DUF4859 - PFAM28P - GREMLIN Contacts

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DUF4859 - Domain of unknown function (DUF4859)

PFAM:	PF16151	Sequences: DYSGTTVDLDLAKIATAFGLTPSEIAAAIGAGPSGGKIKFYAVNPDGTLWDLTSNSTANGPGHWFDADGNVCSWGDGAYVYSEFDPDTLTFNIGQYPGKLKAGDTYTIKQALVYTDKTGT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	120 (112)
Sequences:	856 (744)
Seq/√Len:	70.3
META:	0.926

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_N	83_E	3.959	1.00
81_Y	94_G	3.667	1.00
66_D	70_N	3.615	1.00
21_T	24_E	3.385	1.00
101_K	104_D	3.337	1.00
63_H	110_Q	2.974	1.00
42_A	65_F	2.744	1.00
82_S	110_Q	2.662	1.00
45_P	70_N	2.559	1.00
75_G	78_A	2.271	1.00
6_T	92_N	2.115	1.00
44_N	48_T	1.904	1.00
78_A	96_Y	1.824	1.00
85_D	88_T	1.705	1.00
80_V	108_I	1.631	0.99
95_Q	100_L	1.601	0.99
58_A	94_G	1.594	0.99
19_G	22_P	1.579	0.99
100_L	106_Y	1.572	0.99
10_D	13_K	1.568	0.99
43_V	111_A	1.511	0.99
63_H	82_S	1.507	0.99
67_A	79_Y	1.503	0.99
66_D	72_C	1.484	0.99
79_Y	99_K	1.481	0.99
96_Y	99_K	1.473	0.99
85_D	90_T	1.432	0.98
33_P	36_G	1.413	0.98
56_S	61_P	1.397	0.98
38_I	112_L	1.335	0.98
82_S	108_I	1.329	0.98
19_G	25_I	1.293	0.97
41_Y	113_V	1.293	0.97
58_A	83_E	1.259	0.97
41_Y	54_S	1.253	0.96
72_C	77_G	1.232	0.96
56_S	63_H	1.217	0.96
16_T	19_G	1.213	0.96
64_W	74_W	1.200	0.95
83_E	92_N	1.190	0.95
35_G	117_K	1.187	0.95
33_P	37_K	1.149	0.94
2_Y	74_W	1.145	0.94
44_N	53_T	1.144	0.94
14_I	19_G	1.129	0.94
24_E	28_A	1.117	0.93
42_A	45_P	1.073	0.92
20_L	28_A	1.057	0.91
8_D	11_L	1.056	0.91
71_V	77_G	1.039	0.91
57_T	83_E	1.036	0.90
56_S	59_N	1.033	0.90
57_T	71_V	1.027	0.90
58_A	61_P	1.019	0.90
79_Y	106_Y	1.018	0.90
82_S	93_I	1.012	0.89
32_G	35_G	1.008	0.89
72_C	76_D	0.966	0.87
9_L	14_I	0.956	0.87
84_F	112_L	0.951	0.86
72_C	78_A	0.946	0.86
108_I	111_A	0.941	0.86
10_D	16_T	0.936	0.85
25_I	112_L	0.924	0.85
52_L	55_N	0.916	0.84
41_Y	57_T	0.913	0.84
57_T	61_P	0.906	0.83
8_D	13_K	0.900	0.83
3_S	6_T	0.880	0.82
40_F	110_Q	0.877	0.81
52_L	113_V	0.868	0.81
42_A	71_V	0.855	0.80
82_S	91_F	0.837	0.78
65_F	110_Q	0.836	0.78
23_S	102_A	0.819	0.77
44_N	70_N	0.813	0.76
57_T	60_G	0.812	0.76
12_A	19_G	0.809	0.76
10_D	14_I	0.809	0.76
90_T	105_T	0.803	0.75
12_A	16_T	0.795	0.75
15_A	22_P	0.795	0.75
74_W	97_P	0.793	0.74
91_F	110_Q	0.793	0.74
56_S	64_W	0.784	0.74
4_G	92_N	0.784	0.74
14_I	84_F	0.784	0.74
21_T	28_A	0.778	0.73
20_L	26_A	0.770	0.72
9_L	91_F	0.735	0.69
80_V	110_Q	0.734	0.69
5_T	8_D	0.733	0.69
47_G	109_K	0.729	0.68
66_D	77_G	0.724	0.68
21_T	25_I	0.719	0.67
12_A	86_P	0.713	0.66
100_L	104_D	0.712	0.66
45_P	68_D	0.694	0.64
34_S	53_T	0.687	0.64
44_N	73_S	0.684	0.63
40_F	82_S	0.684	0.63
7_V	43_V	0.656	0.60
86_P	89_L	0.654	0.60
86_P	101_K	0.649	0.59
87_D	91_F	0.646	0.59
62_G	103_G	0.645	0.59
87_D	100_L	0.642	0.58
32_G	36_G	0.639	0.58
6_T	9_L	0.632	0.57
28_A	37_K	0.629	0.57
44_N	71_V	0.627	0.57
18_F	41_Y	0.627	0.57
54_S	96_Y	0.624	0.56
40_F	91_F	0.618	0.55
34_S	107_T	0.617	0.55
84_F	88_T	0.617	0.55
79_Y	83_E	0.612	0.55
67_A	106_Y	0.612	0.55
15_A	91_F	0.609	0.54
63_H	108_I	0.609	0.54
18_F	38_I	0.606	0.54
74_W	96_Y	0.606	0.54
93_I	108_I	0.603	0.54
14_I	18_F	0.603	0.54
63_H	97_P	0.601	0.53
18_F	39_K	0.599	0.53
2_Y	97_P	0.593	0.52
26_A	89_L	0.592	0.52
30_G	33_P	0.591	0.52
96_Y	100_L	0.589	0.52
74_W	94_G	0.588	0.52
18_F	25_I	0.587	0.52
66_D	79_Y	0.586	0.52
43_V	109_K	0.585	0.51
22_P	25_I	0.577	0.50
22_P	26_A	0.575	0.50
12_A	28_A	0.575	0.50
111_A	114_Y	0.571	0.50
42_A	61_P	0.569	0.50
2_Y	7_V	0.569	0.50
67_A	80_V	0.566	0.49
25_I	42_A	0.564	0.49
40_F	63_H	0.564	0.49
32_G	81_Y	0.562	0.49
44_N	47_G	0.562	0.49
32_G	38_I	0.558	0.48
96_Y	106_Y	0.555	0.48
15_A	21_T	0.549	0.47
2_Y	96_Y	0.541	0.46
11_L	22_P	0.540	0.46
84_F	91_F	0.537	0.46
20_L	24_E	0.535	0.45
101_K	106_Y	0.531	0.45
83_E	94_G	0.530	0.45
58_A	62_G	0.527	0.44
82_S	113_V	0.527	0.44
40_F	112_L	0.521	0.44
41_Y	80_V	0.517	0.43
78_A	99_K	0.516	0.43
28_A	87_D	0.515	0.43
68_D	87_D	0.511	0.43
41_Y	85_D	0.507	0.42
13_K	67_A	0.504	0.42
64_W	97_P	0.502	0.41
13_K	17_A	0.502	0.41
64_W	81_Y	0.500	0.41
102_A	117_K	0.500	0.41
30_G	90_T	0.500	0.41

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
1ufmA	1	0.5167	10.6	0.907	Contact Map
4d0pA	1	0.4333	10.3	0.907	Contact Map
3j8bM	1	0.4333	9	0.909	Contact Map
2vf1A	10	0.775	5.9	0.917	Contact Map
4pu7B	2	0.3917	5.1	0.919	Contact Map
4wbhA	2	0	5	0.92	Contact Map
1wi9A	1	0.4917	4.5	0.921	Contact Map
3ipwA	1	0.3333	4.5	0.921	Contact Map
1cx1A	1	0.6333	4.3	0.922	Contact Map
2lnbA	1	0.45	4.2	0.922	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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