Transmemb_17 - PFAM28P - GREMLIN Contacts

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Transmemb_17 - Predicted membrane protein

PFAM:	PF09799	Sequences: MLLYFNGYYFPLYFLAELLLLIYKGQVLPYPDYYLALEVALLFLLLLLEAIRLYLGYKGNLTEKVPPLAGFLLLTLPSQLPLVYFLLWQTYVLPLEVILNAILLVFLV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	108 (107)
Sequences:	633 (467)
Seq/√Len:	45.1
META:	0.352

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_G	68_L	3.441	1.00
6_N	49_E	3.436	1.00
56_G	71_F	3.215	1.00
101_A	105_V	3.115	1.00
83_V	87_L	3.011	1.00
84_Y	89_Q	2.768	1.00
59_G	63_E	2.757	1.00
60_N	63_E	2.708	1.00
85_F	88_W	2.411	1.00
1_M	84_Y	1.985	0.99
97_V	101_A	1.873	0.99
61_L	103_L	1.836	0.99
3_L	56_G	1.744	0.98
42_L	46_L	1.705	0.98
6_N	52_R	1.640	0.97
54_Y	58_K	1.601	0.97
38_E	84_Y	1.571	0.96
21_L	43_F	1.571	0.96
96_E	100_N	1.533	0.96
82_L	103_L	1.522	0.96
55_L	74_L	1.471	0.95
36_A	40_A	1.469	0.95
13_Y	100_N	1.410	0.94
101_A	106_F	1.398	0.93
57_Y	61_L	1.381	0.93
46_L	85_F	1.361	0.92
93_L	96_E	1.344	0.92
19_L	42_L	1.333	0.91
87_L	99_L	1.278	0.90
71_F	75_T	1.208	0.87
49_E	52_R	1.203	0.87
49_E	61_L	1.194	0.86
88_W	92_V	1.192	0.86
3_L	7_G	1.189	0.86
30_Y	38_E	1.184	0.86
52_R	75_T	1.182	0.86
48_L	74_L	1.177	0.85
13_Y	42_L	1.173	0.85
38_E	92_V	1.155	0.84
53_L	96_E	1.115	0.82
98_I	102_I	1.114	0.82
4_Y	8_Y	1.098	0.81
10_F	20_L	1.085	0.80
24_K	89_Q	1.075	0.80
61_L	85_F	1.075	0.80
5_F	70_G	1.073	0.80
68_L	71_F	1.063	0.79
33_Y	73_L	1.042	0.77
48_L	107_L	1.037	0.77
9_Y	20_L	1.032	0.77
41_L	47_L	1.032	0.77
26_Q	47_L	1.030	0.77
75_T	107_L	1.028	0.76
24_K	93_L	1.028	0.76
34_Y	38_E	1.004	0.75
69_A	73_L	0.994	0.74
44_L	100_N	0.982	0.73
4_Y	10_F	0.977	0.73
16_A	99_L	0.959	0.71
51_I	57_Y	0.958	0.71
10_F	45_L	0.948	0.70
14_F	75_T	0.946	0.70
2_L	58_K	0.929	0.69
15_L	18_L	0.926	0.69
89_Q	92_V	0.918	0.68
52_R	71_F	0.912	0.67
39_V	46_L	0.899	0.66
86_L	104_L	0.897	0.66
6_N	61_L	0.893	0.66
22_I	85_F	0.887	0.65
8_Y	21_L	0.886	0.65
41_L	49_E	0.883	0.65
100_N	103_L	0.870	0.64
6_N	10_F	0.864	0.63
46_L	50_A	0.862	0.63
24_K	96_E	0.841	0.61
91_Y	97_V	0.832	0.60
22_I	34_Y	0.830	0.60
30_Y	68_L	0.818	0.59
75_T	85_F	0.793	0.57
31_P	90_T	0.791	0.56
48_L	79_Q	0.783	0.56
33_Y	46_L	0.783	0.56
6_N	64_K	0.774	0.55
2_L	74_L	0.766	0.54
6_N	9_Y	0.765	0.54
84_Y	92_V	0.764	0.54
4_Y	53_L	0.763	0.54
4_Y	106_F	0.763	0.54
18_L	22_I	0.755	0.53
12_L	76_L	0.755	0.53
61_L	82_L	0.751	0.53
8_Y	16_A	0.749	0.52
72_L	76_L	0.749	0.52
66_P	70_G	0.743	0.52
71_F	107_L	0.727	0.50
23_Y	93_L	0.726	0.50
4_Y	73_L	0.714	0.49
21_L	52_R	0.711	0.49
17_E	42_L	0.710	0.49
8_Y	22_I	0.709	0.48
41_L	73_L	0.708	0.48
13_Y	31_P	0.698	0.47
39_V	72_L	0.693	0.47
91_Y	98_I	0.676	0.45
41_L	85_F	0.672	0.45
92_V	105_V	0.663	0.44
35_L	77_P	0.663	0.44
3_L	76_L	0.663	0.44
87_L	90_T	0.662	0.44
37_L	51_I	0.658	0.44
3_L	73_L	0.656	0.43
17_E	21_L	0.653	0.43
74_L	77_P	0.652	0.43
55_L	70_G	0.651	0.43
32_D	69_A	0.648	0.43
23_Y	28_L	0.645	0.42
86_L	100_N	0.635	0.41
49_E	53_L	0.634	0.41
73_L	100_N	0.629	0.41
80_L	88_W	0.624	0.40
31_P	34_Y	0.622	0.40
22_I	98_I	0.620	0.40
11_P	49_E	0.617	0.40
39_V	43_F	0.614	0.39
16_A	23_Y	0.610	0.39
17_E	96_E	0.607	0.39
35_L	41_L	0.606	0.39
76_L	80_L	0.604	0.38
16_A	20_L	0.602	0.38
20_L	103_L	0.601	0.38
27_V	63_E	0.598	0.38
12_L	19_L	0.596	0.38
1_M	11_P	0.591	0.37
31_P	85_F	0.586	0.37
69_A	74_L	0.579	0.36
63_E	73_L	0.571	0.35
28_L	93_L	0.570	0.35
12_L	95_L	0.569	0.35
16_A	26_Q	0.565	0.35
32_D	102_I	0.564	0.35
66_P	75_T	0.562	0.35
13_Y	45_L	0.560	0.34
77_P	89_Q	0.558	0.34
65_V	78_S	0.557	0.34
14_F	43_F	0.548	0.33
45_L	104_L	0.546	0.33
12_L	70_G	0.545	0.33
19_L	76_L	0.534	0.32
48_L	92_V	0.526	0.32
61_L	65_V	0.522	0.31
5_F	78_S	0.509	0.30
12_L	32_D	0.507	0.30
2_L	11_P	0.507	0.30
10_F	103_L	0.503	0.30
18_L	70_G	0.503	0.30
7_G	11_P	0.503	0.30
45_L	78_S	0.502	0.30
37_L	44_L	0.502	0.30
71_F	94_P	0.500	0.29

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
4jq6A	3	0.4074	1.2	0.936	Contact Map
2rmgA	1	0.1667	1	0.938	Contact Map
4pypA	1	0.9444	1	0.939	Contact Map
1b9uA	1	0.3148	0.9	0.94	Contact Map
3wu2Y	1	0.1019	0.7	0.944	Contact Map
2h3oA	1	0.2407	0.7	0.944	Contact Map
2m67A	1	0.4815	0.7	0.945	Contact Map
4pgrA	1	0.5463	0.7	0.945	Contact Map
3wqjA	3	0.5	0.7	0.946	Contact Map
1g0yI	1	0.1944	0.6	0.947	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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