DUF4360 - PFAM28P - GREMLIN Contacts

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DUF4360 - Domain of unknown function (DUF4360)

PFAM:	PF14273	Sequences: DKITIDVVTYNGSGCPAGTASVAVSPDNTAFTVLFDQYLAQAGPGAGPTDDRKNCQLNLPVHVPQGFTYAIASADYRGFASLPAGATATQRAEYYFQGSSQTGSFSHTFTGPLDDDYQITDTLGVASLVWSPCGADRNLNINTELRVTSSNSSATSFITMDSTDGSITTVYHLQWRRC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	178 (176)
Sequences:	1548 (1201)
Seq/√Len:	90.5
META:	0.708

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_Y	143_T	5.164	1.00
88_A	158_I	4.164	1.00
70_A	128_L	3.972	1.00
68_T	131_S	3.695	1.00
81_S	114_D	3.185	1.00
83_P	156_S	3.019	1.00
54_N	142_N	2.786	1.00
56_Q	95_Y	2.709	1.00
31_F	165_G	2.574	1.00
80_A	88_A	2.573	1.00
91_R	104_S	2.447	1.00
20_A	33_V	2.388	1.00
79_F	114_D	2.224	1.00
75_D	120_T	2.154	1.00
95_Y	140_N	2.112	1.00
35_F	163_T	2.102	1.00
80_A	113_L	2.051	1.00
19_T	37_Q	2.041	1.00
94_Y	121_D	2.030	1.00
4_T	62_H	1.987	1.00
76_Y	94_Y	1.984	1.00
67_F	126_A	1.976	1.00
86_A	156_S	1.926	1.00
97_Q	137_R	1.763	1.00
70_A	130_W	1.760	1.00
68_T	176_R	1.736	1.00
73_S	120_T	1.736	1.00
52_R	144_E	1.728	1.00
67_F	177_R	1.711	1.00
42_A	147_V	1.594	1.00
12_G	15_C	1.585	1.00
91_R	106_S	1.560	1.00
148_T	154_A	1.556	1.00
77_R	162_S	1.539	1.00
89_T	106_S	1.528	1.00
62_H	136_D	1.527	1.00
130_W	176_R	1.512	1.00
65_Q	175_W	1.511	1.00
46_A	50_D	1.486	1.00
58_N	138_N	1.474	1.00
87_T	110_T	1.403	0.99
83_P	86_A	1.393	0.99
80_A	158_I	1.375	0.99
82_L	147_V	1.341	0.99
69_Y	173_L	1.326	0.99
73_S	122_T	1.322	0.99
150_S	154_A	1.315	0.99
56_Q	142_N	1.299	0.99
148_T	152_S	1.281	0.99
93_E	102_T	1.278	0.99
33_V	57_L	1.273	0.99
40_A	147_V	1.252	0.98
25_S	30_A	1.248	0.98
13_S	39_L	1.239	0.98
58_N	140_N	1.235	0.98
6_D	60_P	1.226	0.98
169_T	172_H	1.215	0.98
80_A	109_F	1.213	0.98
77_R	164_D	1.209	0.98
109_F	119_I	1.207	0.98
82_L	86_A	1.205	0.98
10_Y	20_A	1.197	0.98
5_I	8_V	1.196	0.98
68_T	127_S	1.193	0.98
117_Y	159_T	1.190	0.98
60_P	138_N	1.153	0.97
16_P	37_Q	1.142	0.97
11_N	17_A	1.142	0.97
77_R	116_D	1.136	0.97
25_S	32_T	1.126	0.97
151_N	154_A	1.116	0.97
63_V	66_G	1.115	0.97
87_T	108_T	1.105	0.97
48_P	51_D	1.091	0.96
34_L	75_D	1.087	0.96
145_L	158_I	1.059	0.96
47_G	50_D	1.054	0.95
56_Q	140_N	1.049	0.95
89_T	108_T	1.046	0.95
43_G	46_A	1.040	0.95
24_V	28_N	1.022	0.95
96_F	132_P	1.018	0.95
90_Q	119_I	1.016	0.94
75_D	118_Q	1.013	0.94
32_T	164_D	1.008	0.94
170_V	173_L	0.994	0.94
65_Q	174_Q	0.987	0.94
59_L	141_I	0.981	0.93
148_T	151_N	0.978	0.93
58_N	97_Q	0.971	0.93
93_E	144_E	0.969	0.93
30_A	34_L	0.954	0.92
107_H	121_D	0.949	0.92
44_P	150_S	0.943	0.92
11_N	36_D	0.941	0.92
161_D	164_D	0.935	0.92
90_Q	107_H	0.927	0.91
9_T	23_A	0.923	0.91
34_L	162_S	0.914	0.91
24_V	31_F	0.905	0.90
32_T	162_S	0.898	0.90
78_G	117_Y	0.891	0.90
97_Q	138_N	0.890	0.90
40_A	51_D	0.886	0.89
22_V	33_V	0.883	0.89
62_H	128_L	0.882	0.89
69_Y	130_W	0.881	0.89
174_Q	177_R	0.875	0.89
52_R	98_G	0.867	0.88
10_Y	17_A	0.864	0.88
69_Y	175_W	0.862	0.88
83_P	154_A	0.862	0.88
15_C	55_C	0.854	0.88
86_A	147_V	0.853	0.87
92_A	141_I	0.852	0.87
84_A	110_T	0.852	0.87
91_R	144_E	0.848	0.87
77_R	161_D	0.844	0.87
25_S	29_T	0.839	0.87
7_V	59_L	0.837	0.86
52_R	142_N	0.823	0.86
74_A	123_L	0.822	0.85
6_D	62_H	0.818	0.85
93_E	104_S	0.809	0.85
41_Q	50_D	0.807	0.84
3_I	7_V	0.803	0.84
130_W	133_C	0.802	0.84
36_D	116_D	0.802	0.84
22_V	31_F	0.798	0.84
105_F	123_L	0.794	0.83
64_P	94_Y	0.791	0.83
170_V	174_Q	0.783	0.83
27_D	76_Y	0.780	0.82
79_F	161_D	0.779	0.82
173_L	178_C	0.774	0.82
90_Q	137_R	0.770	0.82
71_I	175_W	0.766	0.81
148_T	155_T	0.766	0.81
81_S	115_D	0.766	0.81
32_T	161_D	0.756	0.80
19_T	57_L	0.753	0.80
175_W	178_C	0.753	0.80
95_Y	142_N	0.750	0.80
129_V	135_A	0.740	0.79
12_G	55_C	0.736	0.79
53_K	140_N	0.733	0.78
11_N	34_L	0.731	0.78
69_Y	132_P	0.726	0.78
82_L	156_S	0.724	0.77
36_D	161_D	0.703	0.75
9_T	21_S	0.703	0.75
16_P	19_T	0.702	0.75
65_Q	126_A	0.702	0.75
89_T	146_R	0.701	0.75
43_G	52_R	0.698	0.75
57_L	167_I	0.697	0.75
67_F	70_A	0.696	0.75
51_D	147_V	0.693	0.74
60_P	136_D	0.691	0.74
52_R	95_Y	0.690	0.74
11_N	58_N	0.690	0.74
50_D	53_K	0.684	0.73
11_N	16_P	0.684	0.73
128_L	176_R	0.684	0.73
34_L	164_D	0.682	0.73
109_F	168_T	0.681	0.73
74_A	94_Y	0.667	0.71
7_V	60_P	0.666	0.71
63_V	77_R	0.665	0.71
67_F	133_C	0.665	0.71
82_L	88_A	0.664	0.71
35_F	79_F	0.662	0.71
8_V	31_F	0.661	0.71
82_L	111_G	0.655	0.70
96_F	131_S	0.653	0.70
52_R	146_R	0.645	0.69
125_V	166_S	0.644	0.69
47_G	87_T	0.644	0.69
116_D	161_D	0.643	0.69
46_A	51_D	0.643	0.69
130_W	174_Q	0.641	0.68
160_M	163_T	0.635	0.68
56_Q	141_I	0.634	0.68
92_A	96_F	0.631	0.67
30_A	164_D	0.630	0.67
45_G	48_P	0.627	0.67
123_L	127_S	0.625	0.66
42_A	150_S	0.623	0.66
75_D	164_D	0.622	0.66
9_T	58_N	0.621	0.66
42_A	156_S	0.621	0.66
25_S	52_R	0.619	0.66
13_S	54_N	0.618	0.66
73_S	100_S	0.616	0.65
145_L	160_M	0.614	0.65
44_P	154_A	0.614	0.65
40_A	52_R	0.612	0.65
10_Y	21_S	0.608	0.64
149_S	152_S	0.607	0.64
52_R	97_Q	0.607	0.64
147_V	156_S	0.601	0.63
90_Q	165_G	0.599	0.63
32_T	75_D	0.598	0.63
44_P	147_V	0.598	0.63
44_P	148_T	0.597	0.63
107_H	119_I	0.597	0.63
79_F	157_F	0.594	0.63
39_L	159_T	0.594	0.63
55_C	178_C	0.590	0.62
57_L	89_T	0.590	0.62
92_A	121_D	0.587	0.62
96_F	127_S	0.583	0.61
116_D	144_E	0.582	0.61
64_P	175_W	0.579	0.61
166_S	177_R	0.579	0.61
21_S	34_L	0.575	0.60
23_A	30_A	0.573	0.60
54_N	140_N	0.572	0.60
152_S	168_T	0.569	0.59
10_Y	34_L	0.568	0.59
57_L	163_T	0.567	0.59
32_T	79_F	0.560	0.58
165_G	168_T	0.557	0.58
93_E	142_N	0.557	0.58
99_S	131_S	0.551	0.57
95_Y	98_G	0.546	0.56
84_A	104_S	0.543	0.56
159_T	168_T	0.542	0.56
27_D	30_A	0.541	0.55
71_I	111_G	0.539	0.55
99_S	132_P	0.538	0.55
23_A	61_V	0.538	0.55
60_P	93_E	0.534	0.55
73_S	168_T	0.532	0.54
23_A	34_L	0.531	0.54
43_G	144_E	0.531	0.54
13_S	89_T	0.529	0.54
10_Y	36_D	0.529	0.54
157_F	161_D	0.528	0.54
38_Y	42_A	0.528	0.54
62_H	65_Q	0.527	0.54
41_Q	155_T	0.526	0.53
105_F	119_I	0.522	0.53
21_S	36_D	0.521	0.53
152_S	177_R	0.520	0.53
156_S	160_M	0.519	0.52
68_T	130_W	0.518	0.52
22_V	28_N	0.517	0.52
27_D	77_R	0.517	0.52
76_Y	121_D	0.516	0.52
67_F	112_P	0.513	0.52
32_T	77_R	0.512	0.51
44_P	152_S	0.511	0.51
70_A	131_S	0.510	0.51
74_A	141_I	0.509	0.51
40_A	158_I	0.509	0.51
21_S	26_P	0.506	0.51
42_A	83_P	0.505	0.51
131_S	135_A	0.505	0.51
70_A	94_Y	0.504	0.50
88_A	116_D	0.502	0.50
58_N	144_E	0.501	0.50
93_E	97_Q	0.500	0.50
117_Y	160_M	0.500	0.50

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
4pkmA	2	0.9438	7.3	0.939	Contact Map
1ic9A	1	0.1517	6.6	0.94	Contact Map
2lc4A	1	0.2079	3.8	0.946	Contact Map
1w3fA	4	0.6461	2.9	0.949	Contact Map
4a41A	1	0.4438	2.2	0.952	Contact Map
4b9pA	1	0.7978	1.9	0.954	Contact Map
2ag4A	1	0.309	1.7	0.956	Contact Map
3h3iA	1	0.3933	1.5	0.957	Contact Map
4ca9A	5	0.382	1.5	0.957	Contact Map
4tv4A	3	0.3258	1.5	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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