DUF3504 - PFAM28P - GREMLIN Contacts

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DUF3504 - Domain of unknown function (DUF3504)

PFAM:	PF12012	Sequences: VISREEEEKLWESGQLGTDSPQGLLNTVWFFNTKYFGLRGREEHRQLKFSDFVLKTDENGRTKYEYLEYTEPESKTRTGGLKKRKEEPKVVRMYENPTNPERCPVKLYKLYLSKRPPSCKARNDPFYLRPKRSCSPDSPVWYSNQPLGKNTLGKMMKRISM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	161 (153)
Sequences:	832 (728)
Seq/√Len:	58.9
META:	0.571

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
75_K	79_G	3.946	1.00
17_G	23_G	3.898	1.00
65_E	109_K	3.726	1.00
44_H	127_Y	3.446	1.00
110_L	114_K	3.016	1.00
54_L	109_K	2.844	1.00
21_P	141_W	2.475	1.00
116_P	128_L	2.433	1.00
76_T	79_G	2.365	1.00
45_R	146_P	2.358	1.00
25_L	147_L	2.337	1.00
52_F	108_Y	2.307	1.00
54_L	108_Y	2.282	1.00
27_T	107_L	2.237	1.00
41_R	153_G	2.236	1.00
7_E	11_W	2.141	1.00
115_R	128_L	2.098	1.00
47_L	127_Y	2.020	1.00
27_T	31_F	1.968	1.00
77_R	80_G	1.965	1.00
20_S	23_G	1.954	1.00
80_G	83_K	1.839	1.00
49_F	112_L	1.836	1.00
74_S	79_G	1.820	1.00
29_W	33_T	1.757	0.99
17_G	27_T	1.701	0.99
25_L	142_Y	1.665	0.99
49_F	115_R	1.639	0.99
31_F	107_L	1.578	0.99
8_E	102_R	1.564	0.98
38_L	43_E	1.500	0.98
78_T	82_K	1.475	0.98
75_K	78_T	1.470	0.98
131_K	143_S	1.466	0.98
79_G	83_K	1.444	0.97
23_G	27_T	1.441	0.97
93_M	96_N	1.431	0.97
9_K	13_S	1.409	0.97
116_P	127_Y	1.402	0.97
20_S	142_Y	1.364	0.96
42_E	46_Q	1.349	0.96
74_S	77_R	1.335	0.96
76_T	80_G	1.328	0.96
107_L	142_Y	1.318	0.96
57_D	60_G	1.311	0.95
67_L	108_Y	1.221	0.93
32_N	104_P	1.199	0.93
7_E	34_K	1.190	0.92
75_K	81_L	1.188	0.92
25_L	115_R	1.187	0.92
16_L	27_T	1.185	0.92
47_L	51_D	1.179	0.92
55_K	68_E	1.165	0.92
31_F	104_P	1.163	0.91
129_R	145_Q	1.134	0.90
78_T	81_L	1.120	0.90
77_R	82_K	1.117	0.90
41_R	45_R	1.113	0.90
69_Y	72_P	1.111	0.89
65_E	95_E	1.082	0.88
18_T	107_L	1.069	0.88
80_G	86_E	1.066	0.87
48_K	51_D	1.057	0.87
19_D	110_L	1.036	0.86
6_E	9_K	1.027	0.85
32_N	126_F	1.023	0.85
93_M	104_P	1.014	0.85
25_L	32_N	1.000	0.84
49_F	128_L	0.999	0.84
102_R	142_Y	0.999	0.84
74_S	78_T	0.995	0.84
129_R	143_S	0.992	0.83
76_T	83_K	0.976	0.82
41_R	149_K	0.963	0.82
8_E	12_E	0.950	0.81
18_T	27_T	0.948	0.80
32_N	36_F	0.947	0.80
131_K	138_S	0.943	0.80
74_S	80_G	0.917	0.78
128_L	141_W	0.914	0.78
29_W	159_I	0.914	0.78
89_K	94_Y	0.912	0.78
79_G	82_K	0.906	0.77
51_D	127_Y	0.905	0.77
150_N	153_G	0.899	0.77
23_G	107_L	0.893	0.76
66_Y	69_Y	0.890	0.76
38_L	127_Y	0.888	0.76
43_E	116_P	0.887	0.76
78_T	83_K	0.887	0.76
106_K	110_L	0.885	0.76
104_P	141_W	0.885	0.76
65_E	69_Y	0.879	0.75
28_V	115_R	0.872	0.75
83_K	86_E	0.868	0.74
11_W	107_L	0.860	0.74
77_R	81_L	0.853	0.73
25_L	111_Y	0.853	0.73
114_K	141_W	0.851	0.73
49_F	126_F	0.843	0.72
154_K	157_K	0.842	0.72
29_W	157_K	0.841	0.72
3_S	6_E	0.840	0.72
33_T	44_H	0.840	0.72
148_G	152_L	0.834	0.71
50_S	115_R	0.826	0.71
26_N	155_M	0.818	0.70
52_F	126_F	0.807	0.69
110_L	113_S	0.804	0.68
26_N	45_R	0.801	0.68
25_L	44_H	0.799	0.68
54_L	67_L	0.788	0.67
151_T	154_K	0.786	0.67
97_P	100_P	0.786	0.67
36_F	104_P	0.783	0.66
73_E	78_T	0.777	0.66
75_K	83_K	0.774	0.66
7_E	107_L	0.772	0.65
136_P	139_P	0.772	0.65
100_P	106_K	0.770	0.65
23_G	110_L	0.770	0.65
28_V	126_F	0.762	0.64
25_L	155_M	0.761	0.64
77_R	86_E	0.760	0.64
27_T	44_H	0.755	0.64
43_E	51_D	0.748	0.63
32_N	127_Y	0.748	0.63
22_Q	151_T	0.746	0.63
111_Y	126_F	0.743	0.62
114_K	140_V	0.738	0.62
129_R	151_T	0.738	0.62
31_F	35_Y	0.733	0.61
54_L	152_L	0.733	0.61
44_H	49_F	0.731	0.61
29_W	44_H	0.730	0.61
29_W	155_M	0.727	0.61
14_G	19_D	0.727	0.61
14_G	17_G	0.726	0.61
11_W	31_F	0.724	0.60
95_E	106_K	0.724	0.60
33_T	159_I	0.722	0.60
57_D	94_Y	0.720	0.60
65_E	72_P	0.719	0.60
33_T	38_L	0.716	0.59
11_W	27_T	0.716	0.59
39_R	146_P	0.715	0.59
75_K	80_G	0.714	0.59
81_L	86_E	0.713	0.59
71_E	75_K	0.713	0.59
30_F	155_M	0.706	0.58
26_N	158_R	0.704	0.58
45_R	152_L	0.703	0.58
17_G	20_S	0.699	0.58
35_Y	104_P	0.697	0.57
71_E	74_S	0.685	0.56
116_P	143_S	0.681	0.56
133_S	136_P	0.678	0.55
118_S	144_N	0.677	0.55
58_E	142_Y	0.677	0.55
77_R	83_K	0.667	0.54
95_E	103_C	0.658	0.53
43_E	148_G	0.656	0.53
29_W	51_D	0.655	0.53
67_L	113_S	0.654	0.53
50_S	119_C	0.644	0.52
8_E	15_Q	0.640	0.51
92_R	96_N	0.637	0.51
151_T	158_R	0.636	0.51
149_K	153_G	0.634	0.50
10_L	159_I	0.632	0.50
38_L	116_P	0.632	0.50
57_D	61_R	0.629	0.50
82_K	86_E	0.626	0.50
29_W	156_M	0.624	0.49
24_L	48_K	0.621	0.49
79_G	84_R	0.619	0.49
57_D	66_Y	0.619	0.49
5_E	22_Q	0.615	0.48
78_T	84_R	0.606	0.47
33_T	37_G	0.602	0.47
3_S	9_K	0.600	0.47
121_A	132_R	0.598	0.46
85_K	88_P	0.596	0.46
8_E	11_W	0.595	0.46
49_F	120_K	0.591	0.46
33_T	111_Y	0.586	0.45
30_F	33_T	0.585	0.45
40_G	45_R	0.581	0.45
80_G	84_R	0.580	0.45
45_R	155_M	0.580	0.45
135_S	138_S	0.571	0.44
81_L	84_R	0.569	0.43
20_S	154_K	0.567	0.43
25_L	127_Y	0.559	0.42
6_E	23_G	0.559	0.42
54_L	112_L	0.558	0.42
54_L	65_E	0.557	0.42
148_G	151_T	0.555	0.42
76_T	81_L	0.552	0.41
35_Y	108_Y	0.549	0.41
148_G	153_G	0.547	0.41
44_H	80_G	0.546	0.41
103_C	147_L	0.542	0.40
147_L	151_T	0.541	0.40
98_T	106_K	0.541	0.40
94_Y	97_P	0.541	0.40
30_F	111_Y	0.540	0.40
90_V	137_D	0.538	0.40
21_P	71_E	0.537	0.40
3_S	10_L	0.530	0.39
51_D	71_E	0.527	0.39
69_Y	73_E	0.523	0.38
37_G	129_R	0.520	0.38
31_F	44_H	0.519	0.38
4_R	12_E	0.518	0.38
130_P	143_S	0.517	0.38
51_D	120_K	0.515	0.38
11_W	44_H	0.515	0.38
21_P	128_L	0.514	0.37
38_L	44_H	0.513	0.37
96_N	99_N	0.513	0.37
74_S	83_K	0.512	0.37
23_G	138_S	0.511	0.37
156_M	159_I	0.508	0.37
54_L	69_Y	0.508	0.37
41_R	152_L	0.505	0.36
93_M	97_P	0.505	0.36
147_L	155_M	0.504	0.36
95_E	98_T	0.503	0.36
21_P	117_P	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
3nkhA	2	0.8199	85.5	0.891	Contact Map
2a3vA	3	0.7764	80.7	0.897	Contact Map
4a8eA	2	0.7081	80.6	0.897	Contact Map
1xo0A	3	0.8199	78.8	0.899	Contact Map
1a0pA	1	0.7391	78.7	0.899	Contact Map
1ae9A	4	0.7205	72	0.904	Contact Map
1z19A	3	0.7205	70.4	0.905	Contact Map
1z1bA	3	0.7205	61.2	0.911	Contact Map
1aihA	2	0.7267	14.6	0.937	Contact Map
2jubA	1	0.1801	3.6	0.952	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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