DUF4391 - PFAM28P - GREMLIN Contacts

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DUF4391 - Domain of unknown function (DUF4391)

PFAM:	PF14335	Sequences: LGLPKSTEVNRRIPKKKFYENAALTAALKKLFVDQIERITWLYKLAPETINIPPYRDAGREVPEIQVFEIELKTKELDKRVLELIDRAIPYPILFVLEYEDKVQLSAAYKRPSQADAGKWVVEDYFATDWLPEDELRLPLEAPDEIEAAFLESLALSRPPGLNLDALYENLLRQIIGLEAARLTGTFSLRSGESLEERVERLEEIEKLEKEIAKLEAKLKKEKQFNRKVELNAELKKLKKEL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	242 (212)
Sequences:	2364 (1706)
Seq/√Len:	117.2
META:	0.824

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_T	43_Y	3.311	1.00
30_K	34_D	2.890	1.00
217_A	221_K	2.827	1.00
227_R	230_E	2.794	1.00
75_K	102_K	2.650	1.00
69_E	98_E	2.568	1.00
216_E	239_K	2.563	1.00
212_I	235_L	2.528	1.00
234_E	237_K	2.489	1.00
5_K	8_E	2.477	1.00
59_G	165_D	2.469	1.00
42_L	69_E	2.407	1.00
204_E	241_E	2.381	1.00
37_E	73_K	2.285	1.00
219_L	231_L	2.269	1.00
204_E	207_K	2.227	1.00
222_E	227_R	2.208	1.00
214_K	218_K	2.202	1.00
16_K	20_E	2.140	1.00
225_F	229_V	2.115	1.00
230_E	234_E	2.090	1.00
19_Y	33_V	2.047	1.00
107_A	175_I	1.996	1.00
19_Y	32_F	1.995	1.00
35_Q	78_D	1.935	1.00
229_V	232_N	1.917	1.00
41_W	66_Q	1.917	1.00
212_I	238_L	1.884	1.00
225_F	232_N	1.882	1.00
211_E	234_E	1.877	1.00
86_D	106_S	1.824	1.00
160_P	170_N	1.787	1.00
58_A	63_P	1.786	1.00
236_K	239_K	1.751	1.00
193_E	201_R	1.744	1.00
66_Q	91_Y	1.739	1.00
12_R	38_R	1.716	1.00
116_D	119_K	1.712	1.00
219_L	235_L	1.693	1.00
13_I	68_F	1.686	1.00
163_N	166_A	1.678	1.00
237_K	241_E	1.639	1.00
104_Q	127_A	1.579	1.00
113_S	116_D	1.574	1.00
26_A	30_K	1.566	1.00
86_D	110_K	1.553	1.00
209_E	213_A	1.526	1.00
18_F	32_F	1.522	1.00
200_E	204_E	1.514	1.00
94_L	107_A	1.512	1.00
44_K	66_Q	1.504	1.00
67_V	94_L	1.502	1.00
215_L	235_L	1.477	1.00
41_W	64_E	1.476	1.00
211_E	214_K	1.468	1.00
52_I	167_L	1.461	1.00
208_L	241_E	1.447	1.00
10_N	40_T	1.431	1.00
64_E	91_Y	1.413	1.00
41_W	44_K	1.407	1.00
111_R	121_V	1.400	1.00
31_L	35_Q	1.393	1.00
3_L	7_T	1.391	1.00
161_G	167_L	1.382	1.00
18_F	24_L	1.368	1.00
44_K	64_E	1.342	1.00
45_L	50_I	1.332	1.00
226_N	229_V	1.299	1.00
71_E	98_E	1.287	1.00
211_E	238_L	1.268	0.99
18_F	85_I	1.266	0.99
207_K	211_E	1.264	0.99
44_K	49_T	1.207	0.99
171_L	174_Q	1.205	0.99
123_E	203_E	1.195	0.99
7_T	50_I	1.189	0.99
176_I	198_R	1.188	0.99
228_K	236_K	1.187	0.99
205_I	242_L	1.183	0.99
13_I	41_W	1.181	0.99
27_A	80_R	1.170	0.99
106_S	127_A	1.143	0.99
8_E	43_Y	1.134	0.99
94_L	171_L	1.133	0.99
10_N	42_L	1.132	0.99
28_L	84_L	1.129	0.99
24_L	28_L	1.120	0.99
235_L	239_K	1.120	0.99
113_S	121_V	1.108	0.99
213_A	216_E	1.087	0.98
225_F	228_K	1.083	0.98
75_K	99_Y	1.080	0.98
94_L	105_L	1.080	0.98
74_T	99_Y	1.074	0.98
219_L	225_F	1.066	0.98
194_S	197_E	1.056	0.98
45_L	171_L	1.044	0.98
206_E	209_E	1.031	0.98
115_A	119_K	1.029	0.98
35_Q	77_L	1.028	0.98
104_Q	130_W	1.026	0.98
232_N	235_L	1.025	0.98
233_A	236_K	1.023	0.98
212_I	242_L	1.018	0.97
173_R	198_R	1.018	0.97
37_E	71_E	1.013	0.97
62_V	165_D	1.006	0.97
229_V	233_A	1.006	0.97
45_L	65_I	1.002	0.97
224_Q	227_R	1.000	0.97
82_L	97_L	1.000	0.97
231_L	235_L	0.990	0.97
44_K	68_F	0.985	0.97
108_A	122_V	0.980	0.97
205_I	209_E	0.978	0.97
204_E	208_L	0.974	0.97
79_K	83_E	0.974	0.97
26_A	29_K	0.968	0.97
72_L	97_L	0.967	0.97
103_V	133_E	0.961	0.96
219_L	232_N	0.960	0.96
200_E	203_E	0.953	0.96
66_Q	89_I	0.952	0.96
159_P	170_N	0.938	0.96
32_F	85_I	0.931	0.96
190_R	193_E	0.930	0.96
126_F	199_V	0.927	0.96
39_I	70_I	0.910	0.95
205_I	212_I	0.909	0.95
62_V	92_P	0.907	0.95
132_P	135_E	0.904	0.95
41_W	91_Y	0.901	0.95
99_Y	102_K	0.900	0.95
197_E	201_R	0.894	0.95
69_E	96_V	0.894	0.95
64_E	89_I	0.893	0.95
41_W	46_A	0.890	0.94
108_A	125_Y	0.887	0.94
196_E	200_E	0.884	0.94
46_A	62_V	0.882	0.94
45_L	164_L	0.880	0.94
17_K	20_E	0.877	0.94
62_V	164_L	0.872	0.94
107_A	172_L	0.871	0.94
98_E	101_D	0.869	0.94
9_V	44_K	0.867	0.94
112_P	120_W	0.865	0.94
233_A	237_K	0.863	0.94
66_Q	93_I	0.853	0.93
218_K	222_E	0.852	0.93
206_E	210_K	0.848	0.93
213_A	217_A	0.847	0.93
38_R	71_E	0.845	0.93
22_A	88_A	0.842	0.93
197_E	200_E	0.842	0.93
226_N	232_N	0.839	0.93
210_K	214_K	0.836	0.92
234_E	238_L	0.831	0.92
96_V	103_V	0.822	0.92
17_K	21_N	0.822	0.92
219_L	229_V	0.819	0.92
63_P	91_Y	0.819	0.92
161_G	170_N	0.798	0.91
47_P	58_A	0.796	0.90
128_T	175_I	0.795	0.90
11_R	14_P	0.790	0.90
89_I	93_I	0.780	0.90
86_D	95_F	0.780	0.90
80_R	83_E	0.776	0.89
208_L	238_L	0.776	0.89
173_R	176_I	0.773	0.89
44_K	86_D	0.773	0.89
60_R	63_P	0.766	0.89
208_L	212_I	0.765	0.89
70_I	107_A	0.760	0.88
70_I	82_L	0.759	0.88
59_G	62_V	0.758	0.88
176_I	199_V	0.757	0.88
232_N	239_K	0.756	0.88
203_E	206_E	0.752	0.88
228_K	233_A	0.751	0.88
18_F	39_I	0.751	0.88
46_A	49_T	0.750	0.88
97_L	104_Q	0.748	0.88
19_Y	29_K	0.748	0.88
219_L	228_K	0.742	0.87
35_Q	76_E	0.736	0.87
122_V	126_F	0.734	0.87
83_E	87_R	0.731	0.86
46_A	66_Q	0.729	0.86
131_L	138_L	0.726	0.86
46_A	64_E	0.725	0.86
9_V	68_F	0.725	0.86
70_I	88_A	0.724	0.86
232_N	236_K	0.721	0.86
24_L	32_F	0.718	0.85
238_L	241_E	0.716	0.85
162_L	166_A	0.705	0.84
218_K	234_E	0.702	0.84
193_E	197_E	0.700	0.84
169_E	173_R	0.700	0.84
134_D	138_L	0.695	0.83
165_D	169_E	0.694	0.83
40_T	71_E	0.689	0.83
14_P	17_K	0.682	0.82
7_T	45_L	0.677	0.82
12_R	16_K	0.676	0.82
3_L	45_L	0.674	0.82
60_R	165_D	0.670	0.81
6_S	49_T	0.662	0.80
133_E	136_L	0.659	0.80
25_T	28_L	0.657	0.80
214_K	217_A	0.655	0.80
168_Y	232_N	0.650	0.79
22_A	27_A	0.650	0.79
51_N	171_L	0.648	0.79
44_K	65_I	0.647	0.79
12_R	40_T	0.646	0.79
57_D	60_R	0.644	0.79
86_D	125_Y	0.643	0.78
35_Q	74_T	0.641	0.78
180_A	201_R	0.640	0.78
209_E	216_E	0.639	0.78
3_L	96_V	0.636	0.78
77_L	81_V	0.635	0.78
41_W	49_T	0.635	0.78
79_K	127_A	0.634	0.77
47_P	50_I	0.632	0.77
82_L	167_L	0.631	0.77
198_R	202_L	0.631	0.77
216_E	220_K	0.624	0.76
228_K	232_N	0.622	0.76
202_L	206_E	0.620	0.76
203_E	210_K	0.619	0.76
24_L	84_L	0.618	0.76
167_L	172_L	0.615	0.75
59_G	163_N	0.614	0.75
61_E	134_D	0.613	0.75
3_L	43_Y	0.613	0.75
36_I	88_A	0.608	0.75
215_L	238_L	0.607	0.74
124_D	199_V	0.603	0.74
98_E	133_E	0.602	0.74
216_E	227_R	0.601	0.74
8_E	42_L	0.591	0.72
70_I	85_I	0.590	0.72
29_K	128_T	0.588	0.72
85_I	127_A	0.587	0.72
92_P	168_Y	0.586	0.72
11_R	16_K	0.586	0.72
3_L	105_L	0.585	0.72
220_K	223_K	0.585	0.72
46_A	91_Y	0.584	0.72
49_T	110_K	0.582	0.71
95_F	114_Q	0.580	0.71
159_P	171_L	0.580	0.71
98_E	103_V	0.577	0.71
10_N	232_N	0.576	0.71
195_L	218_K	0.573	0.70
235_L	238_L	0.571	0.70
5_K	132_P	0.568	0.69
1_L	4_P	0.568	0.69
204_E	211_E	0.567	0.69
39_I	64_E	0.566	0.69
39_I	98_E	0.562	0.69
106_S	198_R	0.561	0.69
135_E	138_L	0.558	0.68
68_F	93_I	0.558	0.68
19_Y	84_L	0.556	0.68
200_E	206_E	0.554	0.68
65_I	164_L	0.553	0.67
96_V	137_R	0.552	0.67
121_V	124_D	0.549	0.67
116_D	121_V	0.549	0.67
207_K	216_E	0.545	0.66
82_L	95_F	0.545	0.66
32_F	125_Y	0.544	0.66
60_R	87_R	0.543	0.66
32_F	43_Y	0.539	0.65
3_L	50_I	0.538	0.65
192_G	227_R	0.536	0.65
70_I	97_L	0.531	0.64
165_D	176_I	0.529	0.64
11_R	110_K	0.529	0.64
65_I	171_L	0.529	0.64
62_V	223_K	0.528	0.64
83_E	124_D	0.527	0.64
93_I	110_K	0.527	0.64
119_K	205_I	0.526	0.64
132_P	137_R	0.526	0.64
112_P	119_K	0.525	0.63
75_K	97_L	0.525	0.63
2_G	45_L	0.525	0.63
110_K	168_Y	0.524	0.63
17_K	125_Y	0.524	0.63
94_L	241_E	0.522	0.63
66_Q	86_D	0.519	0.63
70_I	95_F	0.518	0.62
90_P	93_I	0.518	0.62
70_I	99_Y	0.518	0.62
6_S	36_I	0.514	0.62
161_G	166_A	0.513	0.62
11_R	18_F	0.512	0.62
140_L	167_L	0.511	0.61
9_V	17_K	0.511	0.61
236_K	240_K	0.509	0.61
97_L	130_W	0.506	0.61
116_D	212_I	0.505	0.60
166_A	169_E	0.505	0.60
179_E	191_S	0.504	0.60
100_E	189_L	0.504	0.60
67_V	161_G	0.504	0.60
189_L	192_G	0.503	0.60
169_E	195_L	0.503	0.60
103_V	136_L	0.502	0.60
28_L	80_R	0.501	0.60
58_A	96_V	0.500	0.60
217_A	234_E	0.500	0.60

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
4etpA	1	0.2355	32.1	0.942	Contact Map
1sesA	2	0.3306	25	0.945	Contact Map
4y66A	1	0.4793	24.7	0.945	Contact Map
3onjA	1	0.314	23.2	0.946	Contact Map
1ysmA	1	0.1736	15.9	0.95	Contact Map
4r3zA	1	0.2521	15.5	0.95	Contact Map
2qywA	1	0.3471	13.8	0.951	Contact Map
2dq0A	2	0.3347	12	0.952	Contact Map
2dq3A	2	0.3347	11.6	0.953	Contact Map
4etpB	1	0.2314	11.6	0.953	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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