DUF2244 - PFAM28P - GREMLIN Contacts

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DUF2244 - Integral membrane protein (DUF2244)

PFAM:	PF10003	Sequences: LRPNRSLSPRGFLLLMAALAAVSLAIGLAFLLLGAWPVLPFAGLEVLLLYWAFRLNYRHARDRERITLTPDELRVERVSRGRVREWEFNPYWVRVELEEPEERGIRLTLRSHGRRVEIGRFLSPEERRSLARALRRAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	138 (138)
Sequences:	8292 (5474)
Seq/√Len:	466.0
META:	0.911

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_E	87_E	3.745	1.00
63_R	78_V	2.487	1.00
55_L	59_H	2.381	1.00
74_R	85_E	2.274	1.00
110_R	115_R	2.249	1.00
51_W	55_L	2.163	1.00
76_E	85_E	2.066	1.00
96_E	110_R	1.999	1.00
74_R	87_E	1.981	1.00
64_E	77_R	1.934	1.00
76_E	83_V	1.805	1.00
31_L	39_L	1.793	1.00
78_V	83_V	1.751	1.00
13_L	17_A	1.744	1.00
19_L	49_L	1.744	1.00
65_R	76_E	1.682	1.00
29_A	33_L	1.664	1.00
73_L	90_P	1.663	1.00
129_S	133_A	1.661	1.00
23_S	42_A	1.650	1.00
67_T	74_R	1.645	1.00
37_P	40_P	1.627	1.00
108_T	115_R	1.575	1.00
20_A	46_V	1.559	1.00
50_Y	54_R	1.552	1.00
106_R	117_E	1.540	1.00
79_S	82_R	1.498	1.00
131_A	135_R	1.480	1.00
68_L	73_L	1.474	1.00
88_F	93_V	1.466	1.00
130_L	134_L	1.465	1.00
8_S	11_G	1.459	1.00
77_R	84_R	1.448	1.00
75_V	116_V	1.416	1.00
1_L	121_F	1.408	1.00
94_R	110_R	1.408	1.00
16_M	50_Y	1.388	1.00
12_F	16_M	1.385	1.00
10_R	14_L	1.380	1.00
96_E	115_R	1.380	1.00
123_S	126_E	1.366	1.00
93_V	109_L	1.365	1.00
107_L	131_A	1.364	1.00
86_W	116_V	1.299	1.00
14_L	18_A	1.289	1.00
28_L	32_L	1.286	1.00
12_F	57_Y	1.277	1.00
48_L	52_A	1.259	1.00
47_L	51_W	1.254	1.00
70_P	90_P	1.248	1.00
7_L	11_G	1.242	1.00
100_P	105_I	1.228	1.00
44_L	48_L	1.222	1.00
108_T	117_E	1.217	1.00
42_A	45_E	1.211	1.00
14_L	17_A	1.204	1.00
77_R	86_W	1.198	1.00
66_I	130_L	1.197	1.00
5_R	60_A	1.191	1.00
89_N	92_W	1.169	1.00
117_E	120_R	1.159	1.00
17_A	21_A	1.141	1.00
31_L	42_A	1.123	1.00
102_E	105_I	1.116	1.00
15_L	18_A	1.116	1.00
67_T	76_E	1.115	1.00
9_P	54_R	1.099	1.00
86_W	114_R	1.099	1.00
31_L	36_W	1.094	1.00
9_P	13_L	1.092	1.00
92_W	112_H	1.092	1.00
7_L	12_F	1.087	1.00
43_G	47_L	1.084	1.00
51_W	54_R	1.069	1.00
15_L	19_L	1.068	1.00
18_A	22_V	1.067	1.00
59_H	62_D	1.065	1.00
30_F	38_V	1.064	1.00
69_T	72_E	1.064	1.00
56_N	59_H	1.064	1.00
73_L	109_L	1.045	1.00
79_S	84_R	1.038	1.00
132_R	136_R	1.033	1.00
65_R	78_V	1.031	1.00
117_E	127_R	1.011	1.00
105_I	124_P	1.009	1.00
100_P	103_R	1.007	1.00
126_E	129_S	0.998	1.00
40_P	43_G	0.967	1.00
16_M	46_V	0.960	1.00
62_D	79_S	0.956	1.00
66_I	75_V	0.953	1.00
95_V	134_L	0.946	1.00
8_S	57_Y	0.943	1.00
77_R	120_R	0.929	1.00
95_V	131_A	0.913	1.00
58_R	80_R	0.912	1.00
26_I	42_A	0.907	1.00
133_A	137_A	0.903	1.00
25_A	29_A	0.899	1.00
41_F	45_E	0.884	1.00
21_A	25_A	0.877	1.00
24_L	46_V	0.867	1.00
29_A	32_L	0.841	1.00
23_S	27_G	0.841	1.00
30_F	34_G	0.838	1.00
23_S	46_V	0.834	1.00
129_S	132_R	0.833	1.00
133_A	136_R	0.829	1.00
54_R	58_R	0.827	1.00
96_E	108_T	0.821	1.00
88_F	111_S	0.810	1.00
88_F	116_V	0.808	1.00
64_E	120_R	0.808	1.00
16_M	53_F	0.792	1.00
16_M	20_A	0.791	1.00
27_G	42_A	0.784	1.00
127_R	131_A	0.784	1.00
19_L	26_I	0.783	1.00
79_S	83_V	0.773	1.00
24_L	27_G	0.760	1.00
56_N	60_A	0.760	1.00
28_L	31_L	0.759	1.00
69_T	90_P	0.757	1.00
89_N	112_H	0.754	1.00
92_W	113_G	0.751	1.00
75_V	109_L	0.747	1.00
98_E	108_T	0.742	1.00
49_L	52_A	0.741	1.00
73_L	93_V	0.738	1.00
95_V	135_R	0.737	1.00
10_R	13_L	0.736	1.00
13_L	20_A	0.732	1.00
69_T	74_R	0.728	1.00
19_L	23_S	0.727	1.00
27_G	39_L	0.722	1.00
48_L	51_W	0.719	1.00
29_A	43_G	0.706	1.00
57_Y	60_A	0.695	1.00
125_E	128_R	0.690	1.00
20_A	24_L	0.689	1.00
98_E	106_R	0.687	1.00
24_L	28_L	0.687	1.00
9_P	12_F	0.685	1.00
2_R	63_R	0.674	1.00
71_D	91_Y	0.668	1.00
99_E	128_R	0.667	1.00
72_E	89_N	0.665	1.00
101_E	104_G	0.663	1.00
97_L	128_R	0.661	1.00
97_L	107_L	0.655	1.00
111_S	114_R	0.651	1.00
100_P	104_G	0.650	1.00
54_R	57_Y	0.649	1.00
128_R	132_R	0.646	1.00
71_D	89_N	0.646	1.00
5_R	57_Y	0.646	1.00
50_Y	57_Y	0.644	1.00
12_F	53_F	0.639	1.00
98_E	115_R	0.635	1.00
78_V	82_R	0.634	1.00
34_G	37_P	0.631	0.99
20_A	23_S	0.630	0.99
12_F	50_Y	0.630	0.99
118_I	130_L	0.628	0.99
22_V	26_I	0.625	0.99
99_E	105_I	0.618	0.99
39_L	42_A	0.618	0.99
75_V	118_I	0.611	0.99
5_R	11_G	0.607	0.99
92_W	111_S	0.598	0.99
38_V	45_E	0.597	0.99
106_R	120_R	0.592	0.99
19_L	22_V	0.584	0.99
101_E	105_I	0.581	0.99
23_S	45_E	0.581	0.99
19_L	46_V	0.578	0.99
68_L	134_L	0.577	0.99
52_A	55_L	0.575	0.99
26_I	29_A	0.569	0.99
89_N	111_S	0.566	0.99
37_P	43_G	0.565	0.99
62_D	77_R	0.560	0.99
26_I	39_L	0.555	0.99
97_L	131_A	0.552	0.99
68_L	90_P	0.551	0.99
109_L	118_I	0.550	0.99
122_L	126_E	0.549	0.99
26_I	31_L	0.547	0.99
99_E	104_G	0.539	0.98
103_R	106_R	0.532	0.98
77_R	121_F	0.530	0.98
53_F	56_N	0.530	0.98
23_S	26_I	0.527	0.98
27_G	34_G	0.526	0.98
40_P	44_L	0.520	0.98
119_G	130_L	0.518	0.98
93_V	112_H	0.518	0.98
53_F	57_Y	0.516	0.98
62_D	121_F	0.514	0.98
128_R	136_R	0.511	0.98
107_L	119_G	0.503	0.98
30_F	35_A	0.503	0.98
9_P	57_Y	0.501	0.97
107_L	130_L	0.501	0.97
105_I	108_T	0.500	0.97
62_D	80_R	0.500	0.97

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
3jtzA	2	0.5072	11.8	0.916	Contact Map
2m67A	1	0.5217	9	0.92	Contact Map
3ju0A	1	0.5072	8.6	0.921	Contact Map
3d9sA	3	0.442	7.1	0.924	Contact Map
1ud0A	4	0.3116	6.3	0.926	Contact Map
2b6oA	6	0.413	6.3	0.926	Contact Map
1j4nA	4	0.413	6.1	0.926	Contact Map
5a63B	1	0.5145	5.5	0.928	Contact Map
3sjdD	1	0.1159	5.5	0.928	Contact Map
4wd8A	3	0.8478	5.2	0.929	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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