DUF2069 - PFAM28P - GREMLIN Contacts

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DUF2069 - Predicted membrane protein (DUF2069)

PFAM:	PF09842	Sequences: LALASLLALIALCLAWELWLAPLRGAPGGSWLALKVLPLLLPLPGLLRGRRYTYQWASLLVLLYFAEGVVRAWSDPGSRLLALLEVALSLLLFAAAVLYVRLRQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	104 (100)
Sequences:	5636 (3534)
Seq/√Len:	353.4
META:	0.876

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_A	92_L	3.625	1.00
44_P	48_R	3.077	1.00
5_S	91_L	2.658	1.00
45_G	53_T	2.526	1.00
13_C	36_V	2.499	1.00
72_A	83_L	2.487	1.00
61_V	92_L	2.295	1.00
51_R	103_R	1.926	1.00
67_E	85_E	1.896	1.00
68_G	86_V	1.828	1.00
80_L	83_L	1.778	1.00
15_A	20_L	1.749	1.00
66_A	70_V	1.724	1.00
65_F	69_V	1.668	1.00
72_A	86_V	1.659	1.00
5_S	95_A	1.615	1.00
51_R	55_Q	1.614	1.00
65_F	89_S	1.569	1.00
76_P	79_R	1.562	1.00
51_R	100_V	1.552	1.00
12_L	84_L	1.550	1.00
38_P	64_Y	1.463	1.00
94_A	98_L	1.425	1.00
75_D	78_S	1.415	1.00
71_R	75_D	1.398	1.00
65_F	86_V	1.271	1.00
40_L	44_P	1.260	1.00
42_P	57_A	1.256	1.00
55_Q	59_L	1.247	1.00
6_L	46_L	1.235	1.00
29_G	32_L	1.223	1.00
18_L	33_A	1.214	1.00
50_R	53_T	1.204	1.00
59_L	62_L	1.196	1.00
3_L	46_L	1.171	1.00
3_L	7_L	1.160	1.00
49_G	99_Y	1.145	1.00
68_G	89_S	1.144	1.00
80_L	84_L	1.139	1.00
79_R	83_L	1.104	1.00
66_A	69_V	1.100	1.00
69_V	86_V	1.081	1.00
71_R	82_A	1.080	1.00
68_G	85_E	1.066	1.00
17_E	35_K	1.049	1.00
83_L	87_A	1.041	1.00
92_L	96_A	1.033	1.00
8_A	88_L	1.009	1.00
14_L	36_V	1.008	1.00
58_S	96_A	1.008	1.00
30_S	33_A	1.002	1.00
41_L	44_P	1.000	1.00
93_F	97_V	0.991	1.00
7_L	11_A	0.978	1.00
46_L	54_Y	0.976	1.00
74_S	77_G	0.959	1.00
52_Y	55_Q	0.956	1.00
14_L	18_L	0.947	1.00
46_L	92_L	0.935	1.00
52_Y	56_W	0.929	1.00
82_A	86_V	0.928	1.00
4_A	8_A	0.927	1.00
83_L	86_V	0.926	1.00
35_K	67_E	0.918	1.00
54_Y	99_Y	0.907	1.00
28_G	32_L	0.905	1.00
42_P	60_L	0.903	1.00
75_D	79_R	0.892	1.00
81_L	85_E	0.891	1.00
61_V	89_S	0.876	1.00
3_L	47_L	0.869	1.00
91_L	95_A	0.864	1.00
39_L	42_P	0.863	1.00
45_G	50_R	0.854	1.00
5_S	92_L	0.844	1.00
55_Q	100_V	0.844	1.00
95_A	98_L	0.839	1.00
68_G	82_A	0.832	1.00
97_V	102_L	0.829	1.00
42_P	53_T	0.827	1.00
49_G	54_Y	0.822	1.00
44_P	50_R	0.822	1.00
90_L	94_A	0.821	1.00
53_T	56_W	0.818	1.00
98_L	102_L	0.813	1.00
67_E	71_R	0.809	1.00
84_L	88_L	0.805	1.00
16_W	22_P	0.799	1.00
70_V	73_W	0.798	1.00
42_P	52_Y	0.797	1.00
12_L	81_L	0.786	1.00
24_R	30_S	0.785	1.00
13_C	16_W	0.775	1.00
58_S	97_V	0.753	1.00
97_V	100_V	0.752	1.00
60_L	64_Y	0.750	1.00
59_L	100_V	0.735	1.00
13_C	17_E	0.726	0.99
24_R	27_P	0.722	0.99
35_K	71_R	0.721	0.99
20_L	81_L	0.716	0.99
27_P	30_S	0.711	0.99
6_L	92_L	0.710	0.99
74_S	79_R	0.700	0.99
23_L	28_G	0.698	0.99
33_A	37_L	0.687	0.99
62_L	65_F	0.685	0.99
7_L	43_L	0.685	0.99
10_I	36_V	0.680	0.99
24_R	28_G	0.679	0.99
69_V	73_W	0.676	0.99
50_R	54_Y	0.675	0.99
86_V	89_S	0.666	0.99
17_E	20_L	0.666	0.99
19_W	22_P	0.666	0.99
46_L	53_T	0.650	0.99
72_A	82_A	0.649	0.99
16_W	20_L	0.645	0.99
62_L	97_V	0.641	0.99
28_G	31_W	0.634	0.99
12_L	20_L	0.634	0.99
98_L	101_R	0.632	0.99
65_F	73_W	0.622	0.98
33_A	44_P	0.616	0.98
17_E	67_E	0.592	0.98
12_L	88_L	0.585	0.98
71_R	74_S	0.583	0.98
58_S	61_V	0.577	0.97
15_A	19_W	0.575	0.97
6_L	43_L	0.574	0.97
65_F	90_L	0.573	0.97
61_V	96_A	0.573	0.97
7_L	47_L	0.564	0.97
61_V	93_F	0.560	0.97
49_G	103_R	0.552	0.97
21_A	24_R	0.546	0.96
23_L	30_S	0.545	0.96
93_F	96_A	0.542	0.96
77_G	80_L	0.536	0.96
70_V	74_S	0.533	0.96
7_L	10_I	0.530	0.96
37_L	40_L	0.530	0.96
6_L	13_C	0.528	0.96
10_I	40_L	0.518	0.95
11_A	14_L	0.515	0.95
85_E	88_L	0.513	0.95
92_L	99_Y	0.512	0.95
96_A	102_L	0.503	0.94
10_I	13_C	0.500	0.94
62_L	66_A	0.500	0.94

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
4p02A	1	0.4615	2.1	0.92	Contact Map
4ryoA	1	0.7596	1.3	0.93	Contact Map
4qncA	2	0.7019	1.3	0.93	Contact Map
4i5sA	2	0.0769	1.2	0.931	Contact Map
3giaA	1	0.9231	1.2	0.931	Contact Map
2m20A	2	0.2885	1.1	0.933	Contact Map
2h8aA	3	0.2885	1.1	0.933	Contact Map
4il3A	1	0.2981	1	0.935	Contact Map
1m56C	2	0.375	1	0.936	Contact Map
4al0A	3	0.3173	0.9	0.936	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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