DUF2189 - PFAM28P - GREMLIN Contacts

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DUF2189 - Predicted integral membrane protein (DUF2189)

PFAM:	PF09955	Sequences: LFPLAAGFALVGPFAAVGLYELSRRRERGEPVSWADALDVWRSPSGAIAALGLLLLVIFLLWLRAAALIYALFFGPAPPPSLSDFLRDVFTTPEGWALLVVGNAVGALFAALVFAISVVSFPLLLD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	126 (125)
Sequences:	9103 (5614)
Seq/√Len:	502.2
META:	0.905

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_R	30_E	3.153	1.00
21_E	25_R	3.041	1.00
33_S	36_D	2.604	1.00
21_E	24_R	2.526	1.00
87_R	91_T	2.525	1.00
107_A	111_A	2.397	1.00
84_D	88_D	2.278	1.00
73_F	97_A	2.183	1.00
51_L	121_F	2.050	1.00
69_I	105_V	2.048	1.00
58_I	113_V	2.011	1.00
7_G	59_F	1.999	1.00
104_A	108_L	1.982	1.00
65_A	109_F	1.970	1.00
25_R	36_D	1.956	1.00
88_D	94_E	1.913	1.00
31_P	36_D	1.753	1.00
66_A	102_G	1.744	1.00
83_S	87_R	1.716	1.00
92_T	95_G	1.704	1.00
69_I	73_F	1.694	1.00
97_A	101_V	1.667	1.00
36_D	39_D	1.596	1.00
51_L	120_S	1.528	1.00
81_S	84_D	1.492	1.00
22_L	26_R	1.467	1.00
57_V	61_L	1.444	1.00
39_D	42_R	1.416	1.00
116_I	120_S	1.396	1.00
42_R	45_S	1.385	1.00
67_A	71_A	1.381	1.00
93_P	97_A	1.373	1.00
2_F	103_N	1.355	1.00
84_D	87_R	1.354	1.00
49_A	52_G	1.345	1.00
104_A	107_A	1.344	1.00
73_F	98_L	1.320	1.00
50_A	54_L	1.314	1.00
58_I	109_F	1.311	1.00
6_A	9_A	1.302	1.00
21_E	36_D	1.296	1.00
55_L	113_V	1.261	1.00
24_R	28_R	1.256	1.00
16_A	20_Y	1.247	1.00
106_G	110_A	1.216	1.00
64_R	68_L	1.207	1.00
32_V	36_D	1.204	1.00
55_L	117_S	1.181	1.00
56_L	60_L	1.175	1.00
25_R	32_V	1.175	1.00
10_L	113_V	1.171	1.00
100_V	103_N	1.156	1.00
51_L	117_S	1.143	1.00
54_L	116_I	1.139	1.00
65_A	105_V	1.124	1.00
46_G	49_A	1.123	1.00
112_L	116_I	1.099	1.00
58_I	112_L	1.096	1.00
68_L	72_L	1.082	1.00
41_W	46_G	1.081	1.00
51_L	124_L	1.070	1.00
64_R	71_A	1.064	1.00
114_F	118_V	1.063	1.00
17_V	48_I	1.061	1.00
80_P	84_D	1.057	1.00
17_V	125_L	1.043	1.00
74_F	88_D	1.039	1.00
70_Y	74_F	1.036	1.00
11_V	59_F	1.032	1.00
96_W	100_V	1.031	1.00
113_V	117_S	1.004	1.00
99_L	103_N	1.002	1.00
3_P	63_L	1.001	1.00
69_I	98_L	0.999	1.00
111_A	115_A	0.991	1.00
47_A	50_A	0.984	1.00
61_L	64_R	0.982	1.00
64_R	67_A	0.951	1.00
93_P	96_W	0.946	1.00
2_F	6_A	0.946	1.00
73_F	101_V	0.945	1.00
14_F	52_G	0.935	1.00
66_A	70_Y	0.925	1.00
108_L	112_L	0.924	1.00
74_F	94_E	0.921	1.00
82_L	86_L	0.900	1.00
94_E	97_A	0.898	1.00
12_G	15_A	0.886	1.00
26_R	32_V	0.873	1.00
52_G	55_L	0.863	1.00
97_A	100_V	0.860	1.00
40_V	44_P	0.859	1.00
85_F	89_V	0.856	1.00
101_V	105_V	0.844	1.00
4_L	8_F	0.842	1.00
61_L	65_A	0.837	1.00
53_L	57_V	0.825	1.00
19_L	37_A	0.822	1.00
80_P	83_S	0.815	1.00
57_V	64_R	0.804	1.00
81_S	85_F	0.790	1.00
79_P	83_S	0.789	1.00
115_A	118_V	0.781	1.00
82_L	85_F	0.781	1.00
8_F	11_V	0.774	1.00
18_G	38_L	0.769	1.00
22_L	37_A	0.768	1.00
47_A	124_L	0.767	1.00
37_A	41_W	0.754	1.00
34_W	37_A	0.754	1.00
43_S	46_G	0.747	1.00
33_S	37_A	0.746	1.00
56_L	67_A	0.742	1.00
31_P	35_A	0.739	1.00
79_P	88_D	0.738	1.00
34_W	38_L	0.734	1.00
89_V	98_L	0.731	1.00
60_L	64_R	0.730	1.00
64_R	72_L	0.715	1.00
14_F	40_V	0.713	1.00
48_I	124_L	0.709	1.00
48_I	125_L	0.704	1.00
103_N	107_A	0.701	1.00
119_V	123_L	0.696	1.00
62_W	106_G	0.695	1.00
30_E	36_D	0.695	1.00
40_V	43_S	0.687	1.00
86_L	90_F	0.669	1.00
7_G	11_V	0.663	1.00
28_R	32_V	0.663	1.00
79_P	82_L	0.655	1.00
59_F	63_L	0.649	1.00
41_W	44_P	0.637	1.00
50_A	53_L	0.636	1.00
35_A	39_D	0.627	1.00
71_A	76_P	0.620	1.00
101_V	104_A	0.615	1.00
33_S	42_R	0.613	1.00
11_V	14_F	0.611	1.00
19_L	23_S	0.609	0.99
115_A	119_V	0.609	0.99
81_S	86_L	0.608	0.99
58_I	116_I	0.604	0.99
37_A	40_V	0.602	0.99
2_F	5_A	0.599	0.99
32_V	37_A	0.595	0.99
9_A	59_F	0.595	0.99
9_A	121_F	0.592	0.99
102_G	106_G	0.588	0.99
83_S	86_L	0.588	0.99
95_G	98_L	0.586	0.99
5_A	9_A	0.575	0.99
8_F	23_S	0.572	0.99
23_S	37_A	0.569	0.99
21_E	26_R	0.566	0.99
100_V	104_A	0.566	0.99
99_L	102_G	0.564	0.99
38_L	41_W	0.563	0.99
50_A	64_R	0.562	0.99
74_F	98_L	0.561	0.99
90_F	94_E	0.560	0.99
62_W	66_A	0.555	0.99
77_A	84_D	0.555	0.99
102_G	105_V	0.553	0.99
57_V	67_A	0.551	0.99
107_A	110_A	0.549	0.99
18_G	40_V	0.548	0.99
105_V	109_F	0.548	0.99
68_L	71_A	0.542	0.99
87_R	93_P	0.542	0.99
26_R	30_E	0.539	0.99
102_G	109_F	0.538	0.99
37_A	52_G	0.538	0.99
49_A	68_L	0.537	0.99
108_L	111_A	0.535	0.99
21_E	43_S	0.534	0.99
14_F	56_L	0.533	0.99
77_A	83_S	0.531	0.99
9_A	15_A	0.527	0.99
35_A	42_R	0.522	0.98
18_G	48_I	0.521	0.98
18_G	36_D	0.514	0.98
77_A	80_P	0.512	0.98
4_L	59_F	0.511	0.98
17_V	40_V	0.509	0.98
19_L	22_L	0.505	0.98
90_F	95_G	0.501	0.98
117_S	120_S	0.500	0.98

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
4ltoA	3	0.619	3.1	0.928	Contact Map
4cbcA	3	0.6111	2.4	0.932	Contact Map
3rkoJ	1	0.2381	2.2	0.933	Contact Map
4k0jA	3	0.1746	1.9	0.935	Contact Map
2wscL	1	0.8016	1.8	0.937	Contact Map
4cadC	1	0.7619	1.7	0.937	Contact Map
3j8eG	3	0.873	1.6	0.938	Contact Map
4gx0A	3	0.6508	1.4	0.94	Contact Map
3rlfF	1	0.9524	1.4	0.94	Contact Map
1q90G	1	0.2143	1.4	0.94	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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