DUF2231 - PFAM28P - GREMLIN Contacts

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DUF2231 - Predicted membrane protein (DUF2231)

PFAM:	PF09990	Sequences: WARAAYWLLAAGLIGALLAAVTGLIDWLGIPPGTRAKRIALLHALLNVVALVLFAVLAVWSLLLRRRDPAAVPPLGLALSLVGVALLLVTGWLGGELVYRHGVG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	104 (98)
Sequences:	19344 (12459)
Seq/√Len:	1258.6
META:	0.953

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_L	90_T	3.485	1.00
47_N	90_T	2.772	1.00
54_F	83_G	2.481	1.00
96_E	100_R	2.308	1.00
27_W	41_L	2.111	1.00
10_A	62_L	1.982	1.00
16_A	51_L	1.938	1.00
53_L	83_G	1.897	1.00
61_S	64_L	1.893	1.00
50_A	90_T	1.810	1.00
42_L	45_L	1.713	1.00
38_R	42_L	1.653	1.00
48_V	52_V	1.584	1.00
20_A	51_L	1.561	1.00
50_A	87_L	1.546	1.00
27_W	40_A	1.470	1.00
95_G	99_Y	1.463	1.00
61_S	80_S	1.459	1.00
73_P	76_G	1.441	1.00
61_S	65_R	1.410	1.00
45_L	49_V	1.397	1.00
39_I	93_L	1.395	1.00
6_Y	66_R	1.371	1.00
42_L	93_L	1.369	1.00
25_I	29_G	1.367	1.00
14_I	18_L	1.348	1.00
41_L	45_L	1.309	1.00
32_P	37_K	1.272	1.00
66_R	69_P	1.266	1.00
47_N	50_A	1.263	1.00
62_L	66_R	1.260	1.00
17_L	55_A	1.254	1.00
6_Y	10_A	1.252	1.00
24_L	28_L	1.251	1.00
12_G	54_F	1.247	1.00
62_L	65_R	1.233	1.00
15_G	18_L	1.231	1.00
72_V	76_G	1.231	1.00
48_V	51_L	1.230	1.00
50_A	86_L	1.223	1.00
76_G	80_S	1.221	1.00
13_L	55_A	1.209	1.00
15_G	19_A	1.203	1.00
24_L	44_A	1.185	1.00
41_L	44_A	1.183	1.00
75_L	78_A	1.171	1.00
91_G	95_G	1.169	1.00
44_A	48_V	1.139	1.00
39_I	101_H	1.122	1.00
89_V	93_L	1.120	1.00
2_A	5_A	1.114	1.00
77_L	81_L	1.080	1.00
4_A	8_L	1.078	1.00
63_L	67_R	1.061	1.00
4_A	7_W	1.059	1.00
31_P	34_T	1.040	1.00
27_W	37_K	1.040	1.00
23_G	43_H	1.024	1.00
46_L	86_L	1.021	1.00
74_P	78_A	1.007	1.00
63_L	66_R	1.006	1.00
11_A	15_G	0.994	1.00
85_A	89_V	0.988	1.00
22_T	25_I	0.987	1.00
52_V	56_V	0.985	1.00
46_L	50_A	0.970	1.00
64_L	67_R	0.960	1.00
36_A	103_V	0.958	1.00
78_A	82_V	0.941	1.00
13_L	17_L	0.940	1.00
84_V	88_L	0.937	1.00
30_I	34_T	0.932	1.00
64_L	68_D	0.931	1.00
18_L	22_T	0.912	1.00
55_A	63_L	0.886	1.00
46_L	89_V	0.877	1.00
26_D	40_A	0.828	1.00
89_V	92_W	0.824	1.00
5_A	9_L	0.819	1.00
86_L	90_T	0.811	1.00
96_E	101_H	0.805	1.00
46_L	93_L	0.794	1.00
81_L	85_A	0.775	1.00
64_L	76_G	0.772	1.00
13_L	62_L	0.765	1.00
27_W	45_L	0.765	1.00
13_L	54_F	0.754	1.00
24_L	48_V	0.747	1.00
84_V	87_L	0.744	1.00
42_L	89_V	0.744	1.00
65_R	68_D	0.742	1.00
39_I	97_L	0.720	1.00
56_V	64_L	0.707	1.00
78_A	81_L	0.705	1.00
20_A	48_V	0.704	1.00
65_R	69_P	0.704	1.00
8_L	11_A	0.700	1.00
16_A	19_A	0.697	1.00
30_I	103_V	0.693	1.00
53_L	86_L	0.690	1.00
61_S	66_R	0.689	1.00
21_V	25_I	0.688	1.00
40_A	44_A	0.683	1.00
50_A	54_F	0.678	1.00
50_A	83_G	0.678	1.00
66_R	70_A	0.675	1.00
92_W	96_E	0.670	1.00
36_A	101_H	0.668	1.00
27_W	44_A	0.662	1.00
30_I	36_A	0.661	1.00
26_D	29_G	0.658	1.00
63_L	68_D	0.650	1.00
74_P	77_L	0.644	1.00
67_R	70_A	0.643	1.00
99_Y	102_G	0.634	1.00
42_L	46_L	0.633	1.00
88_L	92_W	0.613	1.00
35_R	101_H	0.608	1.00
24_L	27_W	0.607	1.00
30_I	33_G	0.587	1.00
13_L	16_A	0.584	1.00
22_T	26_D	0.576	1.00
35_R	38_R	0.576	1.00
51_L	55_A	0.571	1.00
80_S	84_V	0.570	1.00
32_P	36_A	0.568	1.00
3_R	8_L	0.566	1.00
17_L	51_L	0.563	1.00
2_A	7_W	0.562	1.00
5_A	8_L	0.560	1.00
71_A	76_G	0.558	1.00
92_W	95_G	0.552	1.00
64_L	69_P	0.551	1.00
64_L	70_A	0.551	1.00
3_R	6_Y	0.549	1.00
75_L	79_L	0.547	1.00
39_I	96_E	0.542	1.00
14_I	17_L	0.541	1.00
25_I	28_L	0.538	1.00
61_S	68_D	0.536	1.00
13_L	51_L	0.526	1.00
18_L	21_V	0.523	1.00
47_N	51_L	0.518	1.00
49_V	86_L	0.518	1.00
49_V	53_L	0.518	1.00
37_K	40_A	0.503	1.00
61_S	67_R	0.500	1.00

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
4o6yA	2	0.9615	39.7	0.836	Contact Map
4i0uA	4	0.6058	23.2	0.854	Contact Map
4ev6A	3	0.625	18.9	0.86	Contact Map
3ayfA	2	0.9904	17.1	0.863	Contact Map
1kqfC	3	0.9615	7.5	0.883	Contact Map
4gd3A	2	0.9327	6.7	0.886	Contact Map
1rz2A	1	0.0769	6	0.888	Contact Map
3mk7A	1	0.9327	5.2	0.891	Contact Map
2lomA	1	0.6827	3.8	0.899	Contact Map
4pgrA	1	0.625	3	0.904	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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