DUF2703 - PFAM28P - GREMLIN Contacts

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DUF2703 - Domain of unknown function (DUF2703)

PFAM:	PF10865	Sequences: LVIEWLYLDLEGETCERCGGTGEELEEAVEELRPVLAPLGIEVELEKTELDTEEFAKDFLSSNTIRINGRDIEEWLAAEVKESCCESCGDLCGDDVDCRTWEYEGKEYEAIPKELIVEAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	120 (119)
Sequences:	1471 (993)
Seq/√Len:	91.1
META:	0.94

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_E	47_K	4.455	1.00
102_E	107_E	3.585	1.00
24_E	110_A	3.377	1.00
51_D	55_F	2.756	1.00
31_E	113_K	2.664	1.00
20_G	110_A	2.625	1.00
84_C	89_G	2.481	1.00
81_K	100_T	2.369	1.00
58_D	61_S	2.338	1.00
89_G	92_C	2.289	1.00
15_C	18_C	2.245	1.00
83_S	100_T	2.167	1.00
100_T	107_E	2.134	1.00
28_A	117_V	1.746	1.00
4_E	46_E	1.726	1.00
24_E	27_E	1.691	1.00
22_G	47_K	1.642	1.00
70_R	74_E	1.608	1.00
52_T	56_A	1.560	1.00
6_L	64_T	1.553	1.00
65_I	116_I	1.539	1.00
9_D	49_E	1.442	0.99
34_P	43_V	1.439	0.99
25_L	29_V	1.432	0.99
4_E	48_T	1.417	0.99
1_L	67_I	1.408	0.99
43_V	47_K	1.396	0.99
49_E	55_F	1.386	0.99
84_C	97_D	1.379	0.99
71_D	76_L	1.358	0.99
53_E	57_K	1.358	0.99
16_E	86_E	1.338	0.99
10_L	52_T	1.331	0.99
16_E	87_S	1.285	0.99
14_T	17_R	1.277	0.99
80_V	84_C	1.270	0.99
51_D	54_E	1.227	0.98
11_E	19_G	1.206	0.98
4_E	66_R	1.192	0.98
29_V	43_V	1.185	0.98
24_E	113_K	1.172	0.98
85_C	88_C	1.158	0.97
2_V	46_E	1.154	0.97
36_L	43_V	1.147	0.97
61_S	64_T	1.134	0.97
27_E	113_K	1.134	0.97
6_L	9_D	1.133	0.97
18_C	88_C	1.131	0.97
87_S	91_L	1.130	0.97
24_E	116_I	1.126	0.97
6_L	71_D	1.118	0.97
67_I	70_R	1.098	0.96
64_T	71_D	1.088	0.96
2_V	44_E	1.086	0.96
20_G	101_W	1.086	0.96
70_R	75_W	1.071	0.96
66_R	71_D	1.062	0.96
6_L	48_T	1.028	0.95
33_R	42_E	1.024	0.95
9_D	59_F	1.019	0.95
57_K	60_L	1.016	0.95
113_K	116_I	1.010	0.94
24_E	28_A	0.999	0.94
92_C	96_V	0.995	0.94
14_T	62_S	0.983	0.94
54_E	61_S	0.981	0.93
32_L	35_V	0.973	0.93
50_L	55_F	0.969	0.93
24_E	78_A	0.967	0.93
36_L	41_I	0.954	0.93
28_A	113_K	0.950	0.92
108_Y	112_P	0.944	0.92
9_D	64_T	0.936	0.92
88_C	98_C	0.915	0.91
37_A	70_R	0.894	0.90
79_E	102_E	0.891	0.90
32_L	38_P	0.882	0.89
84_C	95_D	0.878	0.89
17_R	83_S	0.866	0.88
3_I	25_L	0.856	0.88
104_E	118_E	0.849	0.87
26_E	45_L	0.842	0.87
77_A	80_V	0.836	0.87
34_P	37_A	0.834	0.86
8_L	92_C	0.827	0.86
54_E	68_N	0.824	0.86
4_E	69_G	0.822	0.86
14_T	91_L	0.817	0.85
102_E	105_G	0.808	0.85
2_V	43_V	0.805	0.84
83_S	97_D	0.804	0.84
6_L	61_S	0.800	0.84
17_R	88_C	0.798	0.84
4_E	43_V	0.788	0.83
11_E	14_T	0.781	0.83
17_R	109_E	0.774	0.82
62_S	99_R	0.769	0.82
62_S	98_C	0.765	0.81
72_I	116_I	0.751	0.80
41_I	44_E	0.744	0.79
45_L	49_E	0.742	0.79
7_Y	49_E	0.739	0.79
67_I	75_W	0.737	0.79
19_G	23_E	0.729	0.78
63_N	71_D	0.725	0.78
32_L	117_V	0.724	0.78
41_I	87_S	0.707	0.76
32_L	39_L	0.707	0.76
2_V	70_R	0.706	0.76
107_E	116_I	0.703	0.75
46_E	116_I	0.693	0.74
76_L	111_I	0.693	0.74
16_E	20_G	0.693	0.74
18_C	62_S	0.692	0.74
55_F	59_F	0.685	0.74
32_L	109_E	0.684	0.73
103_Y	118_E	0.681	0.73
113_K	117_V	0.680	0.73
14_T	109_E	0.670	0.72
35_V	60_L	0.669	0.72
41_I	94_D	0.657	0.70
83_S	95_D	0.655	0.70
9_D	13_E	0.651	0.70
40_G	105_G	0.650	0.70
43_V	68_N	0.649	0.70
56_A	96_V	0.641	0.69
45_L	92_C	0.637	0.68
78_A	81_K	0.633	0.68
8_L	55_F	0.632	0.68
77_A	101_W	0.627	0.67
105_G	118_E	0.624	0.67
17_R	98_C	0.619	0.66
30_E	57_K	0.616	0.66
62_S	69_G	0.612	0.65
19_G	22_G	0.604	0.64
65_I	111_I	0.599	0.63
45_L	108_Y	0.595	0.63
68_N	71_D	0.591	0.62
48_T	66_R	0.590	0.62
38_P	43_V	0.588	0.62
64_T	68_N	0.588	0.62
13_E	65_I	0.585	0.62
18_C	63_N	0.579	0.61
16_E	109_E	0.578	0.61
2_V	116_I	0.577	0.61
44_E	57_K	0.577	0.61
10_L	61_S	0.574	0.60
80_V	83_S	0.574	0.60
92_C	95_D	0.569	0.59
31_E	35_V	0.563	0.59
44_E	54_E	0.560	0.58
16_E	57_K	0.559	0.58
13_E	74_E	0.555	0.58
20_G	87_S	0.553	0.57
12_G	71_D	0.552	0.57
25_L	75_W	0.552	0.57
23_E	38_P	0.548	0.57
30_E	97_D	0.547	0.57
71_D	105_G	0.541	0.56
48_T	58_D	0.540	0.56
25_L	45_L	0.539	0.55
15_C	88_C	0.536	0.55
17_R	62_S	0.534	0.55
46_E	54_E	0.527	0.54
23_E	110_A	0.526	0.54
61_S	111_I	0.524	0.53
30_E	40_G	0.522	0.53
27_E	30_E	0.521	0.53
6_L	10_L	0.521	0.53
98_C	109_E	0.520	0.53
86_E	95_D	0.519	0.53
28_A	67_I	0.512	0.52
58_D	119_A	0.510	0.51
41_I	86_E	0.507	0.51
17_R	110_A	0.505	0.51
8_L	62_S	0.505	0.51
109_E	114_E	0.501	0.50
33_R	37_A	0.500	0.50

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
2r6fA	2	0.9917	46.8	0.903	Contact Map
3pihA	2	0.85	29.1	0.913	Contact Map
2jvfA	1	0.6417	26.6	0.914	Contact Map
4mo1A	1	0.5083	26.3	0.915	Contact Map
3ipzA	3	0.675	24.9	0.916	Contact Map
1k82A	1	0.3333	24.4	0.916	Contact Map
2k8sA	2	0.6667	23.2	0.917	Contact Map
3u6pA	1	0.3083	22.2	0.918	Contact Map
2hzeA	1	0.6833	21.2	0.918	Contact Map
2vf7A	2	0.9083	20.2	0.919	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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