DUF2163 - PFAM28P - GREMLIN Contacts

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DUF2163 - Uncharacterized conserved protein (DUF2163)

PFAM:	PF09931	Sequences: MKTISAALQAHLASGATTLARCWRITRRDGVVLGFTDHDRDLTFDGVTYRAASGLTASAIEQSLGLSVDNLEVTGALSSDAITEADLAAGRYDGARVEIFRVNWADPSQRVLLFRGRIGEVTRGGGAFTAELRGLAAALNQPVGRLYQPTCRAVLGDARCGVD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	163 (158)
Sequences:	5884 (4677)
Seq/√Len:	372.1
META:	0.878

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_D	51_A	4.624	1.00
34_G	47_V	3.296	1.00
9_Q	13_A	2.875	1.00
43_T	48_T	2.565	1.00
145_R	152_R	2.407	1.00
72_E	129_T	2.397	1.00
156_G	162_V	2.392	1.00
153_A	157_D	2.253	1.00
122_T	129_T	2.189	1.00
41_D	48_T	2.169	1.00
96_R	115_R	2.152	1.00
11_H	103_N	2.111	1.00
6_A	10_A	2.035	1.00
26_T	98_E	2.023	1.00
44_F	110_R	2.003	1.00
153_A	159_R	1.991	1.00
24_R	47_V	1.986	1.00
103_N	109_Q	1.928	1.00
22_C	100_F	1.916	1.00
118_I	130_A	1.904	1.00
117_R	138_A	1.882	1.00
58_S	71_L	1.881	1.00
24_R	98_E	1.880	1.00
98_E	112_L	1.872	1.00
100_F	110_R	1.844	1.00
24_R	49_Y	1.841	1.00
24_R	100_F	1.826	1.00
33_L	92_Y	1.826	1.00
41_D	50_R	1.793	1.00
106_D	109_Q	1.777	1.00
24_R	34_G	1.691	1.00
86_D	91_R	1.690	1.00
75_G	128_F	1.632	1.00
21_R	101_R	1.624	1.00
44_F	49_Y	1.572	1.00
21_R	37_D	1.531	1.00
26_T	32_V	1.528	1.00
27_R	31_V	1.521	1.00
152_R	159_R	1.489	1.00
38_H	104_W	1.463	1.00
124_G	129_T	1.453	1.00
58_S	72_E	1.452	1.00
119_G	133_R	1.451	1.00
50_R	79_S	1.447	1.00
98_E	115_R	1.447	1.00
74_T	129_T	1.431	1.00
24_R	32_V	1.429	1.00
11_H	14_S	1.425	1.00
6_A	9_Q	1.420	1.00
21_R	57_A	1.367	1.00
158_A	161_G	1.336	1.00
145_R	159_R	1.327	1.00
117_R	137_A	1.314	1.00
100_F	112_L	1.302	1.00
5_S	8_L	1.280	1.00
97_V	132_L	1.264	1.00
157_D	161_G	1.248	1.00
155_L	162_V	1.239	1.00
148_Q	152_R	1.229	1.00
56_T	74_T	1.208	1.00
45_D	110_R	1.203	1.00
116_G	132_L	1.180	1.00
22_C	102_V	1.171	1.00
20_A	37_D	1.164	1.00
96_R	117_R	1.149	1.00
11_H	109_Q	1.144	1.00
63_S	67_S	1.125	1.00
124_G	127_A	1.121	1.00
74_T	127_A	1.116	1.00
50_R	81_A	1.108	1.00
103_N	106_D	1.080	1.00
32_V	47_V	1.061	1.00
25_I	97_V	1.043	1.00
87_L	121_V	1.039	1.00
78_S	81_A	1.024	1.00
133_R	137_A	1.015	1.00
137_A	140_N	1.009	1.00
121_V	130_A	1.001	1.00
63_S	69_D	0.998	1.00
101_R	111_V	0.958	1.00
14_S	17_T	0.952	1.00
49_Y	100_F	0.950	1.00
70_N	131_E	0.949	1.00
38_H	42_L	0.942	1.00
88_A	123_R	0.942	1.00
21_R	113_L	0.940	1.00
69_D	134_G	0.934	1.00
26_T	96_R	0.928	1.00
18_T	105_A	0.928	1.00
23_W	57_A	0.917	1.00
18_T	103_N	0.915	1.00
144_G	152_R	0.910	1.00
84_E	88_A	0.904	1.00
8_L	11_H	0.892	1.00
79_S	82_I	0.891	1.00
70_N	133_R	0.890	1.00
102_V	110_R	0.882	1.00
94_G	117_R	0.881	1.00
101_R	113_L	0.881	1.00
120_E	131_E	0.881	1.00
7_A	109_Q	0.875	1.00
90_G	93_D	0.871	1.00
62_Q	114_F	0.866	1.00
75_G	130_A	0.866	1.00
11_H	17_T	0.864	1.00
20_A	38_H	0.853	1.00
22_C	49_Y	0.852	1.00
92_Y	95_A	0.848	1.00
71_L	99_I	0.829	1.00
22_C	44_F	0.828	1.00
68_V	137_A	0.824	1.00
94_G	138_A	0.823	1.00
20_A	42_L	0.821	1.00
151_C	160_C	0.820	1.00
72_E	131_E	0.817	1.00
12_L	111_V	0.812	1.00
159_R	162_V	0.809	1.00
44_F	102_V	0.806	1.00
34_G	50_R	0.802	1.00
22_C	42_L	0.800	1.00
60_I	71_L	0.797	1.00
19_L	101_R	0.785	1.00
12_L	19_L	0.784	1.00
138_A	141_Q	0.782	1.00
120_E	133_R	0.779	1.00
27_R	92_Y	0.778	1.00
5_S	9_Q	0.769	1.00
42_L	102_V	0.767	1.00
23_W	97_V	0.763	1.00
25_I	95_A	0.761	1.00
85_A	89_A	0.761	1.00
27_R	91_R	0.754	1.00
71_L	114_F	0.750	1.00
118_I	132_L	0.750	1.00
112_L	115_R	0.739	1.00
86_D	92_Y	0.732	1.00
5_S	13_A	0.732	1.00
117_R	133_R	0.723	1.00
22_C	110_R	0.720	1.00
154_V	157_D	0.719	1.00
28_R	95_A	0.704	0.99
11_H	19_L	0.699	0.99
61_E	69_D	0.693	0.99
20_A	36_T	0.690	0.99
25_I	92_Y	0.684	0.99
69_D	114_F	0.681	0.99
87_L	128_F	0.679	0.99
122_T	131_E	0.678	0.99
12_L	101_R	0.677	0.99
10_A	13_A	0.676	0.99
50_R	53_S	0.669	0.99
153_A	156_G	0.666	0.99
14_S	19_L	0.660	0.99
45_D	49_Y	0.658	0.99
102_V	107_P	0.654	0.99
80_D	83_T	0.649	0.99
28_R	94_G	0.648	0.99
9_Q	19_L	0.647	0.99
47_V	50_R	0.646	0.99
27_R	33_L	0.639	0.99
107_P	110_R	0.639	0.99
5_S	10_A	0.637	0.99
57_A	60_I	0.637	0.99
84_E	123_R	0.637	0.99
60_I	116_G	0.630	0.99
88_A	91_R	0.629	0.99
121_V	128_F	0.628	0.99
119_G	131_E	0.628	0.99
105_A	109_Q	0.620	0.99
8_L	111_V	0.619	0.99
7_A	10_A	0.618	0.99
79_S	83_T	0.616	0.99
86_D	89_A	0.613	0.99
10_A	14_S	0.611	0.98
6_A	14_S	0.610	0.98
83_T	86_D	0.609	0.98
86_D	90_G	0.608	0.98
71_L	132_L	0.606	0.98
29_D	91_R	0.605	0.98
34_G	49_Y	0.603	0.98
6_A	13_A	0.601	0.98
140_N	144_G	0.600	0.98
61_E	70_N	0.600	0.98
43_T	46_G	0.598	0.98
27_R	30_G	0.597	0.98
115_R	135_L	0.590	0.98
44_F	47_V	0.585	0.98
99_I	116_G	0.585	0.98
8_L	12_L	0.584	0.98
137_A	141_Q	0.584	0.98
37_D	57_A	0.584	0.98
77_L	87_L	0.577	0.98
5_S	19_L	0.577	0.98
60_I	114_F	0.570	0.98
114_F	132_L	0.568	0.98
68_V	133_R	0.568	0.98
150_T	154_V	0.568	0.98
12_L	17_T	0.551	0.97
90_G	95_A	0.549	0.97
23_W	37_D	0.547	0.97
69_D	136_A	0.542	0.97
10_A	16_A	0.540	0.97
20_A	104_W	0.536	0.97
42_L	107_P	0.536	0.97
145_R	153_A	0.535	0.97
143_V	149_P	0.535	0.97
44_F	100_F	0.534	0.97
39_D	104_W	0.534	0.97
23_W	35_F	0.532	0.96
38_H	102_V	0.532	0.96
23_W	73_V	0.531	0.96
7_A	11_H	0.530	0.96
92_Y	147_Y	0.529	0.96
18_T	104_W	0.529	0.96
114_F	149_P	0.529	0.96
8_L	19_L	0.528	0.96
99_I	114_F	0.526	0.96
123_R	126_G	0.526	0.96
60_I	64_L	0.525	0.96
62_Q	69_D	0.525	0.96
22_C	36_T	0.525	0.96
11_H	105_A	0.524	0.96
75_G	87_L	0.518	0.96
114_F	134_G	0.518	0.96
53_S	81_A	0.514	0.96
7_A	106_D	0.513	0.96
48_T	51_A	0.513	0.96
9_Q	15_G	0.511	0.96
73_V	132_L	0.510	0.95
24_R	44_F	0.509	0.95
57_A	71_L	0.509	0.95
26_T	47_V	0.505	0.95
152_R	162_V	0.505	0.95
5_S	109_Q	0.504	0.95
84_E	87_L	0.504	0.95
53_S	56_T	0.503	0.95
133_R	140_N	0.500	0.95

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
3d37A	5	0.6503	13.8	0.922	Contact Map
1wruA	3	0.681	12	0.924	Contact Map
3cddA	3	0.7301	8.1	0.93	Contact Map
5a21H	1	0.8712	6	0.934	Contact Map
4lx3A	1	0.3865	3.2	0.942	Contact Map
3fbyA	3	0.411	2.5	0.945	Contact Map
4g4fA	4	0.3006	2.3	0.946	Contact Map
3b64A	3	0.2454	2	0.948	Contact Map
3b9tA	4	0.3497	1.9	0.949	Contact Map
4v2xA	2	0.7239	1.8	0.949	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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