DUF2459 - PFAM28P - GREMLIN Contacts

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DUF2459 - Protein of unknown function (DUF2459)

PFAM:	PF09601	Sequences: IYVVSNGVHTDIVLPVKAELLDWRALFPPSDFAAPDPDARYLAFGWGDRGFYLETPTWADLTPSTALKALFGPGPSVMHVTGYPPPPAPGSDVREIRLSPEQYRRLVAFIRASFARDADGRPIRIGGGGYGPNDAFYEARGRYSLFNTCNTWTARALRAAGLPTSLWTPFD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	171 (170)
Sequences:	4123 (2999)
Seq/√Len:	230.0
META:	0.872

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
109_F	156_A	6.878	1.00
49_R	138_E	3.463	1.00
99_S	102_Q	3.030	1.00
147_N	155_R	2.965	1.00
12_I	156_A	2.247	1.00
50_G	54_E	2.200	1.00
49_R	53_L	2.176	1.00
49_R	75_P	2.158	1.00
113_S	139_A	2.132	1.00
165_S	168_T	2.125	1.00
4_V	13_V	2.080	1.00
55_T	65_T	2.020	1.00
103_Y	107_V	2.008	1.00
48_D	74_G	2.002	1.00
17_K	24_R	1.991	1.00
10_T	153_T	1.985	1.00
50_G	68_K	1.959	1.00
106_L	156_A	1.956	1.00
67_L	71_F	1.873	1.00
117_D	121_R	1.847	1.00
77_V	125_I	1.805	1.00
154_A	164_T	1.782	1.00
79_H	134_D	1.741	1.00
62_T	65_T	1.652	1.00
79_H	130_Y	1.631	1.00
44_F	78_M	1.615	1.00
144_S	147_N	1.565	1.00
124_R	135_A	1.558	1.00
32_F	35_P	1.544	1.00
61_L	66_A	1.529	1.00
156_A	159_A	1.524	1.00
128_G	134_D	1.484	1.00
73_P	144_S	1.449	1.00
17_K	22_D	1.448	1.00
45_G	52_Y	1.448	1.00
21_L	111_R	1.435	1.00
63_P	67_L	1.434	1.00
130_Y	134_D	1.426	1.00
115_A	140_R	1.424	1.00
113_S	141_G	1.424	1.00
27_F	114_F	1.414	1.00
111_R	116_R	1.406	1.00
76_S	141_G	1.392	1.00
154_A	158_R	1.392	1.00
14_L	110_I	1.389	1.00
100_P	104_R	1.389	1.00
1_I	98_L	1.388	1.00
11_D	43_A	1.386	1.00
148_T	151_T	1.365	1.00
109_F	159_A	1.362	1.00
46_W	76_S	1.358	1.00
78_M	114_F	1.329	1.00
14_L	44_F	1.307	1.00
154_A	168_T	1.281	1.00
143_Y	148_T	1.277	1.00
53_L	125_I	1.264	1.00
115_A	123_I	1.261	1.00
51_F	61_L	1.250	1.00
57_T	60_D	1.239	1.00
98_L	162_L	1.235	1.00
78_M	113_S	1.201	1.00
109_F	155_R	1.182	1.00
126_G	129_G	1.172	1.00
108_A	112_A	1.170	1.00
8_V	58_W	1.166	1.00
42_L	82_G	1.162	1.00
147_N	151_T	1.158	1.00
26_L	122_P	1.156	1.00
78_M	139_A	1.156	1.00
74_G	144_S	1.155	1.00
4_V	93_V	1.152	1.00
21_L	26_L	1.128	1.00
30_S	33_A	1.114	1.00
68_K	74_G	1.108	1.00
116_R	122_P	1.105	1.00
141_G	147_N	1.101	1.00
11_D	45_G	1.099	1.00
54_E	65_T	1.094	1.00
10_T	149_C	1.087	1.00
106_L	160_A	1.082	1.00
79_H	136_F	1.077	1.00
46_W	141_G	1.070	1.00
55_T	62_T	1.057	1.00
94_R	97_R	1.051	1.00
129_G	134_D	1.049	1.00
31_D	137_Y	1.030	1.00
123_I	138_E	1.019	1.00
18_A	21_L	1.019	1.00
43_A	83_Y	1.016	1.00
151_T	168_T	1.014	1.00
152_W	156_A	1.012	1.00
64_S	68_K	1.011	1.00
11_D	52_Y	1.011	1.00
2_Y	95_E	0.995	1.00
44_F	114_F	0.983	1.00
39_A	82_G	0.979	1.00
157_L	162_L	0.978	1.00
22_D	25_A	0.972	1.00
151_T	154_A	0.971	1.00
44_F	80_V	0.970	1.00
16_V	21_L	0.964	1.00
44_F	110_I	0.958	1.00
115_A	138_E	0.946	1.00
109_F	113_S	0.943	1.00
89_P	95_E	0.937	1.00
154_A	165_S	0.929	1.00
63_P	66_A	0.917	1.00
105_R	159_A	0.914	1.00
105_R	161_G	0.911	1.00
101_E	105_R	0.907	0.99
117_D	123_I	0.902	0.99
104_R	108_A	0.895	0.99
15_P	18_A	0.895	0.99
6_N	11_D	0.893	0.99
13_V	43_A	0.892	0.99
19_E	23_W	0.878	0.99
114_F	137_Y	0.877	0.99
118_A	121_R	0.869	0.99
129_G	132_P	0.868	0.99
85_P	88_A	0.868	0.99
20_L	104_R	0.858	0.99
16_V	24_R	0.854	0.99
3_V	10_T	0.850	0.99
114_F	122_P	0.849	0.99
52_Y	141_G	0.845	0.99
117_D	120_G	0.838	0.99
14_L	42_L	0.833	0.99
113_S	156_A	0.830	0.99
120_G	123_I	0.828	0.99
106_L	110_I	0.826	0.99
98_L	103_Y	0.822	0.99
10_T	143_Y	0.821	0.99
28_P	37_P	0.815	0.99
98_L	102_Q	0.812	0.99
26_L	116_R	0.807	0.99
52_Y	136_F	0.799	0.99
20_L	107_V	0.792	0.99
26_L	111_R	0.782	0.99
29_P	36_D	0.779	0.98
50_G	65_T	0.778	0.98
6_N	79_H	0.777	0.98
5_S	92_D	0.773	0.98
66_A	69_A	0.772	0.98
22_D	26_L	0.770	0.98
59_A	62_T	0.757	0.98
76_S	113_S	0.756	0.98
55_T	61_L	0.746	0.98
48_D	69_A	0.742	0.98
72_G	142_R	0.736	0.98
54_E	62_T	0.736	0.98
80_V	114_F	0.734	0.98
6_N	91_S	0.728	0.98
4_V	43_A	0.728	0.98
55_T	60_D	0.721	0.97
17_K	21_L	0.718	0.97
50_G	74_G	0.718	0.97
55_T	58_W	0.715	0.97
101_E	104_R	0.715	0.97
29_P	32_F	0.714	0.97
46_W	52_Y	0.706	0.97
20_L	24_R	0.705	0.97
34_A	39_A	0.704	0.97
111_R	122_P	0.703	0.97
16_V	40_R	0.693	0.97
4_V	11_D	0.690	0.97
151_T	155_R	0.682	0.96
52_Y	77_V	0.680	0.96
5_S	51_F	0.679	0.96
84_P	88_A	0.678	0.96
29_P	34_A	0.677	0.96
87_P	108_A	0.675	0.96
48_D	75_P	0.674	0.96
130_Y	136_F	0.673	0.96
89_P	93_V	0.657	0.96
21_L	25_A	0.656	0.96
32_F	36_D	0.655	0.96
155_R	159_A	0.643	0.95
16_V	19_E	0.640	0.95
102_Q	105_R	0.639	0.95
84_P	87_P	0.633	0.95
86_P	95_E	0.631	0.95
107_V	111_R	0.630	0.95
18_A	103_Y	0.628	0.94
98_L	106_L	0.628	0.94
71_F	74_G	0.626	0.94
119_D	140_R	0.626	0.94
21_L	24_R	0.624	0.94
36_D	84_P	0.624	0.94
23_W	26_L	0.621	0.94
28_P	82_G	0.621	0.94
127_G	130_Y	0.620	0.94
46_W	152_W	0.619	0.94
61_L	65_T	0.618	0.94
65_T	68_K	0.618	0.94
46_W	78_M	0.615	0.94
51_F	62_T	0.614	0.94
46_W	143_Y	0.612	0.94
51_F	55_T	0.609	0.94
73_P	142_R	0.608	0.93
102_Q	161_G	0.606	0.93
81_T	133_N	0.605	0.93
101_E	112_A	0.605	0.93
11_D	81_T	0.604	0.93
143_Y	149_C	0.600	0.93
54_E	59_A	0.591	0.92
49_R	77_V	0.591	0.92
3_V	165_S	0.590	0.92
56_P	61_L	0.590	0.92
49_R	54_E	0.590	0.92
43_A	81_T	0.585	0.92
19_E	100_P	0.583	0.92
24_R	28_P	0.579	0.92
78_M	141_G	0.577	0.92
98_L	160_A	0.576	0.92
119_D	123_I	0.572	0.91
18_A	24_R	0.569	0.91
153_T	156_A	0.569	0.91
67_L	73_P	0.565	0.91
72_G	144_S	0.558	0.90
105_R	108_A	0.556	0.90
68_K	72_G	0.553	0.90
18_A	23_W	0.551	0.90
34_A	37_P	0.550	0.90
77_V	81_T	0.549	0.89
18_A	22_D	0.549	0.89
25_A	28_P	0.549	0.89
125_I	128_G	0.548	0.89
66_A	70_L	0.547	0.89
70_L	145_L	0.546	0.89
17_K	20_L	0.545	0.89
102_Q	163_P	0.544	0.89
81_T	134_D	0.542	0.89
151_T	156_A	0.540	0.89
75_P	142_R	0.539	0.89
4_V	10_T	0.538	0.89
53_L	130_Y	0.534	0.88
102_Q	162_L	0.533	0.88
16_V	29_P	0.528	0.88
53_L	127_G	0.524	0.87
163_P	169_P	0.523	0.87
26_L	121_R	0.520	0.87
33_A	36_D	0.516	0.86
12_I	110_I	0.511	0.86
158_R	165_S	0.510	0.86
23_W	28_P	0.510	0.86
165_S	170_F	0.510	0.86
24_R	29_P	0.508	0.86
102_Q	106_L	0.507	0.85
79_H	129_G	0.505	0.85
162_L	165_S	0.504	0.85
8_V	55_T	0.503	0.85
151_T	169_P	0.502	0.85
47_G	152_W	0.501	0.85
101_E	118_A	0.501	0.85
100_P	112_A	0.500	0.85

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
4onzA	1	0.3567	12.5	0.946	Contact Map
2wp7A	2	0.5789	11.6	0.947	Contact Map
3vn5A	1	0.4035	10.6	0.948	Contact Map
4ly1A	2	0.8655	8.6	0.95	Contact Map
4okeA	2	0.3743	7.6	0.951	Contact Map
4bkxB	1	0.8363	5.3	0.955	Contact Map
2e1vA	1	0.5146	4.1	0.957	Contact Map
3rssA	4	0.538	3.9	0.958	Contact Map
3kstA	1	0.5789	3.7	0.958	Contact Map
3ligA	2	0.4561	3.6	0.958	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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