DUF456 - PFAM28P - GREMLIN Contacts

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DUF456 - Protein of unknown function (DUF456)

PFAM:	PF04306	Sequences: VLPVLPGPPLIFAGLLLYAWADGFARVGWWTLVVLAVLALLGEVLDYLAPALGAKKFGASKRGIWGAAIGGIVGLFFGPPVGLILGPFLGAFLGELLRGRKDLRQALRAGLGALLGFLLGTLAKLALALVMIGLFVVAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	139 (136)
Sequences:	13080 (9002)
Seq/√Len:	771.9
META:	0.885

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_W	33_V	3.806	1.00
12_F	36_A	3.121	1.00
92_F	110_G	3.034	1.00
62_R	97_L	2.872	1.00
102_D	105_Q	2.656	1.00
92_F	103_L	2.532	1.00
11_I	128_A	2.298	1.00
62_R	98_R	2.281	1.00
33_V	37_V	2.174	1.00
35_L	131_M	2.122	1.00
54_A	59_A	2.090	1.00
30_W	33_V	2.053	1.00
8_P	128_A	2.003	1.00
30_W	34_V	2.000	1.00
61_K	65_W	1.996	1.00
19_A	24_F	1.983	1.00
31_T	134_L	1.838	1.00
12_F	39_A	1.811	1.00
38_L	127_L	1.777	1.00
66_G	94_G	1.775	1.00
46_D	124_K	1.751	1.00
65_W	69_I	1.670	1.00
99_G	105_Q	1.666	1.00
15_L	35_L	1.615	1.00
31_T	35_L	1.612	1.00
111_L	115_L	1.591	1.00
60_S	63_G	1.533	1.00
42_G	127_L	1.511	1.00
67_A	91_A	1.490	1.00
76_F	79_P	1.476	1.00
83_L	87_P	1.465	1.00
66_G	90_G	1.443	1.00
127_L	131_M	1.407	1.00
15_L	135_F	1.405	1.00
107_L	111_L	1.394	1.00
16_L	24_F	1.385	1.00
66_G	70_G	1.373	1.00
13_A	17_L	1.367	1.00
71_G	87_P	1.342	1.00
90_G	94_G	1.327	1.00
86_G	90_G	1.300	1.00
44_V	48_L	1.290	1.00
11_I	132_I	1.267	1.00
57_F	112_G	1.247	1.00
70_G	90_G	1.234	1.00
96_L	103_L	1.182	1.00
104_R	107_L	1.181	1.00
22_D	26_R	1.178	1.00
95_E	98_R	1.159	1.00
12_F	32_L	1.140	1.00
117_F	121_T	1.134	1.00
94_G	98_R	1.126	1.00
108_R	111_L	1.119	1.00
12_F	16_L	1.118	1.00
51_A	64_I	1.112	1.00
133_G	137_V	1.110	1.00
18_Y	22_D	1.091	1.00
19_A	27_V	1.085	1.00
11_I	15_L	1.071	1.00
28_G	31_T	1.070	1.00
8_P	42_G	1.062	1.00
129_L	133_G	1.060	1.00
12_F	35_L	1.055	1.00
39_A	131_M	1.036	1.00
62_R	65_W	1.015	1.00
35_L	39_A	1.006	1.00
118_L	122_L	1.004	1.00
34_V	134_L	0.994	1.00
78_G	85_L	0.990	1.00
91_A	110_G	0.989	1.00
103_L	107_L	0.984	1.00
57_F	109_A	0.970	1.00
40_L	44_V	0.959	1.00
100_R	105_Q	0.959	1.00
112_G	116_G	0.956	1.00
93_L	97_L	0.955	1.00
19_A	32_L	0.953	1.00
49_A	123_A	0.950	1.00
19_A	29_W	0.948	1.00
37_V	41_L	0.945	1.00
64_I	68_A	0.935	1.00
130_V	134_L	0.927	1.00
88_F	92_F	0.919	1.00
119_L	122_L	0.914	1.00
60_S	98_R	0.912	1.00
104_R	108_R	0.911	1.00
22_D	25_A	0.908	1.00
105_Q	108_R	0.907	1.00
43_E	46_D	0.904	1.00
128_A	132_I	0.876	1.00
9_P	43_E	0.873	1.00
57_F	111_L	0.870	1.00
96_L	99_G	0.864	1.00
51_A	68_A	0.863	1.00
132_I	136_V	0.862	1.00
74_G	86_G	0.857	1.00
45_L	123_A	0.842	1.00
109_A	112_G	0.840	1.00
53_G	112_G	0.833	1.00
119_L	126_A	0.833	1.00
78_G	82_G	0.829	1.00
63_G	95_E	0.829	1.00
8_P	11_I	0.820	1.00
92_F	96_L	0.809	1.00
11_I	131_M	0.809	1.00
33_V	36_A	0.808	1.00
92_F	107_L	0.797	1.00
55_K	61_K	0.797	1.00
99_G	102_D	0.797	1.00
45_L	49_A	0.793	1.00
16_L	32_L	0.783	1.00
23_G	26_R	0.780	1.00
18_Y	21_A	0.775	1.00
54_A	113_A	0.767	1.00
19_A	23_G	0.767	1.00
75_L	79_P	0.759	1.00
49_A	53_G	0.757	1.00
85_L	89_L	0.755	1.00
116_G	120_G	0.751	1.00
79_P	82_G	0.750	1.00
16_L	20_W	0.744	1.00
103_L	106_A	0.744	1.00
74_G	79_P	0.741	1.00
8_P	43_E	0.738	1.00
118_L	121_T	0.734	1.00
82_G	86_G	0.732	1.00
89_L	93_L	0.725	1.00
59_A	112_G	0.724	1.00
68_A	71_G	0.710	1.00
48_L	52_L	0.707	1.00
44_V	47_Y	0.706	1.00
8_P	12_F	0.697	1.00
27_V	31_T	0.696	1.00
1_V	4_V	0.690	1.00
57_F	108_R	0.689	1.00
96_L	102_D	0.688	1.00
115_L	119_L	0.684	1.00
16_L	36_A	0.680	1.00
63_G	94_G	0.674	1.00
81_V	85_L	0.672	1.00
63_G	66_G	0.670	1.00
70_G	74_G	0.669	1.00
62_R	94_G	0.663	1.00
10_L	14_G	0.662	1.00
9_P	13_A	0.661	1.00
36_A	39_A	0.657	1.00
75_L	83_L	0.656	1.00
95_E	109_A	0.650	1.00
32_L	36_A	0.649	1.00
59_A	113_A	0.648	1.00
53_G	119_L	0.648	1.00
39_A	127_L	0.645	1.00
78_G	81_V	0.644	1.00
51_A	54_A	0.643	1.00
88_F	114_L	0.642	1.00
26_R	30_W	0.637	1.00
19_A	22_D	0.630	1.00
60_S	95_E	0.627	1.00
67_A	87_P	0.626	1.00
59_A	109_A	0.623	1.00
121_T	125_L	0.621	1.00
35_L	134_L	0.611	1.00
38_L	134_L	0.606	1.00
40_L	43_E	0.605	1.00
65_W	68_A	0.605	1.00
62_R	66_G	0.605	1.00
70_G	86_G	0.598	1.00
11_I	18_Y	0.597	1.00
15_L	131_M	0.596	1.00
20_W	24_F	0.589	1.00
47_Y	51_A	0.583	1.00
66_G	91_A	0.580	1.00
54_A	116_G	0.578	1.00
77_F	86_G	0.578	1.00
126_A	130_V	0.574	1.00
49_A	52_L	0.573	1.00
74_G	78_G	0.562	1.00
113_A	117_F	0.560	1.00
123_A	130_V	0.558	1.00
9_P	39_A	0.557	1.00
57_F	115_L	0.556	1.00
59_A	116_G	0.555	1.00
52_L	56_K	0.554	1.00
73_V	77_F	0.552	1.00
87_P	113_A	0.551	1.00
27_V	135_F	0.549	1.00
50_P	54_A	0.546	1.00
64_I	67_A	0.544	1.00
35_L	127_L	0.541	1.00
35_L	38_L	0.537	1.00
105_Q	109_A	0.532	1.00
49_A	120_G	0.531	1.00
84_I	117_F	0.529	1.00
11_I	14_G	0.522	1.00
122_L	126_A	0.518	1.00
1_V	125_L	0.518	1.00
88_F	110_G	0.514	1.00
111_L	114_L	0.514	1.00
39_A	43_E	0.513	1.00
66_G	69_I	0.511	1.00
120_G	124_K	0.511	1.00
14_G	17_L	0.511	1.00
17_L	20_W	0.501	1.00
4_V	9_P	0.500	1.00

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
2jwaA	2	0.295	4.9	0.924	Contact Map
2nwlA	3	0.7338	3.2	0.93	Contact Map
3qnqA	2	0.9712	3	0.931	Contact Map
2l2tA	2	0.3094	2.2	0.936	Contact Map
2ks1B	1	0.3094	2	0.937	Contact Map
4pj0K	1	0.1655	1.8	0.939	Contact Map
3wu2K	1	0.1655	1.7	0.94	Contact Map
2jlnA	1	1	1.7	0.94	Contact Map
2a65A	2	0.6115	1.6	0.941	Contact Map
1iijA	1	0.2518	1.6	0.941	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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