DUF2214 - PFAM28P - GREMLIN Contacts

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DUF2214 - Predicted membrane protein (DUF2214)

PFAM:	PF09980	Sequences: DALLAYLHHLAIFLLVGALAAEFVLLRPELDAAAARRLARADAVYGIAAGLVLVTGLLRVFFFEKGAAYYLHNPLFWAKMALFVLVGLLSIYPTVTFIRWRKALRAGAAPVPDAAEVRRLRRILHIELALLVLIPLLAALMARGIG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	146 (146)
Sequences:	4337 (2918)
Seq/√Len:	241.5
META:	0.91

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_L	62_F	3.093	1.00
77_W	81_A	2.868	1.00
67_A	71_L	2.728	1.00
6_Y	136_L	2.714	1.00
23_F	125_H	2.502	1.00
43_A	47_I	2.070	1.00
2_A	140_L	1.976	1.00
4_L	63_F	1.948	1.00
140_L	145_I	1.921	1.00
31_D	34_A	1.898	1.00
34_A	37_R	1.894	1.00
74_P	78_A	1.892	1.00
57_L	61_F	1.862	1.00
26_L	124_L	1.861	1.00
86_V	134_I	1.843	1.00
57_L	80_M	1.770	1.00
5_A	9_H	1.740	1.00
35_A	39_A	1.740	1.00
12_I	52_V	1.739	1.00
96_T	116_E	1.734	1.00
50_G	54_V	1.649	1.00
125_H	129_A	1.597	1.00
78_A	137_L	1.575	1.00
51_L	55_T	1.537	1.00
89_L	123_I	1.537	1.00
53_L	83_F	1.532	1.00
107_G	110_P	1.527	1.00
54_V	58_L	1.520	1.00
96_T	120_L	1.512	1.00
133_L	137_L	1.510	1.00
90_S	94_T	1.500	1.00
113_D	116_E	1.473	1.00
16_V	131_L	1.444	1.00
82_L	133_L	1.428	1.00
77_W	84_V	1.417	1.00
46_G	49_A	1.399	1.00
13_F	16_V	1.389	1.00
75_L	140_L	1.384	1.00
60_V	67_A	1.375	1.00
92_Y	119_R	1.369	1.00
92_Y	96_T	1.365	1.00
61_F	67_A	1.357	1.00
11_A	51_L	1.341	1.00
14_L	48_A	1.331	1.00
19_L	45_Y	1.319	1.00
5_A	59_R	1.317	1.00
20_A	24_V	1.313	1.00
10_L	132_V	1.304	1.00
7_L	55_T	1.282	1.00
88_L	91_I	1.279	1.00
45_Y	87_G	1.276	1.00
75_L	137_L	1.273	1.00
39_A	101_R	1.272	1.00
2_A	6_Y	1.259	1.00
112_P	117_V	1.243	1.00
21_A	41_A	1.225	1.00
122_R	126_I	1.217	1.00
17_G	21_A	1.208	1.00
94_T	98_I	1.202	1.00
40_R	43_A	1.201	1.00
38_L	97_F	1.199	1.00
96_T	99_R	1.195	1.00
121_R	125_H	1.187	1.00
17_G	20_A	1.171	1.00
103_A	108_A	1.165	1.00
77_W	80_M	1.164	1.00
98_I	101_R	1.151	1.00
9_H	55_T	1.150	1.00
92_Y	123_I	1.146	1.00
36_R	105_R	1.135	1.00
118_R	122_R	1.132	1.00
82_L	130_L	1.126	1.00
18_A	44_V	1.123	1.00
26_L	120_L	1.113	1.00
18_A	48_A	1.108	1.00
3_L	7_L	1.108	1.00
119_R	122_R	1.108	1.00
11_A	52_V	1.083	1.00
60_V	71_L	1.082	1.00
57_L	71_L	1.064	1.00
71_L	80_M	1.045	1.00
95_V	99_R	1.042	1.00
69_Y	74_P	1.040	1.00
76_F	80_M	1.035	1.00
82_L	137_L	1.012	1.00
114_A	118_R	1.012	1.00
102_K	106_A	0.991	1.00
136_L	140_L	0.986	1.00
9_H	13_F	0.976	1.00
83_F	134_I	0.965	1.00
11_A	55_T	0.951	1.00
9_H	12_I	0.949	1.00
60_V	66_G	0.940	1.00
92_Y	120_L	0.939	1.00
9_H	139_A	0.926	1.00
37_R	40_R	0.918	1.00
81_A	85_L	0.909	1.00
116_E	119_R	0.907	1.00
92_Y	95_V	0.903	1.00
46_G	50_G	0.902	1.00
13_F	17_G	0.896	1.00
47_I	50_G	0.891	1.00
21_A	24_V	0.882	0.99
87_G	90_S	0.880	0.99
88_L	92_Y	0.871	0.99
53_L	87_G	0.870	0.99
74_P	145_I	0.866	0.99
82_L	134_I	0.856	0.99
119_R	123_I	0.856	0.99
75_L	78_A	0.844	0.99
73_N	145_I	0.844	0.99
91_I	95_V	0.844	0.99
103_A	107_G	0.837	0.99
30_L	38_L	0.832	0.99
21_A	25_L	0.830	0.99
86_V	130_L	0.828	0.99
42_D	46_G	0.823	0.99
36_R	40_R	0.818	0.99
63_F	66_G	0.818	0.99
28_P	33_A	0.818	0.99
68_A	72_H	0.812	0.99
114_A	117_V	0.798	0.99
101_R	105_R	0.794	0.99
32_A	36_R	0.787	0.99
58_L	63_F	0.787	0.99
122_R	129_A	0.786	0.99
122_R	125_H	0.786	0.99
45_Y	127_E	0.786	0.99
30_L	34_A	0.785	0.99
43_A	46_G	0.782	0.99
45_Y	90_S	0.778	0.99
80_M	84_V	0.778	0.99
39_A	104_L	0.773	0.99
53_L	57_L	0.769	0.99
22_E	45_Y	0.760	0.98
38_L	41_A	0.758	0.98
68_A	71_L	0.754	0.98
2_A	145_I	0.746	0.98
128_L	132_V	0.742	0.98
78_A	82_L	0.740	0.98
29_E	114_A	0.738	0.98
131_L	135_P	0.730	0.98
39_A	98_I	0.726	0.98
15_L	52_V	0.724	0.98
48_A	52_V	0.714	0.98
12_I	15_L	0.708	0.98
71_L	77_W	0.707	0.98
6_Y	9_H	0.706	0.98
118_R	125_H	0.694	0.97
23_F	124_L	0.694	0.97
125_H	128_L	0.693	0.97
115_A	119_R	0.691	0.97
33_A	37_R	0.687	0.97
34_A	38_L	0.685	0.97
52_V	134_I	0.682	0.97
99_R	102_K	0.679	0.97
1_D	4_L	0.676	0.97
6_Y	10_L	0.673	0.97
139_A	143_R	0.668	0.97
130_L	135_P	0.661	0.96
131_L	134_I	0.653	0.96
132_V	135_P	0.648	0.96
27_R	34_A	0.631	0.95
4_L	58_L	0.630	0.95
70_Y	142_A	0.630	0.95
22_E	97_F	0.625	0.95
2_A	5_A	0.622	0.95
74_P	77_W	0.618	0.95
44_V	47_I	0.617	0.95
14_L	44_V	0.614	0.95
16_V	24_V	0.613	0.94
52_V	131_L	0.610	0.94
6_Y	135_P	0.609	0.94
12_I	16_V	0.608	0.94
18_A	41_A	0.607	0.94
1_D	63_F	0.597	0.94
115_A	118_R	0.592	0.93
40_R	44_V	0.591	0.93
117_V	124_L	0.587	0.93
11_A	14_L	0.583	0.93
83_F	87_G	0.583	0.93
76_F	141_M	0.580	0.93
42_D	59_R	0.572	0.92
28_P	31_D	0.568	0.92
61_F	71_L	0.567	0.92
16_V	20_A	0.567	0.92
19_L	22_E	0.567	0.92
54_V	62_F	0.565	0.92
129_A	133_L	0.559	0.91
84_V	87_G	0.559	0.91
65_K	69_Y	0.558	0.91
54_V	57_L	0.558	0.91
23_F	128_L	0.557	0.91
35_A	97_F	0.556	0.91
127_E	132_V	0.555	0.91
75_L	145_I	0.554	0.91
110_P	113_D	0.552	0.91
138_A	143_R	0.549	0.91
95_V	102_K	0.548	0.90
86_V	93_P	0.546	0.90
15_L	48_A	0.545	0.90
60_V	80_M	0.544	0.90
90_S	93_P	0.543	0.90
1_D	64_E	0.535	0.89
23_F	129_A	0.534	0.89
36_R	104_L	0.530	0.89
120_L	123_I	0.529	0.89
84_V	88_L	0.527	0.89
95_V	98_I	0.525	0.89
59_R	100_W	0.522	0.88
89_L	93_P	0.522	0.88
138_A	141_M	0.521	0.88
73_N	146_G	0.519	0.88
42_D	49_A	0.517	0.88
57_L	60_V	0.513	0.87
3_L	136_L	0.510	0.87
133_L	136_L	0.507	0.87
103_A	109_A	0.503	0.86
43_A	98_I	0.500	0.86

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
1fftB	1	0.5479	9.4	0.916	Contact Map
4dx5A	3	0.8699	4.5	0.928	Contact Map
3ne5A	3	0.8767	3.6	0.931	Contact Map
4k0jA	3	0.8288	3.5	0.932	Contact Map
4mt1A	3	0.9041	3	0.934	Contact Map
3w9iA	3	0.8699	2.8	0.935	Contact Map
1q16C	2	0.774	2.7	0.935	Contact Map
4humA	1	0.7945	2.3	0.938	Contact Map
4k1cA	4	0.8699	2.1	0.939	Contact Map
4lz6A	1	0.8082	1.9	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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