DUF502 - PFAM28P - GREMLIN Contacts

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DUF502 - Protein of unknown function (DUF502)

PFAM:	PF04367	Sequences: LLTLLLILLVGLLASNFIGRRLLRLGERLLERIPLVRSIYSSVKQLVETFFGDSKKSFKKVVLVEYPRKGIWSIGFVTGEDLGEVGTGEDLVAVFVPTTPNPTS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	104 (103)
Sequences:	25528 (15157)
Seq/√Len:	1493.4
META:	0.942

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_E	72_W	2.875	1.00
62_V	75_G	2.461	1.00
62_V	77_V	2.380	1.00
98_T	101_N	2.367	1.00
8_L	12_L	2.278	1.00
68_R	71_I	2.274	1.00
72_W	91_L	2.193	1.00
27_E	44_K	2.045	1.00
65_E	68_R	2.014	1.00
98_T	103_T	1.974	1.00
21_R	25_L	1.940	1.00
21_R	24_R	1.929	1.00
65_E	70_G	1.885	1.00
77_V	92_V	1.863	1.00
31_E	41_S	1.789	1.00
65_E	69_K	1.780	1.00
64_V	96_V	1.763	1.00
16_N	19_G	1.738	1.00
87_T	91_L	1.731	1.00
6_L	10_V	1.723	1.00
28_R	32_R	1.607	1.00
44_K	48_E	1.606	1.00
79_G	93_A	1.597	1.00
64_V	75_G	1.563	1.00
60_K	80_E	1.549	1.00
12_L	16_N	1.539	1.00
75_G	94_V	1.472	1.00
83_G	86_G	1.411	1.00
47_V	51_F	1.393	1.00
58_F	76_F	1.369	1.00
26_G	29_L	1.361	1.00
73_S	98_T	1.353	1.00
25_L	29_L	1.317	1.00
66_Y	69_K	1.300	1.00
98_T	102_P	1.283	1.00
26_G	30_L	1.283	1.00
81_D	93_A	1.276	1.00
25_L	28_R	1.252	1.00
27_E	31_E	1.245	1.00
3_T	7_I	1.227	1.00
11_G	15_S	1.204	1.00
66_Y	71_I	1.184	1.00
73_S	96_V	1.182	1.00
75_G	96_V	1.182	1.00
60_K	77_V	1.133	1.00
14_A	23_L	1.108	1.00
88_G	91_L	1.085	1.00
95_F	103_T	1.063	1.00
24_R	28_R	1.052	1.00
35_L	38_S	1.052	1.00
38_S	41_S	1.041	1.00
62_V	94_V	1.031	1.00
87_T	90_D	1.028	1.00
34_P	39_I	1.024	1.00
54_S	57_S	0.989	1.00
67_P	73_S	0.977	1.00
82_L	90_D	0.965	1.00
99_T	103_T	0.935	1.00
61_V	74_I	0.922	1.00
31_E	37_R	0.920	1.00
66_Y	73_S	0.920	1.00
2_L	5_L	0.917	1.00
82_L	85_V	0.893	1.00
67_P	70_G	0.891	1.00
4_L	8_L	0.887	1.00
86_G	91_L	0.876	1.00
17_F	21_R	0.870	1.00
20_R	24_R	0.868	1.00
97_P	100_P	0.861	1.00
43_V	47_V	0.859	1.00
23_L	27_E	0.856	1.00
80_E	90_D	0.849	1.00
82_L	86_G	0.846	1.00
73_S	102_P	0.842	1.00
49_T	58_F	0.841	1.00
16_N	21_R	0.840	1.00
69_K	72_W	0.824	1.00
2_L	6_L	0.823	1.00
45_Q	48_E	0.819	1.00
29_L	32_R	0.803	1.00
80_E	92_V	0.788	1.00
63_L	72_W	0.787	1.00
42_S	49_T	0.775	1.00
38_S	42_S	0.771	1.00
66_Y	70_G	0.767	1.00
31_E	44_K	0.766	1.00
1_L	4_L	0.764	1.00
5_L	9_L	0.762	1.00
84_E	87_T	0.753	1.00
52_G	55_K	0.745	1.00
10_V	14_A	0.729	1.00
28_R	31_E	0.719	1.00
49_T	52_G	0.716	1.00
63_L	74_I	0.715	1.00
18_I	21_R	0.712	1.00
23_L	26_G	0.706	1.00
59_K	80_E	0.706	1.00
64_V	71_I	0.703	1.00
95_F	100_P	0.693	1.00
5_L	8_L	0.691	1.00
37_R	41_S	0.690	1.00
67_P	71_I	0.686	1.00
100_P	103_T	0.683	1.00
83_G	87_T	0.678	1.00
27_E	40_Y	0.677	1.00
42_S	46_L	0.673	1.00
61_V	76_F	0.671	1.00
8_L	11_G	0.671	1.00
36_V	40_Y	0.661	1.00
12_L	15_S	0.657	1.00
77_V	94_V	0.656	1.00
15_S	19_G	0.656	1.00
17_F	20_R	0.655	1.00
33_I	36_V	0.642	1.00
23_L	44_K	0.640	1.00
16_N	20_R	0.639	1.00
9_L	12_L	0.631	1.00
29_L	34_P	0.628	1.00
83_G	89_E	0.625	1.00
81_D	85_V	0.624	1.00
82_L	93_A	0.623	1.00
57_S	79_G	0.618	1.00
39_I	42_S	0.618	1.00
37_R	42_S	0.611	1.00
7_I	11_G	0.590	1.00
41_S	49_T	0.589	1.00
85_V	91_L	0.589	1.00
6_L	9_L	0.587	1.00
99_T	102_P	0.582	1.00
53_D	56_K	0.577	1.00
81_D	90_D	0.577	1.00
37_R	51_F	0.572	1.00
14_A	49_T	0.565	1.00
20_R	27_E	0.562	1.00
84_E	88_G	0.562	1.00
85_V	88_G	0.555	1.00
25_L	32_R	0.546	1.00
51_F	58_F	0.545	1.00
11_G	14_A	0.543	1.00
95_F	101_N	0.543	1.00
78_T	95_F	0.540	1.00
78_T	99_T	0.539	1.00
3_T	6_L	0.536	1.00
21_R	26_G	0.534	1.00
9_L	13_L	0.530	1.00
56_K	59_K	0.518	1.00
58_F	77_V	0.516	1.00
35_L	39_I	0.516	1.00
78_T	93_A	0.510	1.00
81_D	86_G	0.508	1.00
21_R	28_R	0.507	1.00
22_L	25_L	0.506	1.00
32_R	35_L	0.504	1.00
40_Y	44_K	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
2fokA	1	0.3077	4.8	0.911	Contact Map
4cq4A	4	0.5962	3.7	0.916	Contact Map
3o3mB	1	0.5769	3.4	0.918	Contact Map
3tqoA	1	0.3558	3.1	0.919	Contact Map
3x2dB	3	0.6827	2.9	0.92	Contact Map
4k0mC	1	0.4712	2.8	0.921	Contact Map
2fyuK	1	0.2596	2.6	0.922	Contact Map
3f6dA	2	0.4808	2.4	0.924	Contact Map
1scfA	4	0	2.4	0.924	Contact Map
4gycB	2	0.1827	2.1	0.926	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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