DUF3316 - PFAM28P - GREMLIN Contacts

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DUF3316 - Protein of unknown function (DUF3316)

PFAM:	PF11777	Sequences: KKILLLLLLLLLSLPLFAQTASATDADSLEANRPVTRSTMIGIGGTNILDTYLSPLKYTGTGLRFLYERMRMTRLANGRWSRQQIFQADLSSTKNPAGNASELSGFYNYSYGLHYRFRPDPNLKLLAGGLADANLGFIYNTRNSN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	145 (135)
Sequences:	815 (686)
Seq/√Len:	59.1
META:	0.887

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_L	96_P	5.242	1.00
112_G	130_L	4.151	1.00
48_I	93_T	3.630	1.00
95_N	99_N	3.054	1.00
100_A	142_R	2.778	1.00
42_G	64_R	2.769	1.00
43_I	61_T	2.729	1.00
112_G	129_G	2.597	1.00
84_Q	109_Y	2.597	1.00
39_T	65_F	2.468	1.00
94_K	98_G	2.321	1.00
105_G	137_F	2.256	1.00
86_F	107_Y	2.174	1.00
62_G	89_D	1.961	1.00
104_S	138_I	1.881	1.00
120_D	123_L	1.859	1.00
82_R	111_Y	1.807	0.99
37_R	69_R	1.800	0.99
67_Y	84_Q	1.714	0.99
47_N	59_T	1.711	0.99
47_N	57_K	1.699	0.99
58_Y	95_N	1.688	0.99
73_T	76_A	1.594	0.99
92_S	103_L	1.571	0.99
16_L	19_Q	1.511	0.98
5_L	8_L	1.478	0.98
106_F	134_N	1.463	0.98
46_T	91_S	1.452	0.98
39_T	67_Y	1.432	0.97
15_P	28_S	1.366	0.96
102_E	140_N	1.364	0.96
81_S	116_R	1.362	0.96
27_D	30_E	1.326	0.96
8_L	14_L	1.301	0.95
81_S	115_Y	1.301	0.95
40_M	66_L	1.272	0.95
55_P	58_Y	1.265	0.94
100_A	143_N	1.265	0.94
116_R	124_K	1.231	0.94
39_T	109_Y	1.224	0.93
90_L	103_L	1.223	0.93
73_T	113_L	1.220	0.93
44_G	51_T	1.202	0.93
69_R	84_Q	1.191	0.92
80_W	115_Y	1.182	0.92
81_S	114_H	1.181	0.92
48_I	138_I	1.180	0.92
92_S	101_S	1.172	0.92
92_S	97_A	1.155	0.91
108_N	134_N	1.152	0.91
70_M	83_Q	1.151	0.91
51_T	90_L	1.142	0.91
56_L	100_A	1.135	0.91
94_K	101_S	1.109	0.89
139_Y	145_N	1.079	0.88
95_N	100_A	1.071	0.88
98_G	101_S	1.039	0.86
37_R	67_Y	1.038	0.86
26_A	30_E	1.029	0.86
35_V	69_R	1.019	0.85
110_S	132_D	1.013	0.85
54_S	143_N	1.012	0.85
112_G	116_R	0.981	0.83
80_W	113_L	0.979	0.83
39_T	68_E	0.970	0.82
7_L	11_L	0.967	0.82
10_L	43_I	0.963	0.82
68_E	85_I	0.963	0.82
85_I	114_H	0.956	0.81
43_I	124_K	0.947	0.81
58_Y	110_S	0.946	0.80
51_T	136_G	0.942	0.80
11_L	17_F	0.922	0.79
58_Y	142_R	0.907	0.78
63_L	141_T	0.896	0.77
99_N	116_R	0.892	0.76
65_F	68_E	0.884	0.76
7_L	14_L	0.884	0.76
61_T	71_R	0.861	0.74
46_T	93_T	0.853	0.73
117_F	127_A	0.844	0.72
95_N	113_L	0.844	0.72
64_R	106_F	0.844	0.72
99_N	144_S	0.832	0.71
19_Q	27_D	0.830	0.71
119_P	123_L	0.824	0.70
83_Q	114_H	0.823	0.70
102_E	138_I	0.817	0.70
41_I	65_F	0.813	0.69
44_G	139_Y	0.813	0.69
65_F	89_D	0.812	0.69
90_L	132_D	0.810	0.69
82_R	113_L	0.804	0.69
83_Q	86_F	0.793	0.68
141_T	144_S	0.792	0.67
49_L	91_S	0.790	0.67
46_T	138_I	0.783	0.67
99_N	142_R	0.781	0.66
85_I	110_S	0.781	0.66
56_L	107_Y	0.781	0.66
114_H	126_L	0.776	0.66
86_F	109_Y	0.776	0.66
49_L	54_S	0.774	0.66
54_S	142_R	0.772	0.65
74_R	77_N	0.759	0.64
35_V	39_T	0.756	0.64
58_Y	100_A	0.754	0.64
36_T	138_I	0.748	0.63
29_L	32_N	0.747	0.63
108_N	132_D	0.745	0.63
37_R	41_I	0.742	0.62
75_L	83_Q	0.742	0.62
53_L	128_G	0.740	0.62
68_E	83_Q	0.737	0.62
38_S	133_A	0.735	0.62
38_S	70_M	0.733	0.61
14_L	18_A	0.730	0.61
27_D	31_A	0.728	0.61
63_L	90_L	0.726	0.61
8_L	16_L	0.721	0.60
95_N	142_R	0.716	0.60
81_S	126_L	0.714	0.59
68_E	86_F	0.705	0.58
11_L	26_A	0.704	0.58
39_T	69_R	0.703	0.58
127_A	137_F	0.703	0.58
5_L	12_L	0.701	0.58
9_L	15_P	0.700	0.58
67_Y	107_Y	0.696	0.57
44_G	70_M	0.692	0.57
140_N	143_N	0.689	0.57
39_T	76_A	0.688	0.57
93_T	102_E	0.686	0.56
115_Y	140_N	0.684	0.56
46_T	66_L	0.684	0.56
66_L	85_I	0.682	0.56
47_N	137_F	0.680	0.56
88_A	103_L	0.680	0.56
121_P	126_L	0.677	0.55
109_Y	133_A	0.674	0.55
53_L	143_N	0.673	0.55
46_T	103_L	0.667	0.54
9_L	12_L	0.667	0.54
131_A	141_T	0.665	0.54
34_P	42_G	0.661	0.54
48_I	96_P	0.661	0.54
91_S	104_S	0.661	0.54
93_T	100_A	0.655	0.53
10_L	13_S	0.651	0.52
62_G	106_F	0.649	0.52
9_L	19_Q	0.644	0.52
27_D	79_R	0.642	0.51
124_K	127_A	0.640	0.51
28_S	31_A	0.634	0.51
33_R	118_R	0.634	0.51
9_L	27_D	0.630	0.50
62_G	81_S	0.629	0.50
64_R	87_Q	0.629	0.50
138_I	144_S	0.624	0.49
7_L	15_P	0.621	0.49
5_L	11_L	0.613	0.48
96_P	102_E	0.609	0.48
6_L	11_L	0.599	0.47
37_R	78_G	0.587	0.45
54_S	105_G	0.585	0.45
91_S	132_D	0.579	0.44
27_D	43_I	0.577	0.44
75_L	80_W	0.575	0.44
103_L	131_A	0.571	0.44
49_L	123_L	0.568	0.43
12_L	18_A	0.567	0.43
9_L	14_L	0.557	0.42
10_L	17_F	0.557	0.42
90_L	106_F	0.557	0.42
105_G	127_A	0.555	0.42
11_L	127_A	0.554	0.42
52_Y	60_G	0.554	0.42
64_R	109_Y	0.552	0.42
5_L	9_L	0.548	0.41
34_P	37_R	0.545	0.41
72_M	116_R	0.541	0.40
37_R	53_L	0.541	0.40
12_L	28_S	0.541	0.40
44_G	144_S	0.540	0.40
90_L	104_S	0.538	0.40
62_G	66_L	0.538	0.40
30_E	51_T	0.536	0.40
63_L	105_G	0.532	0.39
6_L	17_F	0.530	0.39
8_L	15_P	0.530	0.39
60_G	128_G	0.527	0.39
80_W	83_Q	0.527	0.39
120_D	133_A	0.525	0.39
13_S	30_E	0.523	0.38
6_L	14_L	0.520	0.38
36_T	103_L	0.517	0.38
42_G	115_Y	0.517	0.38
36_T	134_N	0.517	0.38
46_T	139_Y	0.513	0.37
89_D	106_F	0.509	0.37
16_L	93_T	0.507	0.37
68_E	97_A	0.500	0.36

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
3nb3A	2	0.6207	86.1	0.882	Contact Map
2k0lA	1	0.7793	21.8	0.926	Contact Map
2f2fC	1	0.6483	6	0.943	Contact Map
2q1fA	1	0.731	5.8	0.943	Contact Map
1vw4F	1	0.4966	5	0.945	Contact Map
4fqeA	1	0.4828	3	0.95	Contact Map
4ymxA	1	0.6207	2.8	0.951	Contact Map
3zbiC	1	0.1931	2.3	0.953	Contact Map
2wjrA	1	0.4966	1.6	0.957	Contact Map
2jenA	5	0.6759	1.6	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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