DUF2157 - PFAM28P - GREMLIN Contacts

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DUF2157 - Predicted membrane protein (DUF2157)

PFAM:	PF09925	Sequences: ERWVEAGLISAEQAERILALYRARPSSSARRRRLLRILLYLGALLLGAGVILFVAANWDELGRLARLALLLALLLAAYAAGALLRRRRRRSPALGEALLLLGALLFGAGIALIGQIYHLGGDWPDLFLLWALLALPLAYLLRSRLLW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	147 (141)
Sequences:	7989 (6160)
Seq/√Len:	518.7
META:	0.891

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
103_A	134_A	3.869	1.00
10_S	13_Q	3.377	1.00
6_A	20_L	3.270	1.00
4_V	14_A	2.976	1.00
70_L	109_G	2.807	1.00
4_V	11_A	2.730	1.00
62_G	65_A	2.568	1.00
11_A	15_E	2.555	1.00
107_G	130_W	2.172	1.00
106_F	133_L	2.130	1.00
15_E	19_A	2.097	1.00
50_V	105_L	1.955	1.00
2_R	6_A	1.943	1.00
47_G	104_L	1.875	1.00
82_A	86_R	1.865	1.00
43_A	97_A	1.846	1.00
77_A	101_L	1.785	1.00
73_L	105_L	1.767	1.00
80_A	98_L	1.753	1.00
106_F	134_A	1.735	1.00
31_R	34_L	1.722	1.00
83_L	86_R	1.673	1.00
51_I	108_A	1.659	1.00
13_Q	16_R	1.625	1.00
121_G	126_L	1.616	1.00
14_A	18_L	1.591	1.00
17_I	20_L	1.588	1.00
99_L	141_L	1.586	1.00
81_G	102_G	1.556	1.00
79_A	83_L	1.538	1.00
77_A	105_L	1.524	1.00
26_S	29_A	1.479	1.00
67_L	113_I	1.454	1.00
8_L	13_Q	1.388	1.00
78_Y	102_G	1.384	1.00
61_L	65_A	1.378	1.00
77_A	102_G	1.361	1.00
124_P	127_F	1.358	1.00
43_A	101_L	1.346	1.00
12_E	15_E	1.337	1.00
123_W	127_F	1.332	1.00
115_Q	118_H	1.327	1.00
16_R	19_A	1.313	1.00
15_E	18_L	1.305	1.00
36_R	40_Y	1.275	1.00
9_I	13_Q	1.272	1.00
47_G	51_I	1.264	1.00
58_W	66_R	1.251	1.00
74_L	78_Y	1.235	1.00
51_I	54_V	1.234	1.00
112_L	116_I	1.220	1.00
57_N	115_Q	1.207	1.00
67_L	71_L	1.201	1.00
96_E	143_S	1.201	1.00
123_W	126_L	1.185	1.00
10_S	16_R	1.168	1.00
114_G	121_G	1.158	1.00
70_L	73_L	1.157	1.00
74_L	109_G	1.156	1.00
94_L	98_L	1.136	1.00
66_R	116_I	1.125	1.00
110_I	126_L	1.118	1.00
63_R	117_Y	1.108	1.00
12_E	16_R	1.096	1.00
20_L	24_R	1.085	1.00
64_L	68_A	1.073	1.00
71_L	109_G	1.072	1.00
93_A	97_A	1.059	1.00
57_N	61_L	1.058	1.00
111_A	115_Q	1.048	1.00
128_L	131_A	1.042	1.00
39_L	97_A	1.040	1.00
137_L	140_L	1.034	1.00
78_Y	99_L	1.031	1.00
78_Y	81_G	1.022	1.00
74_L	77_A	1.021	1.00
60_E	63_R	1.021	1.00
81_G	141_L	0.997	1.00
3_W	8_L	0.994	1.00
120_G	125_D	0.974	1.00
2_R	20_L	0.965	1.00
63_R	116_I	0.956	1.00
84_L	95_G	0.952	1.00
77_A	98_L	0.942	1.00
65_A	68_A	0.942	1.00
74_L	105_L	0.905	1.00
17_I	21_Y	0.896	1.00
122_D	127_F	0.892	1.00
120_G	123_W	0.885	1.00
124_P	128_L	0.877	1.00
120_G	124_P	0.877	1.00
4_V	18_L	0.869	1.00
133_L	136_P	0.865	1.00
11_A	14_A	0.859	1.00
82_A	85_R	0.856	1.00
98_L	102_G	0.845	1.00
61_L	73_L	0.843	1.00
81_G	99_L	0.831	1.00
86_R	89_R	0.830	1.00
13_Q	17_I	0.828	1.00
108_A	112_L	0.824	1.00
114_G	120_G	0.822	1.00
54_V	57_N	0.807	1.00
43_A	47_G	0.804	1.00
52_L	56_A	0.800	1.00
55_A	115_Q	0.796	1.00
126_L	130_W	0.792	1.00
125_D	128_L	0.788	1.00
122_D	125_D	0.783	1.00
140_L	143_S	0.781	1.00
22_R	25_P	0.776	1.00
37_I	42_G	0.770	1.00
91_S	94_L	0.765	1.00
39_L	43_A	0.764	1.00
95_G	102_G	0.763	1.00
125_D	129_L	0.762	1.00
92_P	96_E	0.761	1.00
68_A	72_A	0.759	1.00
79_A	82_A	0.757	1.00
9_I	14_A	0.755	1.00
103_A	137_L	0.755	1.00
135_L	138_A	0.753	1.00
110_I	121_G	0.746	1.00
8_L	21_Y	0.744	1.00
50_V	54_V	0.742	1.00
73_L	77_A	0.714	1.00
126_L	133_L	0.711	1.00
57_N	60_E	0.706	1.00
23_A	26_S	0.705	1.00
21_Y	24_R	0.704	1.00
92_P	95_G	0.703	1.00
109_G	113_I	0.702	1.00
130_W	134_A	0.701	1.00
35_L	39_L	0.693	1.00
69_L	72_A	0.689	1.00
114_G	126_L	0.688	1.00
8_L	20_L	0.687	1.00
52_L	55_A	0.685	1.00
111_A	114_G	0.680	1.00
19_A	23_A	0.679	1.00
67_L	109_G	0.677	1.00
118_H	121_G	0.677	1.00
69_L	73_L	0.669	1.00
22_R	26_S	0.662	1.00
121_G	125_D	0.660	1.00
85_R	96_E	0.658	1.00
135_L	139_Y	0.651	1.00
47_G	101_L	0.649	1.00
80_A	83_L	0.647	1.00
47_G	97_A	0.641	1.00
104_L	108_A	0.636	1.00
16_R	20_L	0.631	1.00
121_G	124_P	0.630	1.00
93_A	96_E	0.629	1.00
3_W	21_Y	0.626	1.00
57_N	117_Y	0.624	1.00
70_L	116_I	0.623	1.00
131_A	135_L	0.617	1.00
54_V	108_A	0.616	1.00
2_R	5_E	0.611	1.00
129_L	132_L	0.611	1.00
37_I	41_L	0.609	1.00
48_A	51_I	0.608	1.00
94_L	97_A	0.606	1.00
24_R	29_A	0.604	1.00
75_L	79_A	0.604	1.00
122_D	126_L	0.601	1.00
81_G	95_G	0.600	1.00
18_L	26_S	0.599	0.99
99_L	103_A	0.598	0.99
6_A	17_I	0.593	0.99
95_G	99_L	0.590	0.99
128_L	132_L	0.587	0.99
76_A	80_A	0.580	0.99
49_G	56_A	0.577	0.99
132_L	136_P	0.576	0.99
136_P	140_L	0.572	0.99
44_L	100_L	0.570	0.99
70_L	74_L	0.568	0.99
58_W	115_Q	0.566	0.99
3_W	9_I	0.557	0.99
22_R	27_S	0.556	0.99
103_A	107_G	0.555	0.99
66_R	70_L	0.553	0.99
18_L	22_R	0.552	0.99
80_A	84_L	0.552	0.99
40_Y	47_G	0.551	0.99
42_G	46_L	0.551	0.99
4_V	13_Q	0.550	0.99
85_R	95_G	0.546	0.99
19_A	22_R	0.543	0.99
76_A	79_A	0.543	0.99
36_R	101_L	0.542	0.99
61_L	69_L	0.542	0.99
70_L	112_L	0.541	0.99
106_F	113_I	0.539	0.99
71_L	113_I	0.536	0.99
26_S	34_L	0.535	0.99
8_L	16_R	0.523	0.99
40_Y	44_L	0.518	0.99
119_L	125_D	0.517	0.99
47_G	108_A	0.515	0.98
111_A	126_L	0.512	0.98
23_A	33_R	0.508	0.98
3_W	17_I	0.508	0.98
120_G	127_F	0.507	0.98
114_G	125_D	0.506	0.98
106_F	109_G	0.505	0.98
99_L	102_G	0.504	0.98
24_R	32_R	0.503	0.98
78_Y	137_L	0.502	0.98
100_L	143_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
4ev6A	3	0.5986	19.1	0.886	Contact Map
4pgrA	1	0.7687	16.4	0.89	Contact Map
4i0uA	4	0.585	14.4	0.892	Contact Map
2xf7A	3	0.1769	13.5	0.894	Contact Map
3pjzA	2	0.7891	12.6	0.895	Contact Map
2vakA	2	0.449	9.6	0.901	Contact Map
2nn4A	1	0.1905	8.1	0.904	Contact Map
4qinA	2	0.7551	8.1	0.904	Contact Map
4ikvA	1	0.8503	7	0.906	Contact Map
4bqqA	2	0.3333	6.3	0.909	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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