DUF1461 - PFAM28P - GREMLIN Contacts

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DUF1461 - Protein of unknown function (DUF1461)

PFAM:	PF07314	Sequences: ILFALLLPLLLLLLSVRLLLNPRPPFYEFEYDKYGVPETTGFSKEELLRVADELLDYLNNGAREDLDVPVTVDGELFNEERELSHMADVKNLFQLALRVLLISLVLLLLLLLLLLRRRKKKRLWRLLRARGLLAGGLLTLALLVVLGLLALIDFDQFFTLFHELFFSNDLWLFDPSTDTLIRLFPEGFF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	189 (182)
Sequences:	4389 (3738)
Seq/√Len:	277.1
META:	0.85

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_D	44_K	3.462	1.00
43_S	46_E	3.391	1.00
14_L	100_L	2.939	1.00
84_S	170_L	2.764	1.00
160_L	163_E	2.740	1.00
159_T	163_E	2.593	1.00
31_Y	51_A	2.528	1.00
78_N	178_D	2.491	1.00
30_E	33_K	2.478	1.00
22_P	25_P	2.389	1.00
10_L	104_L	2.368	1.00
35_G	38_E	2.367	1.00
174_D	177_T	2.356	1.00
60_N	90_K	2.225	1.00
79_E	84_S	2.176	1.00
169_D	172_L	2.118	1.00
29_F	33_K	2.094	1.00
179_T	182_R	2.065	1.00
81_R	170_L	2.057	1.00
28_E	48_L	2.057	1.00
159_T	171_W	1.995	1.00
78_N	81_R	1.969	1.00
113_L	117_R	1.928	1.00
167_S	170_L	1.821	1.00
44_K	48_L	1.771	1.00
125_R	128_R	1.722	1.00
170_L	173_F	1.701	1.00
81_R	173_F	1.666	1.00
20_L	93_F	1.654	1.00
156_Q	160_L	1.654	1.00
46_E	49_R	1.653	1.00
34_Y	187_G	1.644	1.00
78_N	82_E	1.615	1.00
76_L	179_T	1.612	1.00
169_D	173_F	1.605	1.00
26_F	30_E	1.586	1.00
161_F	165_F	1.566	1.00
180_L	183_L	1.545	1.00
72_V	75_E	1.532	1.00
13_L	96_A	1.520	1.00
112_L	116_R	1.491	1.00
91_N	95_L	1.467	1.00
98_R	102_I	1.452	1.00
21_N	59_N	1.433	1.00
92_L	95_L	1.404	1.00
67_D	70_V	1.393	1.00
145_V	149_L	1.389	1.00
84_S	88_D	1.388	1.00
30_E	34_Y	1.377	1.00
178_D	181_I	1.375	1.00
173_F	180_L	1.372	1.00
94_Q	98_R	1.363	1.00
87_A	91_N	1.358	1.00
168_N	173_F	1.349	1.00
10_L	107_L	1.333	1.00
10_L	103_S	1.323	1.00
106_L	110_L	1.314	1.00
150_A	157_F	1.312	1.00
39_T	182_R	1.287	1.00
66_L	86_M	1.284	1.00
153_D	156_Q	1.276	1.00
134_A	138_L	1.268	1.00
137_L	141_A	1.254	1.00
48_L	52_D	1.210	1.00
155_D	186_E	1.207	1.00
149_L	157_F	1.204	1.00
134_A	137_L	1.193	1.00
51_A	184_F	1.189	1.00
124_W	128_R	1.189	1.00
174_D	178_D	1.188	1.00
160_L	164_L	1.177	1.00
71_T	74_G	1.173	1.00
110_L	114_L	1.162	1.00
36_V	39_T	1.139	1.00
86_M	180_L	1.129	1.00
124_W	127_L	1.126	1.00
60_N	63_R	1.123	1.00
54_L	86_M	1.115	1.00
66_L	70_V	1.103	1.00
132_L	136_G	1.099	1.00
42_F	47_L	1.098	1.00
49_R	53_E	1.096	1.00
25_P	29_F	1.091	1.00
27_Y	55_L	1.083	1.00
54_L	184_F	1.074	1.00
17_R	21_N	1.054	1.00
163_E	168_N	1.048	1.00
17_R	100_L	1.037	1.00
54_L	58_L	1.037	1.00
84_S	87_A	1.033	1.00
111_L	115_L	1.022	1.00
57_Y	90_K	1.020	1.00
28_E	52_D	1.018	1.00
101_L	105_V	1.002	1.00
25_P	28_E	1.001	1.00
37_P	40_T	0.995	1.00
4_A	8_P	0.994	1.00
81_R	178_D	0.993	1.00
18_L	22_P	0.989	1.00
184_F	189_F	0.977	1.00
16_V	96_A	0.974	1.00
98_R	101_L	0.973	1.00
92_L	96_A	0.967	1.00
21_N	97_L	0.964	1.00
10_L	100_L	0.959	1.00
168_N	171_W	0.959	1.00
94_Q	97_L	0.958	1.00
13_L	17_R	0.957	1.00
50_V	76_L	0.954	1.00
123_L	127_L	0.951	1.00
21_N	25_P	0.939	1.00
59_N	97_L	0.929	1.00
88_D	167_S	0.928	1.00
9_L	13_L	0.922	1.00
123_L	126_L	0.909	1.00
163_E	167_S	0.900	1.00
51_A	55_L	0.899	1.00
66_L	72_V	0.887	1.00
3_F	107_L	0.880	1.00
50_V	54_L	0.876	1.00
37_P	47_L	0.875	1.00
65_D	68_V	0.873	1.00
81_R	84_S	0.869	1.00
149_L	156_Q	0.865	1.00
95_L	99_V	0.859	1.00
114_L	119_K	0.857	1.00
180_L	184_F	0.856	1.00
133_L	137_L	0.850	1.00
57_Y	87_A	0.850	1.00
50_V	70_V	0.847	1.00
115_L	118_R	0.842	1.00
116_R	120_K	0.835	1.00
49_R	70_V	0.815	0.99
37_P	44_K	0.812	0.99
136_G	139_T	0.811	0.99
28_E	32_D	0.809	0.99
6_L	110_L	0.807	0.99
155_D	159_T	0.807	0.99
31_Y	36_V	0.806	0.99
78_N	83_L	0.806	0.99
54_L	77_F	0.799	0.99
69_P	72_V	0.792	0.99
30_E	36_V	0.783	0.99
53_E	68_V	0.777	0.99
131_G	135_G	0.775	0.99
77_F	82_E	0.769	0.99
42_F	76_L	0.769	0.99
19_L	22_P	0.768	0.99
86_M	89_V	0.763	0.99
149_L	153_D	0.760	0.99
157_F	160_L	0.760	0.99
70_V	76_L	0.754	0.99
103_S	107_L	0.753	0.99
81_R	169_D	0.742	0.99
10_L	13_L	0.737	0.99
29_F	32_D	0.730	0.99
6_L	103_S	0.727	0.99
135_G	139_T	0.724	0.99
157_F	165_F	0.721	0.99
165_F	173_F	0.721	0.99
6_L	106_L	0.717	0.99
76_L	183_L	0.715	0.99
31_Y	34_Y	0.713	0.99
8_P	11_L	0.712	0.99
185_P	189_F	0.708	0.98
159_T	186_E	0.707	0.98
3_F	8_P	0.706	0.98
181_I	184_F	0.705	0.98
15_S	19_L	0.704	0.98
53_E	63_R	0.700	0.98
57_Y	60_N	0.700	0.98
112_L	115_L	0.699	0.98
60_N	64_E	0.699	0.98
117_R	120_K	0.694	0.98
71_T	75_E	0.692	0.98
47_L	183_L	0.692	0.98
31_Y	47_L	0.690	0.98
56_D	60_N	0.690	0.98
154_F	186_E	0.680	0.98
78_N	177_T	0.677	0.98
17_R	97_L	0.675	0.98
153_D	160_L	0.674	0.98
156_Q	159_T	0.672	0.98
130_R	134_A	0.665	0.98
53_E	56_D	0.661	0.98
93_F	184_F	0.661	0.98
18_L	21_N	0.660	0.98
100_L	103_S	0.653	0.97
67_D	71_T	0.652	0.97
47_L	50_V	0.646	0.97
153_D	157_F	0.645	0.97
43_S	49_R	0.644	0.97
85_H	89_V	0.638	0.97
152_I	160_L	0.637	0.97
4_A	138_L	0.635	0.97
122_R	125_R	0.634	0.97
116_R	119_K	0.631	0.97
12_L	22_P	0.630	0.97
85_H	162_H	0.629	0.97
70_V	73_D	0.626	0.97
13_L	100_L	0.625	0.97
51_A	188_F	0.623	0.97
122_R	126_L	0.622	0.97
172_L	178_D	0.621	0.97
143_L	146_L	0.618	0.96
31_Y	48_L	0.614	0.96
149_L	160_L	0.611	0.96
140_L	144_V	0.610	0.96
133_L	136_G	0.608	0.96
158_F	173_F	0.608	0.96
51_A	86_M	0.605	0.96
95_L	98_R	0.601	0.96
165_F	168_N	0.593	0.95
161_F	164_L	0.586	0.95
120_K	123_L	0.585	0.95
165_F	170_L	0.582	0.95
49_R	52_D	0.581	0.95
166_F	171_W	0.579	0.95
93_F	158_F	0.577	0.95
97_L	101_L	0.577	0.95
51_A	54_L	0.577	0.95
68_V	71_T	0.576	0.95
167_S	173_F	0.573	0.95
67_D	72_V	0.573	0.95
158_F	162_H	0.571	0.94
132_L	139_T	0.570	0.94
16_V	19_L	0.567	0.94
63_R	67_D	0.566	0.94
22_P	29_F	0.563	0.94
168_N	172_L	0.561	0.94
47_L	51_A	0.560	0.94
31_Y	37_P	0.558	0.94
184_F	188_F	0.551	0.93
97_L	100_L	0.550	0.93
40_T	47_L	0.550	0.93
13_L	20_L	0.549	0.93
176_S	179_T	0.548	0.93
17_R	96_A	0.548	0.93
130_R	141_A	0.547	0.93
60_N	65_D	0.546	0.93
42_F	46_E	0.546	0.93
58_L	184_F	0.545	0.93
82_E	179_T	0.545	0.93
4_A	134_A	0.543	0.93
13_L	16_V	0.540	0.93
173_F	184_F	0.539	0.93
67_D	83_L	0.538	0.93
6_L	107_L	0.536	0.92
142_L	146_L	0.532	0.92
8_P	17_R	0.532	0.92
45_E	48_L	0.531	0.92
42_F	179_T	0.530	0.92
84_S	168_N	0.526	0.92
13_L	22_P	0.524	0.92
115_L	120_K	0.522	0.91
139_T	143_L	0.521	0.91
36_V	187_G	0.518	0.91
58_L	90_K	0.517	0.91
66_L	83_L	0.515	0.91
147_G	151_L	0.511	0.91
88_D	92_L	0.510	0.90
40_T	182_R	0.509	0.90
178_D	182_R	0.509	0.90
5_L	111_L	0.508	0.90
46_E	72_V	0.508	0.90
65_D	69_P	0.507	0.90
167_S	171_W	0.505	0.90
61_G	64_E	0.505	0.90
132_L	135_G	0.504	0.90
56_D	61_G	0.503	0.90
136_G	140_L	0.501	0.90
82_E	183_L	0.500	0.90
21_N	55_L	0.500	0.90

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
2gsmB	1	0.5979	5.8	0.941	Contact Map
4pd6A	3	0.4233	3	0.949	Contact Map
2kncA	1	0.2116	2.1	0.953	Contact Map
3dctB	1	0.0582	1.8	0.954	Contact Map
2lk9A	1	0.127	1.8	0.955	Contact Map
2mofA	1	0.2222	1.6	0.956	Contact Map
4g6vB	1	0.2434	1.6	0.956	Contact Map
2ks1B	1	0.2328	1.6	0.956	Contact Map
2i53A	1	0.3228	1.5	0.956	Contact Map
4hkrA	3	0.2857	1.4	0.957	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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