DUF4988 - PFAM28P - GREMLIN Contacts

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DUF4988 - Domain of unknown function

PFAM:	PF16378	Sequences: DDSDLRDDIDDLEDRVTALEELVKQLNTNISALQTLVQNGDYITSVEEGDDGGYTITFSDGTTITIYNGKDGDGDTPVIGVDEDGYWTVTGDDGETEWLLDADGNKIPATGEDGKDGVTPQLKIDEDGYWTVSYDGGKTWTRLGDANGNPVKATGGGGGEDGDSFFKSVTVDDDGYVTFTLADGTTITIP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	190 (179)
Sequences:	744 (661)
Seq/√Len:	49.4
META:	0.87

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
123_K	131_T	5.515	1.00
101_D	105_N	3.873	1.00
15_R	20_E	3.675	1.00
12_L	16_V	3.356	1.00
41_D	60_D	3.296	1.00
80_G	88_T	3.075	1.00
8_D	13_E	2.716	1.00
172_D	178_T	2.521	1.00
176_Y	188_T	2.401	1.00
159_G	162_G	2.371	1.00
41_D	61_G	2.344	1.00
58_F	64_I	2.333	1.00
41_D	59_S	2.278	1.00
123_K	126_E	2.209	1.00
135_D	139_T	2.191	1.00
98_W	106_K	2.129	1.00
49_G	52_G	2.095	1.00
69_G	72_G	2.092	1.00
82_D	106_K	2.007	1.00
129_Y	142_R	1.983	0.99
133_S	139_T	1.927	0.99
145_D	149_N	1.847	0.99
125_D	131_T	1.809	0.99
180_T	186_T	1.791	0.99
133_S	140_W	1.772	0.99
5_L	9_I	1.731	0.99
41_D	62_T	1.723	0.99
125_D	142_R	1.705	0.98
48_E	52_G	1.641	0.98
170_T	173_D	1.589	0.97
170_T	174_D	1.575	0.97
6_R	10_D	1.566	0.97
121_Q	133_S	1.544	0.97
48_E	51_D	1.528	0.97
86_Y	89_V	1.527	0.97
45_S	57_T	1.521	0.97
129_Y	143_L	1.519	0.97
133_S	137_G	1.494	0.96
90_T	96_T	1.450	0.96
172_D	176_Y	1.427	0.95
129_Y	145_D	1.427	0.95
11_D	15_R	1.418	0.95
131_T	142_R	1.416	0.95
26_L	30_I	1.408	0.95
19_L	23_V	1.385	0.94
101_D	107_I	1.385	0.94
6_R	9_I	1.370	0.94
7_D	10_D	1.349	0.94
13_E	17_T	1.341	0.93
123_K	140_W	1.335	0.93
86_Y	106_K	1.299	0.92
121_Q	140_W	1.259	0.91
52_G	67_Y	1.242	0.90
114_G	117_G	1.240	0.90
178_T	188_T	1.238	0.90
145_D	153_A	1.225	0.90
47_E	52_G	1.212	0.89
179_F	187_I	1.207	0.89
44_T	59_S	1.194	0.89
89_V	107_I	1.194	0.89
60_D	63_T	1.179	0.88
88_T	92_D	1.178	0.88
56_I	179_F	1.155	0.87
148_G	151_V	1.140	0.86
53_G	68_N	1.138	0.86
117_G	130_W	1.122	0.85
170_T	178_T	1.113	0.85
49_G	53_G	1.110	0.85
169_V	179_F	1.101	0.84
144_G	150_P	1.095	0.84
46_V	166_F	1.087	0.83
170_T	180_T	1.071	0.82
134_Y	143_L	1.071	0.82
46_V	56_I	1.067	0.82
131_T	140_W	1.063	0.82
131_T	153_A	1.058	0.82
47_E	51_D	1.057	0.82
173_D	188_T	1.049	0.81
179_F	189_I	1.047	0.81
99_L	102_A	1.041	0.81
50_D	53_G	1.039	0.81
9_I	12_L	1.039	0.81
135_D	140_W	1.036	0.80
55_T	65_T	1.029	0.80
6_R	11_D	1.025	0.80
158_G	161_D	1.021	0.79
123_K	142_R	1.020	0.79
58_F	72_G	1.015	0.79
58_F	71_D	1.007	0.78
127_D	142_R	1.003	0.78
171_V	187_I	0.995	0.78
124_I	146_A	0.988	0.77
7_D	16_V	0.980	0.76
58_F	69_G	0.979	0.76
170_T	176_Y	0.977	0.76
92_D	96_T	0.976	0.76
15_R	65_T	0.968	0.76
25_Q	29_N	0.966	0.75
178_T	187_I	0.965	0.75
21_E	24_K	0.963	0.75
133_S	136_G	0.960	0.75
143_L	146_A	0.954	0.75
142_R	150_P	0.953	0.74
122_L	143_L	0.948	0.74
91_G	94_G	0.948	0.74
61_G	109_A	0.943	0.74
166_F	181_L	0.936	0.73
9_I	16_V	0.932	0.73
90_T	94_G	0.923	0.72
32_A	64_I	0.922	0.72
72_G	76_T	0.897	0.70
7_D	11_D	0.893	0.70
148_G	152_K	0.879	0.68
12_L	15_R	0.878	0.68
97_E	100_L	0.876	0.68
168_S	180_T	0.876	0.68
41_D	58_F	0.873	0.68
81_V	126_E	0.860	0.67
127_D	153_A	0.857	0.66
100_L	103_D	0.857	0.66
167_K	180_T	0.842	0.65
162_G	165_F	0.842	0.65
5_L	71_D	0.841	0.65
124_I	144_G	0.840	0.65
70_K	73_D	0.840	0.65
46_V	140_W	0.832	0.64
55_T	63_T	0.832	0.64
101_D	104_G	0.830	0.64
64_I	69_G	0.823	0.63
119_T	134_Y	0.817	0.63
56_I	66_I	0.817	0.63
123_K	133_S	0.815	0.62
8_D	11_D	0.815	0.62
26_L	122_L	0.810	0.62
171_V	178_T	0.805	0.61
140_W	144_G	0.804	0.61
12_L	18_A	0.796	0.61
52_G	65_T	0.794	0.60
144_G	151_V	0.791	0.60
29_N	67_Y	0.788	0.60
95_E	98_W	0.778	0.59
16_V	20_E	0.771	0.58
159_G	164_S	0.771	0.58
91_G	96_T	0.769	0.58
14_D	18_A	0.766	0.58
43_I	179_F	0.765	0.57
144_G	148_G	0.763	0.57
77_P	130_W	0.763	0.57
144_G	153_A	0.760	0.57
94_G	98_W	0.757	0.57
142_R	145_D	0.747	0.56
5_L	14_D	0.746	0.56
54_Y	69_G	0.746	0.56
51_D	67_Y	0.739	0.55
125_D	129_Y	0.734	0.54
181_L	187_I	0.728	0.54
4_D	10_D	0.720	0.53
53_G	66_I	0.719	0.53
172_D	177_V	0.717	0.53
129_Y	134_Y	0.711	0.52
108_P	116_D	0.711	0.52
19_L	124_I	0.705	0.51
90_T	93_D	0.703	0.51
29_N	32_A	0.702	0.51
53_G	69_G	0.700	0.51
30_I	34_Q	0.696	0.51
123_K	153_A	0.693	0.50
4_D	16_V	0.687	0.50
26_L	67_Y	0.683	0.49
52_G	63_T	0.682	0.49
51_D	55_T	0.680	0.49
42_Y	60_D	0.677	0.49
38_Q	58_F	0.675	0.48
5_L	21_E	0.666	0.47
8_D	12_L	0.660	0.47
46_V	58_F	0.660	0.47
42_Y	158_G	0.658	0.47
53_G	67_Y	0.653	0.46
66_I	179_F	0.650	0.46
58_F	169_V	0.646	0.45
178_T	186_T	0.640	0.45
132_V	141_T	0.637	0.45
92_D	97_E	0.636	0.44
121_Q	136_G	0.636	0.44
10_D	13_E	0.630	0.44
9_I	178_T	0.630	0.44
22_L	34_Q	0.628	0.44
171_V	174_D	0.626	0.43
12_L	30_I	0.625	0.43
100_L	106_K	0.625	0.43
77_P	87_W	0.621	0.43
76_T	89_V	0.620	0.43
150_P	153_A	0.619	0.43
136_G	139_T	0.618	0.43
20_E	24_K	0.618	0.43
82_D	86_Y	0.617	0.43
59_S	62_T	0.617	0.43
17_T	20_E	0.611	0.42
42_Y	59_S	0.609	0.42
132_V	143_L	0.607	0.42
4_D	7_D	0.606	0.41
18_A	21_E	0.604	0.41
16_V	19_L	0.604	0.41
11_D	14_D	0.603	0.41
7_D	24_K	0.603	0.41
173_D	176_Y	0.601	0.41
145_D	151_V	0.596	0.40
43_I	63_T	0.595	0.40
59_S	64_I	0.594	0.40
86_Y	91_G	0.594	0.40
109_A	180_T	0.592	0.40
58_F	68_N	0.591	0.40
102_A	105_N	0.588	0.40
6_R	13_E	0.587	0.40
88_T	91_G	0.586	0.39
122_L	167_K	0.585	0.39
32_A	36_L	0.579	0.39
87_W	120_P	0.579	0.39
79_I	99_L	0.579	0.39
122_L	127_D	0.576	0.38
177_V	182_A	0.565	0.37
134_Y	145_D	0.565	0.37
55_T	90_T	0.564	0.37
85_G	119_T	0.564	0.37
4_D	25_Q	0.555	0.36
166_F	179_F	0.554	0.36
123_K	135_D	0.553	0.36
6_R	141_T	0.552	0.36
72_G	114_G	0.551	0.36
129_Y	132_V	0.550	0.36
168_S	179_F	0.550	0.36
9_I	13_E	0.549	0.36
84_D	88_T	0.549	0.36
44_T	58_F	0.548	0.36
8_D	109_A	0.543	0.35
40_G	89_V	0.541	0.35
165_F	179_F	0.540	0.35
29_N	34_Q	0.534	0.35
42_Y	61_G	0.534	0.35
3_S	10_D	0.531	0.34
89_V	96_T	0.529	0.34
149_N	152_K	0.529	0.34
122_L	142_R	0.528	0.34
159_G	163_D	0.528	0.34
37_V	81_V	0.526	0.34
68_N	72_G	0.525	0.34
43_I	186_T	0.523	0.34
107_I	152_K	0.519	0.33
144_G	149_N	0.519	0.33
22_L	33_L	0.519	0.33
84_D	106_K	0.518	0.33
84_D	97_E	0.516	0.33
165_F	182_A	0.515	0.33
27_N	54_Y	0.515	0.33
172_D	186_T	0.512	0.33
9_I	110_T	0.511	0.32
24_K	63_T	0.508	0.32
99_L	107_I	0.508	0.32
11_D	25_Q	0.507	0.32
79_I	87_W	0.506	0.32
161_D	164_S	0.506	0.32
21_E	25_Q	0.505	0.32
28_T	37_V	0.504	0.32
4_D	9_I	0.503	0.32
13_E	66_I	0.501	0.32
87_W	130_W	0.500	0.31
43_I	173_D	0.500	0.31
26_L	159_G	0.500	0.31

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
2pnvA	5	0.1789	74.5	0.912	Contact Map
3zifN	3	0.1684	68	0.916	Contact Map
2yy0A	6	0.1789	65.9	0.917	Contact Map
3w92A	3	0.1632	58.5	0.921	Contact Map
2oqqA	3	0.2053	48.6	0.926	Contact Map
4dznA	3	0.1684	47.7	0.926	Contact Map
4g1aA	3	0.1474	47.6	0.926	Contact Map
3a2aA	2	0.2105	47.1	0.926	Contact Map
1kd8A	1	0.1842	45.3	0.927	Contact Map
2ynyA	3	0.1947	42.9	0.928	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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