DUF3661 - PFAM28P - GREMLIN Contacts

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DUF3661 - Vaculolar membrane protein

PFAM:	PF12400	Sequences: CSWYFLNFLIDTTLGVPILYLLLRLLTRLASKTPLPESIESGNYGDPPSAKWWLKQLLIYLLILLLMKLIVLLLLLLFPWPLAWVGDWLLSWTEGNPKLELVFVMLIFPLIMNALQFWIIDSFLKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	126 (125)
Sequences:	576 (435)
Seq/√Len:	38.9
META:	0.431

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
45_G	48_P	4.553	1.00
1_C	4_Y	2.870	1.00
19_L	60_Y	2.843	1.00
115_L	119_I	2.770	1.00
93_T	96_N	2.595	1.00
101_L	106_L	2.540	1.00
60_Y	63_I	2.419	1.00
68_K	90_L	2.418	1.00
53_W	57_L	2.321	1.00
16_V	112_M	2.210	0.99
102_V	107_I	2.141	0.99
40_E	43_N	2.111	0.99
60_Y	64_L	2.006	0.99
5_F	108_F	1.957	0.99
12_T	112_M	1.868	0.98
19_L	120_I	1.793	0.97
84_W	102_V	1.742	0.97
42_G	56_Q	1.623	0.95
18_I	32_K	1.559	0.94
104_V	109_P	1.536	0.94
60_Y	120_I	1.526	0.94
14_L	21_L	1.525	0.94
7_N	86_G	1.524	0.94
69_L	73_L	1.504	0.93
14_L	40_E	1.485	0.93
7_N	68_K	1.485	0.93
118_W	122_S	1.480	0.93
109_P	113_N	1.463	0.92
41_S	82_L	1.459	0.92
120_I	124_L	1.348	0.88
59_I	123_F	1.344	0.88
112_M	116_Q	1.336	0.88
102_V	125_K	1.326	0.88
103_F	108_F	1.320	0.87
8_F	16_V	1.296	0.86
121_D	125_K	1.282	0.86
25_L	32_K	1.268	0.85
118_W	124_L	1.263	0.85
23_L	63_I	1.252	0.84
2_S	90_L	1.248	0.84
76_L	85_V	1.238	0.84
57_L	61_L	1.238	0.84
47_P	60_Y	1.207	0.82
29_L	46_D	1.192	0.81
107_I	111_I	1.173	0.80
6_L	86_G	1.159	0.79
54_L	57_L	1.155	0.79
43_N	46_D	1.153	0.79
21_L	24_R	1.150	0.79
2_S	86_G	1.137	0.78
38_S	90_L	1.133	0.78
70_I	89_L	1.114	0.77
44_Y	56_Q	1.102	0.76
27_T	69_L	1.092	0.75
60_Y	106_L	1.083	0.75
25_L	54_L	1.075	0.74
121_D	124_L	1.075	0.74
120_I	123_F	1.073	0.74
22_L	119_I	1.071	0.74
78_F	81_P	1.058	0.73
4_Y	121_D	1.036	0.71
68_K	100_E	1.020	0.70
29_L	33_T	1.019	0.70
68_K	105_M	1.009	0.69
28_R	32_K	1.006	0.69
65_L	111_I	1.005	0.69
106_L	110_L	1.004	0.69
46_D	54_L	1.004	0.69
57_L	60_Y	0.986	0.67
59_I	114_A	0.985	0.67
59_I	110_L	0.981	0.67
3_W	36_P	0.975	0.67
1_C	11_D	0.972	0.66
90_L	100_E	0.969	0.66
53_W	56_Q	0.967	0.66
2_S	10_I	0.959	0.65
19_L	124_L	0.923	0.62
32_K	58_L	0.915	0.62
53_W	105_M	0.910	0.61
15_G	68_K	0.908	0.61
22_L	63_I	0.906	0.61
66_L	70_I	0.901	0.60
11_D	15_G	0.892	0.60
104_V	111_I	0.891	0.59
58_L	124_L	0.882	0.59
16_V	116_Q	0.881	0.59
33_T	61_L	0.878	0.58
52_W	97_P	0.874	0.58
40_E	94_E	0.861	0.57
101_L	105_M	0.846	0.56
60_Y	101_L	0.839	0.55
68_K	71_V	0.828	0.54
21_L	111_I	0.824	0.54
51_K	54_L	0.822	0.53
23_L	67_M	0.814	0.53
62_L	70_I	0.812	0.52
12_T	16_V	0.810	0.52
4_Y	15_G	0.806	0.52
30_A	39_I	0.796	0.51
12_T	116_Q	0.792	0.51
55_K	116_Q	0.769	0.49
87_D	93_T	0.762	0.48
53_W	125_K	0.760	0.48
47_P	100_E	0.758	0.48
20_Y	83_A	0.755	0.47
21_L	28_R	0.754	0.47
116_Q	125_K	0.745	0.46
25_L	51_K	0.740	0.46
42_G	82_L	0.736	0.46
53_W	123_F	0.735	0.46
114_A	117_F	0.727	0.45
119_I	123_F	0.727	0.45
85_V	88_W	0.724	0.45
118_W	121_D	0.722	0.44
33_T	51_K	0.716	0.44
32_K	66_L	0.715	0.44
11_D	14_L	0.714	0.44
76_L	79_P	0.714	0.44
49_S	115_L	0.714	0.44
80_W	85_V	0.714	0.44
80_W	93_T	0.712	0.43
22_L	62_L	0.712	0.43
53_W	117_F	0.699	0.42
61_L	123_F	0.699	0.42
62_L	80_W	0.691	0.42
70_I	74_L	0.690	0.42
118_W	125_K	0.686	0.41
106_L	124_L	0.681	0.41
18_I	51_K	0.679	0.41
2_S	5_F	0.678	0.40
31_S	87_D	0.664	0.39
22_L	66_L	0.661	0.39
8_F	100_E	0.657	0.39
21_L	102_V	0.652	0.38
21_L	84_W	0.651	0.38
30_A	82_L	0.648	0.38
106_L	120_I	0.648	0.38
26_L	41_S	0.644	0.38
14_L	66_L	0.635	0.37
37_E	55_K	0.635	0.37
36_P	39_I	0.634	0.37
116_Q	120_I	0.632	0.37
36_P	123_F	0.625	0.36
9_L	18_I	0.620	0.36
39_I	90_L	0.618	0.35
13_T	125_K	0.616	0.35
13_T	18_I	0.614	0.35
54_L	66_L	0.610	0.35
7_N	90_L	0.610	0.35
107_I	115_L	0.608	0.35
81_P	100_E	0.608	0.35
81_P	89_L	0.605	0.34
24_R	70_I	0.603	0.34
101_L	113_N	0.603	0.34
77_L	84_W	0.602	0.34
71_V	79_P	0.601	0.34
64_L	71_V	0.586	0.33
19_L	47_P	0.584	0.33
64_L	108_F	0.583	0.33
20_Y	98_K	0.581	0.32
26_L	50_A	0.574	0.32
30_A	75_L	0.574	0.32
54_L	58_L	0.574	0.32
68_K	120_I	0.564	0.31
38_S	52_W	0.563	0.31
81_P	85_V	0.557	0.31
20_Y	85_V	0.553	0.30
78_F	102_V	0.550	0.30
33_T	37_E	0.548	0.30
85_V	111_I	0.542	0.29
32_K	114_A	0.534	0.29
38_S	89_L	0.533	0.29
109_P	121_D	0.533	0.29
72_L	78_F	0.528	0.28
81_P	88_W	0.527	0.28
73_L	99_L	0.525	0.28
26_L	62_L	0.524	0.28
10_I	29_L	0.524	0.28
89_L	123_F	0.523	0.28
7_N	64_L	0.520	0.28
51_K	77_L	0.516	0.27
12_T	108_F	0.516	0.27
115_L	125_K	0.511	0.27
21_L	62_L	0.508	0.27
68_K	122_S	0.506	0.27
64_L	102_V	0.506	0.27
9_L	101_L	0.502	0.26
28_R	115_L	0.500	0.26

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
1vjeA	2	0.254	2.4	0.95	Contact Map
3al9A	2	0.2857	1.4	0.956	Contact Map
2kv5A	1	0.2143	1	0.96	Contact Map
4il3A	1	0.8016	0.9	0.961	Contact Map
3zo5A	1	0.3333	0.9	0.961	Contact Map
2xphA	1	0.3333	0.8	0.962	Contact Map
4k5yA	1	0.9127	0.8	0.962	Contact Map
1euvA	1	0.3333	0.8	0.963	Contact Map
3r15A	1	0.1429	0.7	0.964	Contact Map
1b3tA	2	0.3413	0.6	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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