DUF4410 - PFAM28P - GREMLIN Contacts

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DUF4410 - Domain of unknown function (DUF4410)

PFAM:	PF14366	Sequences: IYVYDFAASPADVPLDSGPQTAEQIALGRKLGAALAEELVAELRKMGLPAERASGGTPPGNDLVIRGYFLSVDEGNRAKRVVIGFGAGASELKTAVEVYQMTAGLRKLGSFTTDAGSGKMPGAAVTLGVGAAAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	134 (132)
Sequences:	3038 (2212)
Seq/√Len:	192.6
META:	0.958

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
79_K	87_A	3.535	1.00
68_Y	97_E	2.668	1.00
126_T	129_V	2.537	1.00
33_A	52_R	2.448	1.00
35_L	69_F	2.418	1.00
85_F	125_V	2.374	1.00
5_D	52_R	2.231	1.00
76_N	79_K	2.226	1.00
70_L	95_A	2.164	1.00
61_N	100_Q	1.996	1.00
59_P	62_D	1.993	1.00
43_L	46_M	1.961	1.00
75_G	86_G	1.929	1.00
34_A	38_E	1.922	1.00
36_A	52_R	1.911	1.00
7_A	12_D	1.880	1.00
65_I	98_V	1.866	1.00
105_L	109_G	1.765	1.00
26_A	30_K	1.746	1.00
38_E	42_E	1.714	1.00
33_A	37_E	1.705	1.00
37_E	52_R	1.699	1.00
36_A	40_V	1.646	1.00
21_T	24_Q	1.624	1.00
64_V	105_L	1.621	1.00
3_V	40_V	1.615	1.00
69_F	72_V	1.584	1.00
38_E	41_A	1.553	1.00
93_K	114_D	1.541	1.00
126_T	130_G	1.534	1.00
104_G	109_G	1.532	1.00
123_A	126_T	1.526	1.00
40_V	50_A	1.514	1.00
101_M	105_L	1.433	1.00
110_S	113_T	1.416	1.00
80_R	88_G	1.378	1.00
20_Q	25_I	1.375	1.00
127_L	130_G	1.367	1.00
5_D	36_A	1.342	1.00
28_G	32_G	1.340	1.00
44_R	49_P	1.329	1.00
105_L	108_L	1.303	1.00
2_Y	53_A	1.297	1.00
35_L	94_T	1.294	1.00
111_F	115_A	1.284	1.00
30_K	34_A	1.280	1.00
42_E	45_K	1.270	1.00
14_P	17_S	1.259	1.00
94_T	113_T	1.244	1.00
66_R	99_Y	1.243	1.00
40_V	52_R	1.241	1.00
41_A	45_K	1.218	1.00
75_G	85_F	1.205	1.00
91_E	114_D	1.190	1.00
4_Y	64_V	1.188	1.00
1_I	48_L	1.181	1.00
13_V	16_D	1.166	1.00
128_G	131_A	1.160	1.00
41_A	44_R	1.158	1.00
37_E	41_A	1.154	1.00
40_V	44_R	1.148	1.00
51_E	57_T	1.130	1.00
31_L	72_V	1.119	1.00
15_L	18_G	1.098	1.00
125_V	129_V	1.098	1.00
78_A	82_V	1.097	1.00
6_F	96_V	1.090	1.00
25_I	28_G	1.086	1.00
106_R	109_G	1.084	1.00
10_P	13_V	1.057	1.00
73_D	77_R	1.017	1.00
34_A	37_E	1.007	1.00
12_D	29_R	0.992	0.99
68_Y	95_A	0.991	0.99
26_A	29_R	0.960	0.99
124_A	129_V	0.957	0.99
95_A	110_S	0.942	0.99
123_A	130_G	0.921	0.99
110_S	114_D	0.893	0.99
49_P	52_R	0.890	0.99
111_F	114_D	0.882	0.99
74_E	79_K	0.879	0.99
66_R	97_E	0.875	0.99
104_G	108_L	0.863	0.99
13_V	18_G	0.860	0.99
21_T	29_R	0.858	0.99
85_F	88_G	0.854	0.98
104_G	107_K	0.853	0.98
55_G	66_R	0.850	0.98
39_L	65_I	0.838	0.98
14_P	18_G	0.837	0.98
4_Y	7_A	0.835	0.98
85_F	121_P	0.834	0.98
20_Q	24_Q	0.834	0.98
54_S	57_T	0.833	0.98
124_A	128_G	0.831	0.98
92_L	100_Q	0.827	0.98
75_G	88_G	0.825	0.98
7_A	68_Y	0.823	0.98
27_L	30_K	0.819	0.98
44_R	51_E	0.808	0.98
28_G	31_L	0.800	0.98
23_E	26_A	0.796	0.98
51_E	55_G	0.794	0.98
112_T	115_A	0.791	0.97
29_R	32_G	0.786	0.97
93_K	112_T	0.785	0.97
75_G	80_R	0.771	0.97
79_K	83_I	0.769	0.97
7_A	13_V	0.767	0.97
123_A	128_G	0.759	0.97
62_D	101_M	0.742	0.96
89_A	119_K	0.741	0.96
89_A	117_S	0.737	0.96
39_L	43_L	0.735	0.96
98_V	111_F	0.735	0.96
4_Y	66_R	0.731	0.96
100_Q	106_R	0.728	0.96
62_D	100_Q	0.727	0.96
9_S	12_D	0.718	0.96
5_D	54_S	0.712	0.95
8_A	12_D	0.712	0.95
73_D	79_K	0.706	0.95
3_V	43_L	0.703	0.95
43_L	48_L	0.698	0.95
64_V	101_M	0.697	0.95
30_K	33_A	0.696	0.95
8_A	11_A	0.696	0.95
81_V	123_A	0.694	0.95
125_V	128_G	0.689	0.94
25_I	29_R	0.688	0.94
27_L	74_E	0.686	0.94
18_G	78_A	0.679	0.94
116_G	119_K	0.675	0.94
45_K	54_S	0.666	0.93
60_G	98_V	0.665	0.93
74_E	77_R	0.665	0.93
9_S	25_I	0.664	0.93
110_S	115_A	0.658	0.93
65_I	96_V	0.657	0.93
44_R	48_L	0.647	0.92
2_Y	51_E	0.640	0.92
113_T	117_S	0.639	0.92
5_D	33_A	0.639	0.92
80_R	90_S	0.637	0.92
58_P	61_N	0.637	0.92
73_D	91_E	0.632	0.92
88_G	122_G	0.631	0.91
41_A	52_R	0.629	0.91
36_A	43_L	0.625	0.91
31_L	94_T	0.624	0.91
39_L	46_M	0.622	0.91
95_A	112_T	0.621	0.91
89_A	116_G	0.616	0.90
8_A	14_P	0.614	0.90
36_A	67_G	0.614	0.90
31_L	35_L	0.613	0.90
117_S	120_M	0.610	0.90
124_A	130_G	0.606	0.90
58_P	101_M	0.605	0.90
84_G	88_G	0.603	0.90
101_M	106_R	0.602	0.89
79_K	82_V	0.602	0.89
123_A	127_L	0.601	0.89
86_G	118_G	0.600	0.89
41_A	107_K	0.598	0.89
40_V	53_A	0.581	0.88
102_T	105_L	0.578	0.88
22_A	44_R	0.574	0.87
75_G	90_S	0.572	0.87
10_P	14_P	0.570	0.87
35_L	70_L	0.569	0.87
1_I	4_Y	0.562	0.86
34_A	41_A	0.560	0.86
6_F	36_A	0.559	0.86
55_G	59_P	0.556	0.85
47_G	50_A	0.551	0.85
29_R	33_A	0.551	0.85
89_A	118_G	0.544	0.84
3_V	50_A	0.542	0.84
24_Q	28_G	0.540	0.84
51_E	54_S	0.534	0.83
74_E	81_V	0.533	0.83
83_I	88_G	0.530	0.83
4_Y	8_A	0.528	0.82
3_V	6_F	0.527	0.82
3_V	39_L	0.526	0.82
123_A	132_A	0.524	0.82
77_R	81_V	0.520	0.81
32_G	92_L	0.517	0.81
79_K	89_A	0.511	0.80
9_S	16_D	0.511	0.80
107_K	110_S	0.509	0.80
17_S	43_L	0.504	0.79
4_Y	10_P	0.502	0.79
11_A	14_P	0.501	0.79
89_A	115_A	0.500	0.79
63_L	98_V	0.500	0.79

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
4uv2A	3	0.9478	57.6	0.867	Contact Map
3w1eA	1	0.8955	44.4	0.877	Contact Map
2iqiA	1	0.9328	37.9	0.881	Contact Map
2miiA	1	0.6343	20.4	0.896	Contact Map
4hrvA	2	0.8134	13.9	0.904	Contact Map
4q6vA	1	0.6194	8.6	0.912	Contact Map
4ltoA	3	0.3134	4.8	0.922	Contact Map
3zyyX	2	0.8657	4.7	0.922	Contact Map
2mhjA	1	0.5299	4.1	0.925	Contact Map
2hqsA	2	0.8582	3.9	0.925	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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