G	2.068	1.00
81_S	84_K	2.047	1.00
22_L	53_V	2.042	1.00
127_F	130_L	2.033	1.00
176_R	179_I	2.004	1.00
131_F	134_W	1.985	1.00
177_S	181_I	1.973	1.00
183_G	187_W	1.857	1.00
184_L	188_A	1.829	1.00
86_L	193_L	1.787	1.00
27_L	32_Y	1.759	1.00
11_L	15_L	1.753	1.00
177_S	180_G	1.720	1.00
93_T	97_L	1.701	1.00
157_L	160_L	1.640	0.99
184_L	187_W	1.634	0.99
180_G	184_L	1.625	0.99
129_L	156_L	1.609	0.99
31_M	53_V	1.606	0.99
80_D	84_K	1.567	0.99
131_F	135_N	1.567	0.99
122_L	126_G	1.567	0.99
155_L	159_L	1.564	0.99
178_W	181_I	1.558	0.99
201_N	204_L	1.532	0.99
10_G	13_I	1.494	0.99
75_R	88_H	1.492	0.99
176_R	181_I	1.478	0.99
212_L	215_L	1.457	0.99
172_F	179_I	1.450	0.98
127_F	131_F	1.449	0.98
180_G	185_I	1.447	0.98
163_I	166_Y	1.441	0.98
122_L	134_W	1.441	0.98
34_A	48_D	1.440	0.98
159_L	163_I	1.430	0.98
122_L	129_L	1.417	0.98
118_S	122_L	1.398	0.98
53_V	56_V	1.372	0.98
129_L	134_W	1.371	0.98
131_F	137_Y	1.332	0.97
179_I	183_G	1.331	0.97
194_I	208_V	1.320	0.97
182_L	185_I	1.320	0.97
124_L	128_I	1.310	0.97
5_I	66_M	1.306	0.97
111_L	114_A	1.300	0.97
151_I	155_L	1.290	0.97
147_L	151_I	1.290	0.97
84_K	87_L	1.282	0.97
149_L	153_G	1.274	0.97
122_L	127_F	1.266	0.96
187_W	190_F	1.263	0.96
76_L	85_I	1.255	0.96
145_L	148_I	1.251	0.96
148_I	151_I	1.247	0.96
76_L	82_K	1.247	0.96
185_I	189_L	1.246	0.96
132_L	137_Y	1.246	0.96
5_I	67_S	1.233	0.96
181_I	185_I	1.232	0.96
126_G	129_L	1.228	0.96
52_F	55_L	1.222	0.96
103_M	127_F	1.219	0.96
130_L	134_W	1.216	0.95
15_L	52_F	1.204	0.95
142_P	146_F	1.196	0.95
110_V	115_P	1.177	0.95
162_L	166_Y	1.173	0.95
173_S	178_W	1.170	0.94
161_A	164_Y	1.167	0.94
149_L	157_L	1.146	0.94
111_L	115_P	1.134	0.93
117_L	122_L	1.133	0.93
82_K	199_R	1.132	0.93
145_L	149_L	1.126	0.93
179_I	182_L	1.110	0.93
183_G	188_A	1.102	0.92
144_K	148_I	1.098	0.92
212_L	216_F	1.097	0.92
30_W	33_H	1.089	0.92
91_L	95_A	1.088	0.92
6_D	9_R	1.085	0.92
216_F	219_A	1.082	0.92
122_L	131_F	1.076	0.92
172_F	177_S	1.076	0.92
157_L	166_Y	1.037	0.90
70_F	74_R	1.034	0.90
157_L	165_R	1.030	0.90
115_P	118_S	1.029	0.90
75_R	80_D	1.023	0.89
121_L	125_L	1.022	0.89
132_L	135_N	1.011	0.89
204_L	208_V	1.010	0.89
174_L	179_I	1.001	0.88
173_S	176_R	0.989	0.88
213_L	216_F	0.983	0.87
205_R	208_V	0.980	0.87
175_T	179_I	0.978	0.87
89_I	192_S	0.976	0.87
179_I	184_L	0.973	0.87
7_A	11_L	0.971	0.87
13_I	53_V	0.970	0.87
83_W	87_L	0.962	0.86
156_L	159_L	0.953	0.86
152_A	159_L	0.951	0.86
186_G	189_L	0.951	0.86
153_G	156_L	0.951	0.86
182_L	186_G	0.945	0.85
31_M	52_F	0.940	0.85
128_I	131_F	0.939	0.85
180_G	186_G	0.930	0.84
198_T	204_L	0.927	0.84
13_I	66_M	0.924	0.84
122_L	132_L	0.921	0.84
28_P	33_H	0.920	0.84
111_L	116_G	0.909	0.83
45_P	48_D	0.904	0.83
5_I	13_I	0.904	0.83
172_F	180_G	0.903	0.82
134_W	137_Y	0.897	0.82
207_G	214_A	0.892	0.82
35_Q	49_G	0.891	0.82
32_Y	53_V	0.890	0.82
161_A	165_R	0.883	0.81
13_I	51_T	0.882	0.81
99_F	130_L	0.880	0.81
178_W	184_L	0.867	0.80
94_L	144_K	0.863	0.80
147_L	155_L	0.863	0.80
150_R	158_I	0.857	0.79
87_L	90_L	0.845	0.78
85_I	206_L	0.845	0.78
209_L	216_F	0.837	0.77
125_L	129_L	0.831	0.77
173_S	179_I	0.830	0.77
163_I	167_R	0.818	0.76
203_L	206_L	0.816	0.76
22_L	56_V	0.815	0.76
161_A	166_Y	0.813	0.75
161_A	167_R	0.808	0.75
143_K	148_I	0.799	0.74
201_N	205_R	0.794	0.74
130_L	137_Y	0.783	0.73
68_I	196_L	0.778	0.72
172_F	178_W	0.771	0.71
210_A	213_L	0.767	0.71
48_D	51_T	0.761	0.70
162_L	165_R	0.758	0.70
172_F	181_I	0.756	0.70
80_D	85_I	0.749	0.69
130_L	133_I	0.748	0.69
179_I	187_W	0.748	0.69
111_L	118_S	0.747	0.69
82_K	86_L	0.747	0.69
13_I	23_A	0.746	0.69
3_L	11_L	0.743	0.69
165_R	168_D	0.743	0.69
4_S	8_L	0.743	0.69
30_W	53_V	0.743	0.69
134_W	138_P	0.739	0.68
58_P	65_G	0.736	0.68
173_S	177_S	0.736	0.68
10_G	53_V	0.735	0.68
7_A	12_T	0.735	0.68
104_V	107_E	0.733	0.68
95_A	134_W	0.732	0.67
115_P	119_K	0.728	0.67
123_A	126_G	0.728	0.67
97_L	182_L	0.727	0.67
114_A	118_S	0.726	0.67
27_L	53_V	0.713	0.65
198_T	202_L	0.712	0.65
126_G	132_L	0.710	0.65
160_L	165_R	0.710	0.65
150_R	157_L	0.709	0.65
195_Y	205_R	0.707	0.65
210_A	214_A	0.707	0.65
87_L	91_L	0.702	0.64
179_I	185_I	0.701	0.64
71_A	75_R	0.700	0.64
32_Y	52_F	0.699	0.64
131_F	136_R	0.698	0.64
56_V	101_V	0.695	0.63
211_F	217_L	0.691	0.63
150_R	155_L	0.689	0.63
138_P	146_F	0.689	0.63
122_L	125_L	0.688	0.63
123_A	127_F	0.688	0.63
29_A	53_V	0.686	0.62
190_F	208_V	0.686	0.62
198_T	208_V	0.685	0.62
5_I	70_F	0.685	0.62
133_I	137_Y	0.684	0.62
175_T	180_G	0.683	0.62
129_L	133_I	0.683	0.62
124_L	133_I	0.681	0.62
18_F	22_L	0.676	0.61
97_L	104_V	0.676	0.61
86_L	196_L	0.676	0.61
127_F	134_W	0.675	0.61
116_G	119_K	0.673	0.61
127_F	136_R	0.670	0.61
126_G	160_L	0.668	0.60
205_R	209_L	0.667	0.60
119_K	123_A	0.666	0.60
11_L	49_G	0.662	0.60
174_L	181_I	0.658	0.59
10_G	99_F	0.658	0.59
112_S	115_P	0.654	0.59
22_L	34_A	0.653	0.59
72_I	195_Y	0.652	0.59
157_L	164_Y	0.651	0.58
119_K	122_L	0.650	0.58
148_I	152_A	0.649	0.58
15_L	53_V	0.648	0.58
8_L	12_T	0.646	0.58
76_L	124_L	0.644	0.58
13_I	21_D	0.641	0.57
8_L	59_A	0.637	0.57
23_A	32_Y	0.636	0.57
173_S	180_G	0.634	0.56
2_I	5_I	0.633	0.56
21_D	24_G	0.626	0.55
188_A	192_S	0.626	0.55
12_T	30_W	0.620	0.55
17_I	21_D	0.619	0.55
172_F	176_R	0.618	0.54
20_N	183_G	0.618	0.54
32_Y	35_Q	0.613	0.54
89_I	196_L	0.612	0.54
209_L	212_L	0.608	0.53
181_I	186_G	0.608	0.53
24_G	32_Y	0.600	0.52
113_A	116_G	0.600	0.52
128_I	132_L	0.598	0.52
142_P	145_L	0.596	0.52
113_A	118_S	0.594	0.52
22_L	32_Y	0.593	0.52
91_L	98_V	0.593	0.52
25_K	32_Y	0.593	0.52
12_T	19_V	0.592	0.51
189_L	193_L	0.590	0.51
124_L	127_F	0.590	0.51
106_A	126_G	0.589	0.51
210_A	216_F	0.589	0.51
149_L	152_A	0.588	0.51
101_V	105_N	0.583	0.50
87_L	154_I	0.582	0.50
12_T	20_N	0.577	0.50
138_P	142_P	0.576	0.49
29_A	32_Y	0.574	0.49
103_M	126_G	0.574	0.49
8_L	31_M	0.573	0.49
33_H	57_F	0.573	0.49
132_L	153_G	0.572	0.49
126_G	134_W	0.572	0.49
7_A	14_L	0.572	0.49
54_D	60_F	0.572	0.49
78_K	84_K	0.571	0.49
13_I	52_F	0.570	0.49
34_A	47_V	0.570	0.49
22_L	27_L	0.565	0.48
34_A	46_D	0.565	0.48
102_F	157_L	0.564	0.48
17_I	103_M	0.561	0.48
72_I	196_L	0.560	0.48
167_R	171_G	0.560	0.48
65_G	71_A	0.560	0.48
48_D	52_F	0.560	0.48
136_R	145_L	0.557	0.47
20_N	63_I	0.557	0.47
55_L	59_A	0.551	0.46
10_G	55_L	0.551	0.46
85_I	196_L	0.551	0.46
64_V	68_I	0.549	0.46
16_M	28_P	0.546	0.46
174_L	180_G	0.545	0.46
147_L	156_L	0.544	0.46
111_L	122_L	0.541	0.45
210_A	217_L	0.541	0.45
10_G	51_T	0.540	0.45
193_L	197_F	0.540	0.45
213_L	217_L	0.539	0.45
61_L	187_W	0.536	0.45
153_G	164_Y	0.533	0.44
170_E	173_S	0.532	0.44
194_I	215_L	0.532	0.44
64_V	185_I	0.531	0.44
51_T	56_V	0.531	0.44
120_W	127_F	0.529	0.44
144_K	147_L	0.529	0.44
142_P	147_L	0.528	0.44
211_F	214_A	0.526	0.43
6_D	10_G	0.517	0.42
23_A	51_T	0.514	0.42
14_L	218_A	0.500	0.40
126_G	130_L	0.500	0.40
15_L	56_V	0.500	0.40

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
2mkvA	1	0.2423	34.1	0.959	Contact Map
3wguG	1	0.1269	26.7	0.961	Contact Map
2jo1A	1	0.2462	22	0.962	Contact Map
2zxeG	1	0.15	7.2	0.97	Contact Map
3l32A	2	0.1385	6	0.971	Contact Map
2jp3A	1	0.2577	5.2	0.972	Contact Map
4f35D	2	0.3577	3.6	0.974	Contact Map
2mgyA	1	0.6115	3.3	0.974	Contact Map
4ryoA	1	0.5615	2.1	0.977	Contact Map
2nq2A	2	0.6692	2.1	0.977	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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