DUF4409 - PFAM28P - GREMLIN Contacts

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DUF4409 - Domain of unknown function (DUF4409)

PFAM:	PF14365	Sequences: TIQSPDGDIIDCVPIHKQPAFDHPLLKNHKIQMRPSERPEGLFDESSNSKSSSKPITQLWHKNGESCPEGTIPIRRTTKEDLLRASSLKRFGRKKPPNPRSVRPDSVSSNGHEHAIAY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	118 (117)
Sequences:	979 (724)
Seq/√Len:	66.9
META:	0.225

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
81_D	84_R	3.923	1.00
91_F	94_K	3.583	1.00
11_D	76_R	3.511	1.00
14_P	17_K	3.204	1.00
19_P	74_I	2.858	1.00
98_N	101_S	2.688	1.00
75_R	81_D	2.676	1.00
109_S	113_E	2.612	1.00
13_V	74_I	2.452	1.00
59_L	62_K	2.124	1.00
23_H	26_L	2.097	1.00
84_R	91_F	1.949	1.00
60_W	64_G	1.898	1.00
68_P	74_I	1.825	1.00
22_D	83_L	1.785	1.00
29_H	32_Q	1.779	1.00
109_S	117_A	1.684	0.99
109_S	114_H	1.676	0.99
8_D	20_A	1.633	0.99
100_R	105_D	1.614	0.99
77_T	81_D	1.584	0.99
105_D	114_H	1.520	0.99
36_S	39_P	1.518	0.99
52_S	59_L	1.494	0.99
15_I	31_I	1.459	0.98
26_L	29_H	1.426	0.98
19_P	73_P	1.397	0.98
85_A	92_G	1.367	0.98
18_Q	21_F	1.364	0.98
110_N	113_E	1.345	0.97
111_G	114_H	1.324	0.97
107_V	110_N	1.322	0.97
110_N	116_I	1.300	0.97
21_F	24_P	1.256	0.96
25_L	29_H	1.229	0.95
4_S	60_W	1.197	0.95
18_Q	26_L	1.183	0.94
106_S	113_E	1.152	0.94
100_R	103_R	1.149	0.93
53_S	56_I	1.136	0.93
28_N	32_Q	1.125	0.93
24_P	29_H	1.123	0.93
111_G	116_I	1.112	0.92
51_S	54_K	1.110	0.92
85_A	88_L	1.107	0.92
108_S	114_H	1.105	0.92
106_S	114_H	1.093	0.92
99_P	103_R	1.086	0.91
108_S	111_G	1.086	0.91
6_D	10_I	1.068	0.91
50_K	78_T	1.066	0.91
10_I	31_I	1.057	0.90
103_R	113_E	1.036	0.89
106_S	109_S	1.022	0.89
23_H	32_Q	1.007	0.88
50_K	53_S	1.006	0.88
23_H	29_H	1.002	0.88
7_G	68_P	0.996	0.87
102_V	107_V	0.996	0.87
4_S	10_I	0.993	0.87
13_V	26_L	0.989	0.87
5_P	10_I	0.979	0.86
15_I	18_Q	0.960	0.85
48_N	53_S	0.956	0.85
15_I	72_I	0.936	0.84
100_R	104_P	0.930	0.83
21_F	26_L	0.930	0.83
98_N	102_V	0.928	0.83
78_T	86_S	0.925	0.83
14_P	78_T	0.913	0.82
20_A	26_L	0.910	0.82
10_I	60_W	0.904	0.82
7_G	35_P	0.895	0.81
103_R	114_H	0.892	0.81
48_N	52_S	0.891	0.81
4_S	64_G	0.890	0.81
87_S	94_K	0.886	0.80
58_Q	61_H	0.871	0.79
8_D	60_W	0.867	0.79
23_H	28_N	0.848	0.77
103_R	106_S	0.837	0.76
82_L	86_S	0.836	0.76
58_Q	75_R	0.808	0.74
98_N	103_R	0.796	0.73
103_R	108_S	0.795	0.73
107_V	113_E	0.792	0.72
33_M	36_S	0.788	0.72
53_S	62_K	0.784	0.72
17_K	28_N	0.783	0.72
79_K	82_L	0.782	0.71
35_P	39_P	0.781	0.71
8_D	64_G	0.765	0.70
10_I	15_I	0.765	0.70
75_R	84_R	0.764	0.70
28_N	31_I	0.745	0.68
58_Q	64_G	0.744	0.68
8_D	58_Q	0.739	0.67
12_C	18_Q	0.734	0.67
69_E	86_S	0.734	0.67
17_K	80_E	0.728	0.66
32_Q	35_P	0.721	0.65
15_I	32_Q	0.721	0.65
41_G	45_E	0.721	0.65
101_S	117_A	0.717	0.65
25_L	54_K	0.715	0.65
24_P	32_Q	0.714	0.64
59_L	117_A	0.714	0.64
75_R	89_K	0.713	0.64
98_N	105_D	0.711	0.64
8_D	81_D	0.710	0.64
47_S	57_T	0.707	0.64
14_P	70_G	0.707	0.64
107_V	114_H	0.700	0.63
72_I	105_D	0.699	0.63
105_D	110_N	0.697	0.63
106_S	116_I	0.692	0.62
9_I	76_R	0.692	0.62
18_Q	71_T	0.691	0.62
10_I	65_E	0.686	0.61
105_D	111_G	0.680	0.61
108_S	117_A	0.673	0.60
106_S	110_N	0.673	0.60
102_V	106_S	0.672	0.60
52_S	57_T	0.653	0.58
9_I	22_D	0.652	0.57
49_S	52_S	0.645	0.57
106_S	117_A	0.636	0.56
101_S	105_D	0.635	0.56
100_R	106_S	0.635	0.56
54_K	72_I	0.635	0.56
2_I	73_P	0.635	0.56
56_I	62_K	0.629	0.55
54_K	62_K	0.627	0.55
49_S	55_P	0.621	0.54
26_L	32_Q	0.621	0.54
42_L	46_S	0.621	0.54
107_V	116_I	0.617	0.53
84_R	87_S	0.613	0.53
49_S	86_S	0.611	0.53
10_I	24_P	0.608	0.52
3_Q	79_K	0.601	0.51
7_G	23_H	0.598	0.51
67_C	81_D	0.594	0.51
5_P	62_K	0.594	0.51
22_D	27_K	0.592	0.50
43_F	46_S	0.591	0.50
25_L	88_L	0.588	0.50
5_P	30_K	0.584	0.49
70_G	117_A	0.579	0.49
38_R	91_F	0.578	0.49
105_D	108_S	0.577	0.49
64_G	71_T	0.576	0.49
69_E	89_K	0.572	0.48
34_R	37_E	0.570	0.48
18_Q	67_C	0.565	0.47
9_I	17_K	0.561	0.47
9_I	93_R	0.556	0.46
72_I	92_G	0.553	0.46
87_S	91_F	0.552	0.46
32_Q	36_S	0.550	0.45
80_E	94_K	0.544	0.45
6_D	58_Q	0.542	0.45
20_A	29_H	0.539	0.44
82_L	93_R	0.533	0.43
27_K	83_L	0.531	0.43
44_D	63_N	0.528	0.43
99_P	102_V	0.523	0.42
6_D	23_H	0.521	0.42
17_K	22_D	0.520	0.42
98_N	106_S	0.519	0.42
47_S	51_S	0.517	0.42
110_N	114_H	0.515	0.41
83_L	86_S	0.514	0.41
2_I	60_W	0.512	0.41
97_P	103_R	0.507	0.40
17_K	70_G	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
1akpA	1	0.322	7.3	0.936	Contact Map
4aenA	1	0.2458	5.9	0.938	Contact Map
1acxA	1	0.3051	4.4	0.942	Contact Map
1u58A	1	0.2373	4	0.943	Contact Map
2bc4B	1	0.3136	3.3	0.946	Contact Map
4d6qA	2	0.339	2.6	0.948	Contact Map
4v2wA	1	0.3644	2.5	0.949	Contact Map
1uvqA	1	0.2458	2.5	0.949	Contact Map
1ytqA	4	0.4322	2.2	0.95	Contact Map
2grrB	1	0.3644	2.1	0.951	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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