DUF92 - PFAM28P - GREMLIN Contacts

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DUF92 - Integral membrane protein DUF92

PFAM:	PF01940	Sequences: LALLLALLAYRARSLTLSGALAAALVGTLIFGGGGWGWFLLLLAFFVSSSLLTRLGYARKAALGIAEEKGGRRDAGQVLANGGVAALLALLYALTPSPAWDLLLLAFAAALAAAAADTWASEIGVLSGRRPRLITTLKPVPPGTSGGVSLLGTLAGLAGALLIALVAALAGFLGSLVDSLLGATLQARYYCPVCGKETERRVHCGTRTVRGWRWLNNDAVNFLSTLIGAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	230 (216)
Sequences:	5929 (4158)
Seq/√Len:	282.9
META:	0.827

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_A	166_V	3.806	1.00
191_C	194_C	3.780	1.00
114_A	225_T	3.562	1.00
177_V	227_I	3.211	1.00
34_G	38_W	3.051	1.00
156_G	175_S	3.017	1.00
130_R	139_P	2.959	1.00
215_L	219_A	2.846	1.00
52_L	119_W	2.758	1.00
26_V	86_A	2.746	1.00
119_W	159_G	2.675	1.00
153_T	176_L	2.642	1.00
120_A	156_G	2.603	1.00
22_A	75_A	2.553	1.00
56_G	59_R	2.495	1.00
44_A	162_L	2.463	1.00
88_L	106_A	2.413	1.00
109_A	228_G	2.376	1.00
108_A	167_A	2.356	1.00
140_V	147_G	2.327	1.00
85_A	111_L	2.307	1.00
161_L	168_A	2.266	1.00
15_L	23_A	2.229	1.00
48_S	119_W	2.224	1.00
41_L	108_A	2.047	1.00
157_L	172_F	1.960	1.00
190_Y	195_G	1.878	1.00
88_L	103_L	1.823	1.00
127_S	151_L	1.796	1.00
10_Y	17_L	1.761	1.00
7_L	11_R	1.758	1.00
140_V	144_T	1.744	1.00
29_L	86_A	1.718	1.00
6_A	24_A	1.706	1.00
56_G	60_K	1.634	1.00
145_S	187_A	1.630	1.00
131_P	147_G	1.625	1.00
135_T	184_T	1.622	1.00
132_R	139_P	1.619	1.00
113_A	224_S	1.604	1.00
3_L	24_A	1.588	1.00
115_A	163_I	1.586	1.00
133_L	183_A	1.575	1.00
123_I	155_A	1.568	1.00
131_P	149_S	1.531	1.00
154_L	158_A	1.519	1.00
141_P	144_T	1.506	1.00
109_A	170_A	1.484	1.00
38_W	107_F	1.483	1.00
14_S	50_S	1.474	1.00
13_R	72_R	1.473	1.00
84_V	226_L	1.440	1.00
172_F	176_L	1.406	1.00
148_V	153_T	1.382	1.00
58_A	61_A	1.378	1.00
59_R	63_L	1.369	1.00
120_A	175_S	1.368	1.00
45_F	49_S	1.364	1.00
133_L	140_V	1.363	1.00
75_A	79_L	1.338	1.00
31_F	39_F	1.332	1.00
113_A	228_G	1.314	1.00
24_A	28_T	1.314	1.00
33_G	93_A	1.294	1.00
48_S	162_L	1.289	1.00
41_L	167_A	1.289	1.00
181_L	185_L	1.275	1.00
33_G	89_A	1.273	1.00
134_I	176_L	1.261	1.00
49_S	119_W	1.241	1.00
48_S	115_A	1.231	1.00
20_A	24_A	1.226	1.00
53_T	71_G	1.216	1.00
30_I	107_F	1.197	1.00
135_T	180_L	1.184	1.00
153_T	156_G	1.178	1.00
22_A	79_L	1.176	1.00
123_I	151_L	1.167	1.00
85_A	107_F	1.160	1.00
69_K	74_D	1.151	1.00
74_D	77_Q	1.131	1.00
130_R	141_P	1.128	1.00
39_F	43_L	1.115	1.00
133_L	136_T	1.114	1.00
44_A	48_S	1.110	1.00
215_L	223_L	1.109	1.00
145_S	182_G	1.109	1.00
45_F	114_A	1.107	1.00
135_T	183_A	1.105	1.00
23_A	27_G	1.104	1.00
8_L	12_A	1.092	1.00
170_A	228_G	1.087	1.00
105_L	109_A	1.086	1.00
116_A	160_A	1.080	1.00
2_A	39_F	1.075	1.00
115_A	119_W	1.071	1.00
9_A	14_S	1.050	1.00
224_S	228_G	1.048	1.00
187_A	214_W	1.032	1.00
18_S	75_A	1.027	1.00
116_A	175_S	1.016	1.00
130_R	149_S	1.008	1.00
82_G	111_L	0.993	1.00
160_A	164_A	0.991	1.00
41_L	107_F	0.988	1.00
88_L	91_L	0.986	1.00
164_A	171_G	0.986	1.00
17_L	21_L	0.985	1.00
93_A	96_P	0.974	1.00
92_Y	96_P	0.970	1.00
53_T	60_K	0.949	1.00
113_A	174_G	0.946	1.00
156_G	176_L	0.946	1.00
151_L	154_L	0.942	1.00
156_G	172_F	0.938	1.00
144_T	147_G	0.936	1.00
44_A	163_I	0.934	1.00
38_W	89_A	0.928	1.00
115_A	159_G	0.927	1.00
23_A	82_G	0.923	1.00
129_R	151_L	0.922	1.00
59_R	62_A	0.913	1.00
15_L	78_V	0.905	1.00
150_L	153_T	0.904	1.00
219_A	222_F	0.896	1.00
224_S	227_I	0.894	1.00
43_L	47_V	0.887	1.00
128_G	151_L	0.887	1.00
164_A	168_A	0.876	1.00
86_A	89_A	0.866	1.00
81_N	218_D	0.861	1.00
112_A	171_G	0.859	1.00
66_A	71_G	0.856	1.00
173_L	227_I	0.853	1.00
111_L	163_I	0.853	1.00
95_T	103_L	0.851	1.00
76_G	216_N	0.851	1.00
157_L	168_A	0.848	1.00
41_L	163_I	0.843	1.00
50_S	53_T	0.841	1.00
29_L	33_G	0.840	1.00
10_Y	72_R	0.838	1.00
153_T	175_S	0.828	1.00
188_R	197_E	0.828	1.00
155_A	158_A	0.827	1.00
84_V	88_L	0.827	1.00
85_A	110_A	0.824	1.00
129_R	149_S	0.818	1.00
15_L	82_G	0.816	0.99
84_V	110_A	0.811	0.99
27_G	42_L	0.809	0.99
34_G	107_F	0.804	0.99
174_G	178_D	0.804	0.99
57_Y	61_A	0.801	0.99
6_A	20_A	0.790	0.99
1_L	4_L	0.789	0.99
107_F	111_L	0.788	0.99
97_S	100_W	0.787	0.99
112_A	163_I	0.785	0.99
34_G	89_A	0.783	0.99
145_S	186_Q	0.779	0.99
150_L	154_L	0.774	0.99
78_V	82_G	0.769	0.99
214_W	219_A	0.766	0.99
147_G	179_S	0.766	0.99
60_K	63_L	0.766	0.99
171_G	178_D	0.764	0.99
57_Y	66_A	0.764	0.99
219_A	223_L	0.763	0.99
194_C	199_E	0.763	0.99
3_L	7_L	0.763	0.99
84_V	222_F	0.761	0.99
133_L	144_T	0.760	0.99
130_R	142_P	0.752	0.99
225_T	228_G	0.744	0.99
5_L	43_L	0.744	0.99
15_L	19_G	0.743	0.99
10_Y	20_A	0.742	0.99
14_S	54_R	0.742	0.99
26_V	82_G	0.740	0.99
110_A	225_T	0.738	0.99
22_A	78_V	0.733	0.99
49_S	52_L	0.732	0.99
133_L	147_G	0.732	0.99
159_G	163_I	0.729	0.99
46_F	77_Q	0.724	0.99
45_F	82_G	0.722	0.99
173_L	177_V	0.717	0.99
65_I	125_V	0.713	0.99
19_G	22_A	0.712	0.99
63_L	142_P	0.712	0.99
26_V	78_V	0.709	0.99
132_R	137_L	0.705	0.99
191_C	199_E	0.705	0.99
49_S	115_A	0.702	0.98
55_L	59_R	0.702	0.98
67_E	71_G	0.701	0.98
33_G	86_A	0.701	0.98
20_A	23_A	0.698	0.98
190_Y	193_V	0.696	0.98
64_G	67_E	0.696	0.98
92_Y	103_L	0.692	0.98
134_I	183_A	0.691	0.98
181_L	184_T	0.690	0.98
52_L	121_S	0.689	0.98
42_L	111_L	0.688	0.98
16_T	74_D	0.687	0.98
27_G	30_I	0.682	0.98
121_S	125_V	0.679	0.98
185_L	215_L	0.679	0.98
49_S	118_T	0.677	0.98
19_G	23_A	0.675	0.98
76_G	218_D	0.671	0.98
111_L	225_T	0.668	0.98
222_F	226_L	0.667	0.98
8_L	11_R	0.660	0.98
127_S	131_P	0.658	0.98
83_G	87_L	0.653	0.98
45_F	115_A	0.647	0.97
190_Y	194_C	0.646	0.97
190_Y	197_E	0.645	0.97
149_S	176_L	0.643	0.97
18_S	22_A	0.642	0.97
145_S	178_D	0.638	0.97
121_S	228_G	0.637	0.97
134_I	147_G	0.636	0.97
177_V	181_L	0.635	0.97
87_L	91_L	0.634	0.97
172_F	175_S	0.629	0.97
6_A	10_Y	0.628	0.97
121_S	145_S	0.624	0.97
66_A	69_K	0.623	0.97
132_R	136_T	0.622	0.97
136_T	183_A	0.622	0.97
81_N	174_G	0.619	0.97
38_W	92_Y	0.618	0.97
81_N	114_A	0.616	0.97
170_A	174_G	0.616	0.97
151_L	155_A	0.614	0.96
108_A	164_A	0.612	0.96
181_L	223_L	0.610	0.96
52_L	123_I	0.605	0.96
58_A	62_A	0.604	0.96
135_T	179_S	0.604	0.96
53_T	122_E	0.601	0.96
30_I	35_G	0.601	0.96
67_E	77_Q	0.598	0.96
91_L	103_L	0.597	0.96
92_Y	104_L	0.596	0.96
91_L	95_T	0.596	0.96
95_T	98_P	0.594	0.96
14_S	46_F	0.593	0.96
56_G	126_L	0.590	0.96
60_K	126_L	0.590	0.96
30_I	85_A	0.584	0.95
127_S	149_S	0.583	0.95
89_A	107_F	0.581	0.95
22_A	26_V	0.579	0.95
109_A	113_A	0.578	0.95
32_G	39_F	0.577	0.95
79_L	222_F	0.574	0.95
216_N	219_A	0.574	0.95
109_A	225_T	0.573	0.95
192_P	195_G	0.573	0.95
41_L	166_V	0.572	0.95
86_A	111_L	0.568	0.95
181_L	220_V	0.568	0.95
173_L	176_L	0.567	0.95
85_A	225_T	0.566	0.95
212_W	215_L	0.564	0.94
2_A	28_T	0.564	0.94
30_I	89_A	0.563	0.94
68_E	216_N	0.562	0.94
125_V	128_G	0.562	0.94
9_A	15_L	0.558	0.94
171_G	174_G	0.557	0.94
67_E	70_G	0.557	0.94
4_L	7_L	0.556	0.94
24_A	31_F	0.555	0.94
92_Y	95_T	0.555	0.94
53_T	74_D	0.554	0.94
38_W	43_L	0.552	0.94
148_V	176_L	0.552	0.94
77_Q	119_W	0.548	0.94
131_P	140_V	0.546	0.93
61_A	64_G	0.544	0.93
123_I	131_P	0.542	0.93
136_T	139_P	0.541	0.93
42_L	107_F	0.541	0.93
159_G	171_G	0.540	0.93
67_E	125_V	0.540	0.93
135_T	140_V	0.539	0.93
121_S	217_N	0.539	0.93
9_A	46_F	0.536	0.93
109_A	121_S	0.535	0.93
178_D	182_G	0.535	0.93
55_L	127_S	0.530	0.92
37_G	40_L	0.530	0.92
98_P	103_L	0.529	0.92
88_L	107_F	0.526	0.92
31_F	35_G	0.526	0.92
80_A	222_F	0.524	0.92
94_L	98_P	0.522	0.92
180_L	184_T	0.521	0.92
77_Q	218_D	0.521	0.92
29_L	90_L	0.519	0.92
76_G	186_Q	0.519	0.92
63_L	67_E	0.516	0.91
97_S	103_L	0.516	0.91
89_A	92_Y	0.515	0.91
30_I	86_A	0.515	0.91
114_A	145_S	0.513	0.91
46_F	82_G	0.512	0.91
18_S	74_D	0.509	0.91
26_V	42_L	0.508	0.91
97_S	102_L	0.507	0.91
76_G	79_L	0.507	0.91
92_Y	97_S	0.507	0.91
30_I	82_G	0.506	0.91
38_W	41_L	0.505	0.90
185_L	212_W	0.504	0.90
31_F	34_G	0.503	0.90
63_L	66_A	0.500	0.90
112_A	164_A	0.500	0.90

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
2xq2A	2	0.5348	76.3	0.937	Contact Map
4q2eA	2	0.8652	45.1	0.949	Contact Map
3dh4A	3	0.4304	40.8	0.95	Contact Map
3l1lA	2	0.3	26.5	0.955	Contact Map
1dlcA	1	0.3217	16.1	0.959	Contact Map
3qnqA	2	0.3174	10.2	0.962	Contact Map
4czbA	2	0.813	9.5	0.963	Contact Map
2jwaA	2	0.1913	9.5	0.963	Contact Map
2c9kA	1	0.3087	9.3	0.963	Contact Map
4w6vA	1	0.2609	9.3	0.963	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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