DUF2165 - PFAM28P - GREMLIN Contacts

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DUF2165 - Predicted small integral membrane protein (DUF2165)

PFAM:	PF09933	Sequences: IRLAKILLVAAVALFALLVAFNNITDYGSNYQFVRHVLSMDTTFPGNALMWRAITSPALHHAAYALIIAWEALTALLCWIGAVRLLRALRAPAAAFNRAKRLAIAGLTLGFLLWFVGFMVVGGEWFLMWQSKTWNGQEAAFRFFTVIGLVLIFVAQP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	157 (155)
Sequences:	2808 (1989)
Seq/√Len:	159.7
META:	0.84

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_L	79_W	4.120	1.00
10_A	82_A	3.098	1.00
86_L	89_L	2.917	1.00
78_C	106_G	2.820	1.00
4_A	108_T	2.674	1.00
27_Y	61_H	2.574	1.00
70_W	113_L	2.569	1.00
13_A	79_W	2.511	1.00
20_A	72_A	2.436	1.00
110_G	147_I	2.298	1.00
49_L	127_L	2.192	1.00
43_T	47_N	2.179	1.00
92_P	95_A	2.158	1.00
145_T	149_L	2.153	1.00
31_Y	60_H	2.131	1.00
36_H	41_D	2.119	1.00
32_Q	35_R	2.094	1.00
9_V	103_A	2.053	1.00
25_T	51_W	2.029	1.00
17_L	75_A	2.009	1.00
28_G	32_Q	1.972	1.00
4_A	153_F	1.916	1.00
31_Y	61_H	1.872	1.00
43_T	50_M	1.837	1.00
141_F	145_T	1.771	1.00
80_I	102_L	1.710	1.00
11_A	116_V	1.708	1.00
21_F	51_W	1.700	1.00
22_N	127_L	1.646	1.00
13_A	17_L	1.589	1.00
21_F	25_T	1.559	1.00
138_E	142_R	1.548	1.00
47_N	50_M	1.532	1.00
39_S	60_H	1.487	1.00
139_A	142_R	1.477	1.00
103_A	154_V	1.464	1.00
16_A	74_T	1.444	1.00
84_R	87_R	1.408	1.00
97_N	100_K	1.400	1.00
42_T	131_S	1.370	1.00
15_F	19_V	1.362	1.00
12_V	78_C	1.359	1.00
15_F	143_F	1.349	1.00
74_T	109_L	1.333	1.00
27_Y	64_Y	1.332	1.00
61_H	65_A	1.318	1.00
104_I	155_A	1.311	1.00
39_S	55_T	1.307	1.00
54_I	59_L	1.287	1.00
27_Y	68_I	1.260	1.00
85_L	99_A	1.236	1.00
122_G	128_M	1.231	1.00
77_L	105_A	1.218	1.00
58_A	62_A	1.217	1.00
11_A	112_L	1.199	1.00
96_F	100_K	1.196	1.00
64_Y	68_I	1.193	1.00
74_T	113_L	1.165	1.00
14_L	116_V	1.157	1.00
33_F	136_G	1.156	1.00
149_L	152_I	1.148	1.00
84_R	102_L	1.138	1.00
77_L	109_L	1.131	1.00
139_A	143_F	1.131	1.00
85_L	97_N	1.127	1.00
6_I	89_L	1.112	1.00
20_A	75_A	1.111	1.00
27_Y	31_Y	1.089	0.99
146_V	149_L	1.082	0.99
63_A	117_G	1.076	0.99
46_G	50_M	1.064	0.99
80_I	84_R	1.062	0.99
74_T	110_G	1.057	0.99
34_V	67_I	1.055	0.99
26_D	29_S	1.052	0.99
78_C	107_L	1.041	0.99
36_H	42_T	1.038	0.99
93_A	97_N	1.038	0.99
8_L	150_V	1.035	0.99
75_A	79_W	1.027	0.99
22_N	25_T	1.026	0.99
30_N	64_Y	1.024	0.99
84_R	88_A	1.013	0.99
84_R	101_R	1.006	0.99
38_L	63_A	0.973	0.99
70_W	109_L	0.969	0.99
12_V	147_I	0.965	0.99
104_I	151_L	0.961	0.99
24_I	72_A	0.958	0.99
111_F	147_I	0.957	0.99
127_L	130_Q	0.957	0.99
20_A	24_I	0.954	0.99
115_F	120_V	0.952	0.99
80_I	83_V	0.950	0.99
83_V	86_L	0.928	0.98
44_F	130_Q	0.922	0.98
40_M	53_A	0.916	0.98
91_A	95_A	0.904	0.98
81_G	106_G	0.902	0.98
71_E	114_W	0.889	0.98
35_R	39_S	0.883	0.98
86_L	155_A	0.878	0.98
144_F	148_G	0.864	0.97
9_V	154_V	0.863	0.97
3_L	6_I	0.860	0.97
37_V	136_G	0.848	0.97
70_W	117_G	0.845	0.97
131_S	134_W	0.838	0.97
14_L	18_L	0.831	0.97
116_V	120_V	0.826	0.97
132_K	138_E	0.825	0.97
70_W	74_T	0.825	0.97
7_L	112_L	0.824	0.97
29_S	48_A	0.818	0.96
103_A	106_G	0.812	0.96
137_Q	141_F	0.795	0.96
76_L	80_I	0.793	0.96
110_G	113_L	0.790	0.96
88_A	91_A	0.786	0.95
107_L	151_L	0.784	0.95
38_L	122_G	0.780	0.95
6_I	86_L	0.777	0.95
2_R	5_K	0.777	0.95
16_A	120_V	0.775	0.95
138_E	141_F	0.773	0.95
128_M	140_A	0.769	0.95
82_A	86_L	0.763	0.95
16_A	110_G	0.754	0.94
115_F	146_V	0.750	0.94
81_G	103_A	0.739	0.94
74_T	106_G	0.736	0.94
21_F	24_I	0.719	0.93
78_C	81_G	0.718	0.93
14_L	120_V	0.714	0.93
21_F	49_L	0.705	0.92
51_W	125_W	0.696	0.92
27_Y	30_N	0.693	0.91
4_A	104_I	0.689	0.91
26_D	30_N	0.689	0.91
152_I	156_Q	0.688	0.91
38_L	117_G	0.686	0.91
43_T	127_L	0.685	0.91
85_L	96_F	0.681	0.91
3_L	7_L	0.675	0.90
123_G	137_Q	0.675	0.90
119_M	137_Q	0.671	0.90
8_L	111_F	0.668	0.90
137_Q	142_R	0.664	0.90
128_M	135_N	0.658	0.89
124_E	128_M	0.654	0.89
119_M	146_V	0.651	0.89
33_F	134_W	0.647	0.88
16_A	75_A	0.643	0.88
148_G	152_I	0.641	0.88
141_F	146_V	0.631	0.87
144_F	150_V	0.629	0.87
76_L	91_A	0.628	0.87
98_R	101_R	0.627	0.87
36_H	134_W	0.624	0.86
29_S	127_L	0.621	0.86
88_A	92_P	0.620	0.86
146_V	150_V	0.619	0.86
111_F	144_F	0.619	0.86
94_A	125_W	0.616	0.86
6_I	9_V	0.614	0.86
88_A	99_A	0.613	0.85
40_M	125_W	0.613	0.85
45_P	50_M	0.610	0.85
149_L	156_Q	0.610	0.85
10_A	14_L	0.605	0.85
12_V	150_V	0.603	0.85
15_F	120_V	0.602	0.84
143_F	147_I	0.596	0.84
35_R	57_P	0.595	0.84
29_S	49_L	0.594	0.84
26_D	40_M	0.591	0.83
12_V	107_L	0.590	0.83
8_L	148_G	0.588	0.83
90_R	94_A	0.585	0.83
30_N	41_D	0.585	0.83
104_I	108_T	0.582	0.82
30_N	33_F	0.581	0.82
23_N	71_E	0.581	0.82
6_I	85_L	0.580	0.82
16_A	114_W	0.577	0.82
143_F	146_V	0.575	0.82
22_N	137_Q	0.569	0.81
71_E	124_E	0.569	0.81
112_L	116_V	0.567	0.81
12_V	18_L	0.563	0.80
46_G	49_L	0.562	0.80
16_A	115_F	0.561	0.80
43_T	48_A	0.560	0.80
52_R	125_W	0.556	0.80
79_W	82_A	0.555	0.79
28_G	35_R	0.555	0.79
73_L	109_L	0.553	0.79
50_M	53_A	0.552	0.79
110_G	114_W	0.552	0.79
105_A	109_L	0.552	0.79
49_L	52_R	0.552	0.79
90_R	101_R	0.550	0.79
111_F	148_G	0.550	0.79
71_E	113_L	0.550	0.79
2_R	96_F	0.549	0.79
95_A	99_A	0.548	0.79
146_V	154_V	0.548	0.79
58_A	89_L	0.541	0.78
111_F	150_V	0.541	0.78
6_I	82_A	0.539	0.77
77_L	102_L	0.538	0.77
88_A	95_A	0.533	0.77
133_T	136_G	0.531	0.76
31_Y	68_I	0.528	0.76
148_G	153_F	0.528	0.76
22_N	49_L	0.527	0.76
137_Q	143_F	0.523	0.75
18_L	120_V	0.521	0.75
72_A	76_L	0.517	0.74
7_L	80_I	0.515	0.74
19_V	30_N	0.514	0.74
3_L	89_L	0.511	0.74
124_E	131_S	0.510	0.73
10_A	79_W	0.508	0.73
24_I	65_A	0.508	0.73
117_G	120_V	0.507	0.73
103_A	107_L	0.506	0.73
133_T	137_Q	0.505	0.73
9_V	106_G	0.505	0.73
97_N	101_R	0.504	0.73
11_A	14_L	0.503	0.72
114_W	119_M	0.500	0.72

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
4or2A	2	0.8344	6.7	0.944	Contact Map
2h88C	2	0.7898	2.6	0.954	Contact Map
1zoyC	1	0.7771	2.5	0.955	Contact Map
4od4A	1	0.8854	2.4	0.955	Contact Map
4ytpC	1	0.7134	2.3	0.955	Contact Map
1m56D	1	0.1465	1.2	0.962	Contact Map
1qleD	1	0.1465	1.2	0.962	Contact Map
4oo9A	1	0.3949	1.1	0.963	Contact Map
5a63B	1	0.6051	1.1	0.963	Contact Map
2wdqC	1	0.6752	0.9	0.965	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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