DUF1983 - PFAM28P - GREMLIN Contacts

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DUF1983 - Domain of unknown function (DUF1983)

PFAM:	PF09327	Sequences: VQQVSTAVADLDGKLSAQYTVKVQVNGNGQYYVAGFGLGSENNNGGPTSQFLVLADRFAIVNPSGGTVTPPFVVQGGQVFI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	81 (81)
Sequences:	1751 (1194)
Seq/√Len:	132.7
META:	0.681

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_V	8_V	4.271	1.00
52_L	59_A	3.469	1.00
19_Y	36_F	2.433	1.00
60_I	74_V	2.366	1.00
8_V	11_L	2.269	1.00
10_D	14_K	2.129	1.00
53_V	58_F	2.099	1.00
36_F	53_V	2.084	1.00
20_T	39_G	1.994	1.00
50_Q	57_R	1.919	1.00
36_F	51_F	1.905	1.00
53_V	60_I	1.811	1.00
23_V	40_S	1.739	1.00
3_Q	19_Y	1.656	1.00
74_V	79_V	1.570	1.00
8_V	12_D	1.542	1.00
34_A	49_S	1.509	1.00
22_K	37_G	1.448	1.00
5_S	8_V	1.420	1.00
15_L	39_G	1.358	1.00
61_V	70_P	1.330	1.00
71_P	74_V	1.279	1.00
7_A	10_D	1.269	1.00
1_V	7_A	1.261	1.00
57_R	75_Q	1.244	1.00
43_N	46_G	1.241	1.00
17_A	25_V	1.230	1.00
51_F	58_F	1.225	1.00
23_V	38_L	1.212	1.00
54_L	61_V	1.203	1.00
59_A	73_V	1.193	0.99
56_D	62_N	1.185	0.99
62_N	65_G	1.160	0.99
60_I	72_F	1.155	0.99
11_L	15_L	1.148	0.99
62_N	77_G	1.100	0.99
3_Q	21_V	1.085	0.99
26_N	30_Q	1.065	0.99
15_L	18_Q	1.027	0.98
18_Q	39_G	1.005	0.98
24_Q	27_G	0.968	0.98
51_F	55_A	0.962	0.98
1_V	5_S	0.960	0.98
24_Q	54_L	0.958	0.98
21_V	36_F	0.950	0.97
50_Q	59_A	0.949	0.97
34_A	40_S	0.947	0.97
4_V	11_L	0.931	0.97
52_L	61_V	0.931	0.97
75_Q	78_Q	0.928	0.97
73_V	80_F	0.916	0.97
18_Q	43_N	0.911	0.97
48_T	57_R	0.906	0.97
17_A	23_V	0.903	0.96
9_A	13_G	0.889	0.96
42_N	47_P	0.888	0.96
54_L	63_P	0.888	0.96
7_A	11_L	0.884	0.96
32_Y	40_S	0.873	0.96
9_A	15_L	0.859	0.95
25_V	31_Y	0.828	0.94
20_T	37_G	0.825	0.94
38_L	51_F	0.823	0.94
70_P	73_V	0.809	0.94
11_L	14_K	0.801	0.93
25_V	40_S	0.785	0.92
76_G	80_F	0.770	0.92
41_E	47_P	0.770	0.92
33_V	53_V	0.756	0.91
1_V	4_V	0.750	0.91
24_Q	33_V	0.729	0.89
26_N	31_Y	0.726	0.89
40_S	49_S	0.721	0.89
24_Q	31_Y	0.699	0.87
18_Q	37_G	0.693	0.87
9_A	12_D	0.691	0.87
2_Q	22_K	0.688	0.87
59_A	70_P	0.682	0.86
12_D	16_S	0.674	0.85
1_V	11_L	0.670	0.85
8_V	16_S	0.670	0.85
56_D	63_P	0.669	0.85
1_V	9_A	0.666	0.85
2_Q	5_S	0.661	0.84
60_I	79_V	0.656	0.84
57_R	61_V	0.649	0.83
16_S	25_V	0.646	0.83
38_L	49_S	0.618	0.80
23_V	31_Y	0.615	0.80
6_T	10_D	0.611	0.79
68_V	71_P	0.609	0.79
59_A	71_P	0.605	0.79
5_S	9_A	0.602	0.78
43_N	47_P	0.601	0.78
42_N	48_T	0.595	0.78
4_V	16_S	0.593	0.77
51_F	60_I	0.590	0.77
63_P	66_G	0.590	0.77
42_N	46_G	0.587	0.77
66_G	70_P	0.587	0.77
34_A	55_A	0.586	0.77
34_A	38_L	0.576	0.75
4_V	12_D	0.572	0.75
75_Q	80_F	0.571	0.75
33_V	36_F	0.564	0.74
60_I	69_T	0.552	0.72
68_V	73_V	0.551	0.72
62_N	76_G	0.547	0.72
25_V	32_Y	0.538	0.70
69_T	79_V	0.534	0.70
54_L	64_S	0.532	0.69
31_Y	48_T	0.514	0.67
5_S	10_D	0.512	0.67
19_Y	23_V	0.508	0.66
68_V	77_G	0.508	0.66
11_L	16_S	0.505	0.65
7_A	12_D	0.504	0.65
40_S	51_F	0.503	0.65
12_D	15_L	0.503	0.65
44_N	47_P	0.502	0.65
30_Q	50_Q	0.500	0.65
54_L	62_N	0.500	0.65

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
2k49A	1	0.3457	8.7	0.873	Contact Map
4pdcE	1	0.642	3.7	0.894	Contact Map
2k8eA	1	0.3827	2.7	0.901	Contact Map
3bidA	2	0.321	2.2	0.905	Contact Map
3a1mA	5	0.8395	2.2	0.906	Contact Map
3if8A	1	0.8272	1.8	0.91	Contact Map
1zruA	3	0.2222	1.8	0.91	Contact Map
1xgsA	2	0.4321	1.6	0.912	Contact Map
3ogiA	1	0	1.4	0.915	Contact Map
4qs4A	3	0.7901	1.4	0.915	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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