DUF4942 - PFAM28P - GREMLIN Contacts

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DUF4942 - Domain of unknown function (DUF4942)

PFAM:	PF13708	Sequences: MKELKRKYWRALFDKTGITKLMTSKAREEWNKQLEEQDTPEFTEENIYATLEQLIANRGEIFEEGVLEVFDKLSNRHYYEGYKTNSPYKIGKRIILPGLVSYGWWGFFSLSYSARDKLDDLEKVFAYLDGKPIPDHRNGITSRLLDAIRRGFYSENGEGKWIETEYFRVRFYKKGTAHLEFKRPDLLDKLNRIVARHYG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	199 (192)
Sequences:	1949 (1623)
Seq/√Len:	117.1
META:	0.819

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
168_R	180_E	4.859	1.00
163_E	182_K	4.831	1.00
28_E	32_K	3.447	1.00
129_D	166_Y	2.950	1.00
92_K	180_E	2.764	1.00
26_A	64_E	2.340	1.00
163_E	168_R	2.240	1.00
94_I	179_L	2.229	1.00
43_T	46_N	2.166	1.00
12_L	42_F	2.136	1.00
6_R	35_E	2.128	1.00
29_E	33_Q	2.110	1.00
144_L	148_I	2.092	1.00
72_K	117_K	2.069	1.00
52_E	56_A	2.042	1.00
8_Y	42_F	2.022	1.00
5_K	41_E	1.970	1.00
92_K	184_P	1.956	1.00
11_A	15_K	1.946	1.00
94_I	181_F	1.934	1.00
57_N	60_E	1.887	1.00
97_P	174_K	1.867	1.00
184_P	188_D	1.810	1.00
25_K	68_E	1.786	1.00
53_Q	57_N	1.771	1.00
44_E	48_Y	1.732	1.00
145_L	148_I	1.704	1.00
25_K	28_E	1.694	1.00
162_I	169_V	1.683	1.00
32_K	36_E	1.682	1.00
168_R	182_K	1.664	1.00
93_R	170_R	1.656	1.00
24_S	116_D	1.614	1.00
129_D	183_R	1.595	1.00
185_D	188_D	1.579	1.00
183_R	186_L	1.571	1.00
141_T	145_L	1.554	1.00
157_G	160_K	1.529	1.00
169_V	177_A	1.525	1.00
131_K	165_E	1.524	1.00
194_V	198_Y	1.520	1.00
23_T	26_A	1.477	1.00
193_I	196_R	1.476	1.00
10_R	14_D	1.467	1.00
144_L	147_A	1.466	1.00
189_K	193_I	1.458	1.00
62_F	127_Y	1.456	1.00
137_R	140_I	1.445	1.00
141_T	144_L	1.441	1.00
19_T	31_N	1.411	1.00
113_S	116_D	1.395	1.00
23_T	68_E	1.383	1.00
25_K	29_E	1.376	1.00
67_L	198_Y	1.376	1.00
24_S	28_E	1.373	1.00
22_M	30_W	1.359	1.00
63_E	193_I	1.340	1.00
17_G	20_K	1.340	1.00
187_L	190_L	1.339	1.00
142_S	146_D	1.337	1.00
114_A	117_K	1.325	1.00
169_V	179_L	1.322	1.00
90_I	190_L	1.318	1.00
102_Y	106_G	1.316	1.00
99_L	177_A	1.302	1.00
143_R	146_D	1.301	1.00
84_T	93_R	1.299	1.00
125_F	186_L	1.297	1.00
184_P	187_L	1.267	0.99
73_L	94_I	1.265	0.99
140_I	144_L	1.261	0.99
181_F	187_L	1.253	0.99
102_Y	105_W	1.230	0.99
76_R	79_Y	1.222	0.99
84_T	95_I	1.220	0.99
100_V	103_G	1.212	0.99
189_K	192_R	1.203	0.99
66_V	193_I	1.196	0.99
71_D	198_Y	1.195	0.99
192_R	196_R	1.194	0.99
32_K	35_E	1.194	0.99
126_A	166_Y	1.171	0.99
26_A	29_E	1.166	0.99
12_L	47_I	1.159	0.99
100_V	106_G	1.132	0.99
101_S	106_G	1.124	0.99
116_D	119_D	1.118	0.99
171_F	177_A	1.106	0.99
84_T	180_E	1.102	0.98
66_V	190_L	1.101	0.98
97_P	176_T	1.099	0.98
90_I	194_V	1.082	0.98
80_E	174_K	1.081	0.98
122_E	164_T	1.079	0.98
89_K	188_D	1.049	0.98
161_W	168_R	1.043	0.98
49_A	53_Q	1.037	0.98
16_T	51_L	1.033	0.98
188_D	192_R	1.026	0.98
48_Y	52_E	1.025	0.98
136_H	140_I	1.022	0.98
74_S	81_G	1.020	0.97
28_E	31_N	1.012	0.97
144_L	149_R	1.006	0.97
128_L	189_K	0.982	0.97
70_F	194_V	0.981	0.97
60_E	64_E	0.975	0.97
10_R	31_N	0.968	0.97
161_W	180_E	0.960	0.96
137_R	141_T	0.932	0.96
23_T	64_E	0.926	0.96
125_F	187_L	0.923	0.95
194_V	197_H	0.912	0.95
71_D	85_N	0.898	0.95
100_V	104_W	0.897	0.95
40_P	50_T	0.896	0.95
18_I	22_M	0.889	0.94
54_L	58_R	0.884	0.94
91_G	187_L	0.883	0.94
71_D	74_S	0.882	0.94
49_A	52_E	0.882	0.94
43_T	177_A	0.879	0.94
63_E	197_H	0.879	0.94
63_E	196_R	0.876	0.94
19_T	27_R	0.874	0.94
24_S	120_D	0.869	0.94
73_L	179_L	0.864	0.94
146_D	149_R	0.855	0.93
131_K	166_Y	0.840	0.93
16_T	54_L	0.836	0.92
122_E	167_F	0.835	0.92
14_D	19_T	0.832	0.92
111_S	114_A	0.824	0.92
93_R	180_E	0.821	0.92
161_W	170_R	0.820	0.92
58_R	61_I	0.815	0.91
140_I	145_L	0.810	0.91
129_D	186_L	0.808	0.91
74_S	87_P	0.807	0.91
101_S	109_S	0.807	0.91
140_I	143_R	0.805	0.91
22_M	54_L	0.797	0.91
190_L	194_V	0.795	0.90
12_L	15_K	0.790	0.90
67_L	197_H	0.790	0.90
44_E	47_I	0.786	0.90
65_G	123_K	0.783	0.90
22_M	26_A	0.778	0.89
96_L	177_A	0.761	0.88
55_I	58_R	0.761	0.88
46_N	49_A	0.761	0.88
133_I	136_H	0.760	0.88
63_E	67_L	0.759	0.88
27_R	116_D	0.759	0.88
101_S	104_W	0.758	0.88
139_G	142_S	0.757	0.88
96_L	99_L	0.756	0.88
103_G	106_G	0.754	0.88
158_E	161_W	0.752	0.88
90_I	187_L	0.747	0.87
75_N	82_Y	0.742	0.87
141_T	146_D	0.739	0.87
135_D	138_N	0.735	0.87
69_V	124_V	0.735	0.87
142_S	145_L	0.733	0.86
73_L	195_A	0.726	0.86
26_A	61_I	0.721	0.86
60_E	63_E	0.721	0.86
70_F	90_I	0.721	0.86
72_K	120_D	0.720	0.85
134_P	138_N	0.714	0.85
143_R	148_I	0.711	0.85
167_F	179_L	0.710	0.85
5_K	8_Y	0.708	0.85
185_D	189_K	0.705	0.84
129_D	165_E	0.704	0.84
6_R	15_K	0.704	0.84
98_G	114_A	0.702	0.84
4_L	8_Y	0.700	0.84
137_R	142_S	0.697	0.84
6_R	34_L	0.697	0.84
74_S	82_Y	0.696	0.84
54_L	61_I	0.691	0.83
95_I	178_H	0.688	0.83
27_R	31_N	0.686	0.83
101_S	105_W	0.685	0.83
73_L	77_H	0.682	0.82
57_N	61_I	0.682	0.82
132_P	136_H	0.682	0.82
129_D	189_K	0.678	0.82
193_I	197_H	0.677	0.82
149_R	155_E	0.677	0.82
166_Y	186_L	0.675	0.82
87_P	195_A	0.666	0.81
22_M	61_I	0.661	0.80
71_D	172_Y	0.658	0.80
170_R	180_E	0.654	0.80
34_L	40_P	0.653	0.79
70_F	73_L	0.651	0.79
77_H	80_E	0.648	0.79
73_L	90_I	0.648	0.79
4_L	126_A	0.642	0.78
52_E	55_I	0.638	0.78
58_R	62_F	0.638	0.78
159_G	170_R	0.634	0.77
61_I	123_K	0.633	0.77
118_L	122_E	0.622	0.76
136_H	139_G	0.621	0.76
29_E	64_E	0.621	0.76
86_S	89_K	0.621	0.76
80_E	84_T	0.619	0.76
114_A	143_R	0.616	0.75
136_H	141_T	0.613	0.75
85_N	178_H	0.613	0.75
105_W	113_S	0.612	0.75
47_I	68_E	0.611	0.75
139_G	144_L	0.610	0.75
68_E	72_K	0.608	0.74
122_E	165_E	0.603	0.74
77_H	87_P	0.601	0.74
33_Q	41_E	0.601	0.74
88_Y	96_L	0.597	0.73
132_P	135_D	0.596	0.73
107_F	111_S	0.596	0.73
65_G	124_V	0.594	0.73
125_F	167_F	0.593	0.73
41_E	44_E	0.593	0.73
157_G	161_W	0.593	0.73
3_E	7_K	0.589	0.72
36_E	39_T	0.587	0.72
81_G	87_P	0.587	0.72
138_N	141_T	0.585	0.72
18_I	26_A	0.584	0.72
135_D	141_T	0.583	0.71
98_G	113_S	0.583	0.71
134_P	137_R	0.583	0.71
142_S	147_A	0.580	0.71
13_F	26_A	0.580	0.71
143_R	147_A	0.579	0.71
67_L	194_V	0.579	0.71
119_D	122_E	0.578	0.71
41_E	46_N	0.577	0.71
100_V	105_W	0.576	0.70
148_I	171_F	0.576	0.70
160_K	171_F	0.573	0.70
75_N	81_G	0.570	0.70
53_Q	56_A	0.569	0.70
6_R	38_D	0.568	0.69
64_E	68_E	0.568	0.69
15_K	20_K	0.567	0.69
81_G	97_P	0.567	0.69
74_S	79_Y	0.564	0.69
55_I	59_G	0.563	0.69
36_E	52_E	0.561	0.68
33_Q	36_E	0.559	0.68
25_K	64_E	0.556	0.68
69_V	121_L	0.552	0.67
82_Y	97_P	0.547	0.67
124_V	128_L	0.546	0.66
10_R	35_E	0.543	0.66
34_L	37_Q	0.541	0.66
66_V	124_V	0.539	0.65
64_E	197_H	0.539	0.65
82_Y	190_L	0.536	0.65
27_R	119_D	0.535	0.65
69_V	73_L	0.533	0.65
75_N	78_Y	0.533	0.65
111_S	146_D	0.530	0.64
15_K	18_I	0.529	0.64
73_L	96_L	0.528	0.64
109_S	112_Y	0.528	0.64
18_I	51_L	0.525	0.63
139_G	145_L	0.525	0.63
99_L	115_R	0.525	0.63
59_G	63_E	0.522	0.63
183_R	187_L	0.518	0.62
66_V	194_V	0.516	0.62
8_Y	18_I	0.515	0.62
112_Y	117_K	0.514	0.62
82_Y	176_T	0.514	0.62
125_F	181_F	0.512	0.61
94_I	159_G	0.511	0.61
103_G	144_L	0.509	0.61
13_F	34_L	0.506	0.61
125_F	128_L	0.506	0.61
34_L	54_L	0.501	0.60
40_P	78_Y	0.501	0.60
66_V	76_R	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
2qneA	2	0.3166	16.4	0.942	Contact Map
4yycA	2	0.2764	11.7	0.946	Contact Map
1n4cA	1	0.3769	8.8	0.949	Contact Map
4yiiA	1	0.3367	8.4	0.949	Contact Map
1z5hA	3	0.3417	6.7	0.951	Contact Map
1mg4A	1	0.1809	5.3	0.954	Contact Map
4ie5A	1	0.2915	5.2	0.954	Contact Map
4kx7A	1	0.3819	4.9	0.954	Contact Map
2x6hA	2	0.3719	4.7	0.955	Contact Map
2k6lA	2	0.1357	4.5	0.955	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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