DUF3106 - PFAM28P - GREMLIN Contacts

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DUF3106 - Protein of unknown function (DUF3106)

PFAM:	PF11304	Sequences: WSELSPEQQQVLAPLAPRWDSLPPERQQRLLERAQRWPSMPPEERQRLQERMERWAKLTPEQRQQARERFQRFRQLPPEERQRLRQAWRRYQALPPEERQQLRE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	104 (102)
Sequences:	10394 (7055)
Seq/√Len:	698.6
META:	0.962

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_E	101_Q	2.978	1.00
23_P	26_R	2.952	1.00
5_S	8_Q	2.653	1.00
59_T	62_Q	2.608	1.00
95_P	98_E	2.593	1.00
77_P	80_E	2.521	1.00
41_P	44_E	2.431	1.00
8_Q	31_L	2.135	1.00
37_W	45_R	2.115	1.00
87_A	90_R	1.947	1.00
32_E	35_Q	1.939	1.00
53_E	57_K	1.916	1.00
62_Q	65_Q	1.799	1.00
6_P	9_Q	1.755	1.00
35_Q	39_S	1.688	1.00
7_E	10_Q	1.644	1.00
80_E	83_R	1.635	1.00
18_R	21_S	1.604	1.00
54_R	57_K	1.572	1.00
40_M	48_L	1.519	1.00
26_R	29_R	1.499	1.00
64_Q	68_E	1.489	1.00
90_R	93_A	1.485	1.00
70_F	74_R	1.464	1.00
34_A	38_P	1.460	1.00
36_R	40_M	1.443	1.00
88_W	91_Y	1.368	1.00
55_W	67_R	1.315	1.00
13_A	16_A	1.301	1.00
96_P	99_R	1.293	1.00
16_A	20_D	1.276	1.00
87_A	91_Y	1.257	1.00
61_E	64_Q	1.247	1.00
72_R	75_Q	1.246	1.00
42_P	45_R	1.243	1.00
19_W	27_Q	1.233	1.00
10_Q	13_A	1.218	1.00
37_W	49_Q	1.215	1.00
44_E	47_R	1.190	1.00
36_R	39_S	1.188	1.00
46_Q	50_E	1.184	1.00
78_P	81_R	1.182	1.00
82_Q	86_Q	1.163	1.00
28_Q	32_E	1.157	1.00
69_R	72_R	1.147	1.00
86_Q	89_R	1.091	1.00
30_L	52_M	1.071	1.00
29_R	32_E	1.065	1.00
65_Q	69_R	1.063	1.00
27_Q	31_L	1.041	1.00
83_R	87_A	1.041	1.00
30_L	33_R	1.036	1.00
62_Q	66_A	1.032	1.00
65_Q	68_E	1.023	1.00
22_L	27_Q	1.021	1.00
89_R	93_A	1.017	1.00
96_P	100_Q	1.007	1.00
1_W	16_A	1.003	1.00
71_Q	75_Q	0.996	1.00
68_E	72_R	0.990	1.00
1_W	5_S	0.989	1.00
29_R	33_R	0.964	1.00
24_P	28_Q	0.960	1.00
51_R	54_R	0.959	1.00
43_E	46_Q	0.959	1.00
44_E	48_L	0.957	1.00
68_E	71_Q	0.935	1.00
47_R	51_R	0.924	1.00
50_E	53_E	0.923	1.00
66_A	70_F	0.922	1.00
66_A	69_R	0.898	1.00
81_R	85_R	0.883	1.00
19_W	37_W	0.883	1.00
82_Q	85_R	0.882	1.00
55_W	63_R	0.875	1.00
91_Y	94_L	0.857	1.00
74_R	81_R	0.855	1.00
84_L	87_A	0.852	1.00
90_R	94_L	0.836	1.00
58_L	66_A	0.829	1.00
24_P	27_Q	0.823	1.00
9_Q	16_A	0.810	1.00
15_L	19_W	0.807	1.00
45_R	49_Q	0.793	1.00
33_R	36_R	0.792	1.00
86_Q	90_R	0.785	1.00
9_Q	13_A	0.782	1.00
52_M	56_A	0.767	1.00
89_R	92_Q	0.763	1.00
8_Q	35_Q	0.761	1.00
35_Q	38_P	0.761	1.00
6_P	10_Q	0.721	1.00
73_F	81_R	0.713	1.00
28_Q	31_L	0.708	1.00
37_W	48_L	0.704	1.00
88_W	92_Q	0.700	1.00
22_L	30_L	0.692	1.00
30_L	34_A	0.690	1.00
50_E	54_R	0.683	1.00
94_L	98_E	0.680	1.00
19_W	34_A	0.668	1.00
73_F	76_L	0.666	1.00
47_R	50_E	0.661	1.00
1_W	12_L	0.660	1.00
83_R	86_Q	0.645	1.00
40_M	45_R	0.641	1.00
11_V	14_P	0.638	1.00
26_R	30_L	0.637	1.00
31_L	34_A	0.626	1.00
67_R	70_F	0.623	1.00
61_E	65_Q	0.622	1.00
94_L	102_L	0.613	1.00
33_R	48_L	0.609	1.00
55_W	66_A	0.608	1.00
42_P	46_Q	0.606	1.00
25_E	28_Q	0.605	1.00
54_R	58_L	0.600	1.00
91_Y	95_P	0.597	1.00
40_M	44_E	0.593	1.00
48_L	51_R	0.591	1.00
97_E	101_Q	0.577	1.00
37_W	52_M	0.577	1.00
46_Q	49_Q	0.576	1.00
8_Q	11_V	0.568	1.00
34_A	70_F	0.565	1.00
49_Q	53_E	0.565	1.00
63_R	67_R	0.555	1.00
64_Q	67_R	0.554	1.00
85_R	88_W	0.554	1.00
14_P	17_P	0.553	1.00
97_E	100_Q	0.553	1.00
93_A	101_Q	0.552	1.00
55_W	70_F	0.549	1.00
73_F	77_P	0.542	1.00
53_E	56_A	0.536	1.00
27_Q	30_L	0.529	1.00
23_P	30_L	0.528	1.00
11_V	19_W	0.527	1.00
75_Q	78_P	0.526	1.00
69_R	73_F	0.525	1.00
55_W	74_R	0.523	1.00
48_L	52_M	0.523	1.00
57_K	60_P	0.522	1.00
33_R	52_M	0.521	1.00
15_L	22_L	0.517	1.00
55_W	69_R	0.511	0.99
11_V	15_L	0.510	0.99
37_W	56_A	0.507	0.99
85_R	89_R	0.504	0.99
5_S	10_Q	0.502	0.99
49_Q	52_M	0.502	0.99
58_L	62_Q	0.500	0.99
17_P	20_D	0.500	0.99

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
2w9yA	1	0.9135	83.9	0.751	Contact Map
4mncA	1	0.7596	51.8	0.804	Contact Map
1j7nA	2	0.7019	47.8	0.808	Contact Map
2ouxA	2	0.8269	46.9	0.81	Contact Map
4wwfA	2	0.9038	45.7	0.811	Contact Map
2zy9A	2	0.7981	42.8	0.814	Contact Map
3u65B	1	0.7596	40	0.817	Contact Map
3oeoA	3	0.7981	37.5	0.82	Contact Map
3o39A	2	0.7981	37.1	0.821	Contact Map
3zg1A	2	0.9135	35.6	0.822	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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