DUF389 - PFAM28P - GREMLIN Contacts

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DUF389 - Domain of unknown function (DUF389)

PFAM:	PF04087	Sequences: MLIAPLMGPILGLGLGLVLGDRRLLRRSLKTLLVGVLLAIAVSALLGLLLPLGPPALLEAPTSEILARTSPTLLDLLVALAAGAAGALALTRKKSSALPGVAIAVALVPPLATAGIGLALGNWSLALGALLLFLTNLVAIVL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	142 (138)
Sequences:	11742 (7213)
Seq/√Len:	614.0
META:	0.874

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_G	25_L	3.796	1.00
36_V	133_F	3.037	1.00
40_I	114_A	3.029	1.00
114_A	130_L	2.964	1.00
117_G	125_L	2.704	1.00
47_G	116_I	2.625	1.00
44_A	118_L	2.369	1.00
65_I	113_T	2.265	1.00
44_A	48_L	2.264	1.00
114_A	126_A	2.246	1.00
26_R	30_K	2.243	1.00
118_L	126_A	2.220	1.00
30_K	34_V	2.204	1.00
13_L	25_L	2.123	1.00
122_N	125_L	2.122	1.00
40_I	111_L	2.075	1.00
23_R	27_R	2.033	1.00
22_R	26_R	1.998	1.00
113_T	117_G	1.993	1.00
64_E	68_R	1.984	1.00
44_A	119_A	1.944	1.00
66_L	69_T	1.910	1.00
62_T	65_I	1.867	1.00
16_G	24_L	1.773	1.00
111_L	133_F	1.707	1.00
82_A	105_V	1.640	1.00
43_S	112_A	1.580	1.00
36_V	111_L	1.562	1.00
76_L	139_A	1.545	1.00
130_L	134_L	1.530	1.00
27_R	30_K	1.528	1.00
33_L	37_L	1.478	1.00
16_G	28_S	1.431	1.00
12_G	28_S	1.403	1.00
46_L	50_L	1.402	1.00
96_S	99_P	1.394	1.00
123_W	127_L	1.358	1.00
133_F	137_L	1.355	1.00
131_L	135_T	1.354	1.00
113_T	129_A	1.344	1.00
39_A	108_V	1.306	1.00
118_L	123_W	1.273	1.00
124_S	127_L	1.270	1.00
126_A	130_L	1.260	1.00
15_L	19_L	1.256	1.00
31_T	35_G	1.231	1.00
117_G	126_A	1.224	1.00
63_S	67_A	1.220	1.00
73_L	77_L	1.205	1.00
3_I	97_A	1.204	1.00
127_L	131_L	1.197	1.00
47_G	119_A	1.185	1.00
23_R	26_R	1.182	1.00
37_L	41_A	1.159	1.00
13_L	32_L	1.147	1.00
58_L	61_P	1.139	1.00
13_L	29_L	1.130	1.00
108_V	112_A	1.122	1.00
21_D	24_L	1.119	1.00
127_L	130_L	1.114	1.00
86_G	101_V	1.101	1.00
114_A	129_A	1.097	1.00
40_I	118_L	1.094	1.00
59_E	62_T	1.086	1.00
32_L	137_L	1.070	1.00
95_S	99_P	1.039	1.00
22_R	27_R	1.035	1.00
68_R	132_L	1.028	1.00
48_L	119_A	1.024	1.00
76_L	135_T	1.021	1.00
64_E	67_A	1.018	1.00
23_R	30_K	1.009	1.00
41_A	45_L	0.979	1.00
40_I	44_A	0.973	1.00
80_L	84_A	0.965	1.00
135_T	140_I	0.959	1.00
65_I	117_G	0.958	1.00
34_V	37_L	0.934	1.00
123_W	126_A	0.918	1.00
80_L	139_A	0.916	1.00
2_L	7_M	0.916	1.00
138_V	141_V	0.913	1.00
13_L	28_S	0.891	1.00
7_M	11_L	0.883	1.00
4_A	107_L	0.869	1.00
41_A	44_A	0.866	1.00
115_G	119_A	0.865	1.00
10_I	141_V	0.859	1.00
13_L	141_V	0.849	1.00
29_L	33_L	0.840	1.00
106_A	109_P	0.835	1.00
74_L	77_L	0.830	1.00
65_I	68_R	0.823	1.00
87_A	91_T	0.819	1.00
69_T	117_G	0.809	1.00
88_L	92_R	0.809	1.00
79_A	136_N	0.809	1.00
131_L	134_L	0.808	1.00
134_L	138_V	0.806	1.00
71_P	75_D	0.796	1.00
74_L	78_V	0.793	1.00
80_L	83_G	0.790	1.00
4_A	102_A	0.790	1.00
43_S	115_G	0.785	1.00
8_G	11_L	0.764	1.00
14_G	141_V	0.756	1.00
114_A	117_G	0.751	1.00
121_G	124_S	0.751	1.00
100_G	109_P	0.751	1.00
65_I	125_L	0.745	1.00
45_L	48_L	0.745	1.00
75_D	135_T	0.736	1.00
90_L	99_P	0.736	1.00
40_I	115_G	0.734	1.00
66_L	70_S	0.727	1.00
17_L	141_V	0.721	1.00
116_I	120_L	0.721	1.00
50_L	53_G	0.719	1.00
68_R	106_A	0.715	1.00
43_S	47_G	0.714	1.00
61_P	65_I	0.711	1.00
63_S	66_L	0.707	1.00
40_I	43_S	0.707	1.00
15_L	21_D	0.707	1.00
79_A	82_A	0.706	1.00
7_M	102_A	0.702	1.00
50_L	74_L	0.698	1.00
71_P	128_G	0.688	1.00
58_L	63_S	0.686	1.00
6_L	10_I	0.684	1.00
67_A	75_D	0.681	1.00
11_L	90_L	0.681	1.00
76_L	80_L	0.673	1.00
27_R	31_T	0.669	1.00
45_L	49_L	0.658	1.00
103_I	108_V	0.656	1.00
53_G	59_E	0.649	1.00
78_V	82_A	0.647	1.00
48_L	51_P	0.637	1.00
68_R	107_L	0.636	1.00
128_G	132_L	0.633	1.00
4_A	7_M	0.632	1.00
1_M	4_A	0.631	1.00
101_V	104_A	0.628	1.00
117_G	122_N	0.626	1.00
68_R	113_T	0.625	1.00
11_L	86_G	0.621	1.00
3_I	102_A	0.620	1.00
10_I	102_A	0.618	1.00
25_L	29_L	0.617	1.00
69_T	129_A	0.616	1.00
11_L	87_A	0.615	1.00
112_A	115_G	0.608	1.00
106_A	110_P	0.603	1.00
92_R	97_A	0.602	1.00
121_G	126_A	0.601	1.00
44_A	121_G	0.598	1.00
26_R	29_L	0.591	1.00
6_L	110_P	0.588	1.00
66_L	125_L	0.587	1.00
25_L	32_L	0.585	1.00
106_A	132_L	0.582	1.00
74_L	88_L	0.579	1.00
7_M	86_G	0.578	1.00
89_A	99_P	0.576	1.00
32_L	36_V	0.575	1.00
42_V	45_L	0.575	1.00
2_L	6_L	0.574	1.00
34_V	38_L	0.574	1.00
3_I	85_A	0.571	1.00
77_L	81_A	0.570	1.00
114_A	118_L	0.568	1.00
39_A	133_F	0.568	1.00
64_E	69_T	0.568	1.00
47_G	50_L	0.567	1.00
126_A	129_A	0.566	1.00
82_A	94_K	0.566	1.00
35_G	99_P	0.566	1.00
124_S	128_G	0.565	1.00
48_L	121_G	0.560	1.00
102_A	106_A	0.558	1.00
34_V	121_G	0.556	1.00
90_L	96_S	0.552	1.00
13_L	16_G	0.551	1.00
71_P	135_T	0.550	0.99
35_G	38_L	0.550	0.99
61_P	66_L	0.548	0.99
79_A	109_P	0.548	0.99
62_T	66_L	0.547	0.99
135_T	139_A	0.547	0.99
22_R	41_A	0.537	0.99
9_P	35_G	0.534	0.99
12_G	105_V	0.528	0.99
14_G	18_V	0.528	0.99
29_L	32_L	0.528	0.99
129_A	132_L	0.528	0.99
79_A	106_A	0.524	0.99
86_G	100_G	0.521	0.99
48_L	52_L	0.519	0.99
83_G	87_A	0.516	0.99
105_V	139_A	0.515	0.99
104_A	108_V	0.511	0.99
137_L	141_V	0.505	0.99
68_R	71_P	0.504	0.99
58_L	62_T	0.504	0.99
69_T	113_T	0.503	0.99
85_A	97_A	0.500	0.99

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
2nwlA	3	0.9014	5.4	0.92	Contact Map
2zy9A	2	0.5915	1.5	0.94	Contact Map
2nq2A	2	0.8099	1.5	0.94	Contact Map
3trkA	1	0.3521	1.3	0.942	Contact Map
4httA	1	0.9296	1.1	0.945	Contact Map
4m5bA	1	0.7887	1	0.945	Contact Map
2j5dA	2	0.1831	1	0.946	Contact Map
1afoA	2	0.2817	1	0.946	Contact Map
2mgyA	1	0.7817	1	0.946	Contact Map
4p79A	1	0.6127	1	0.946	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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