DUF4359 - PFAM28P - GREMLIN Contacts

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DUF4359 - Domain of unknown function (DUF4359)

PFAM:	PF14271	Sequences: VALALTNPSKEDYEEFAKEQLTEYLKEELCEKTPNILGNLQSNCKSLVASGGPLIESLIDNNTERQNYGLFSIYTTELGGESPSYKVVTLGIFGNFFTLDA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	101 (95)
Sequences:	1169 (947)
Seq/√Len:	97.1
META:	0.83

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_L	93_F	5.338	1.00
13_Y	76_T	2.884	1.00
66_Q	75_T	2.569	1.00
9_S	12_D	2.454	1.00
16_F	96_F	2.318	1.00
65_R	74_Y	2.226	1.00
65_R	72_S	2.214	1.00
3_L	92_I	2.192	1.00
74_Y	96_F	2.170	1.00
13_Y	74_Y	2.072	1.00
13_Y	63_T	2.045	1.00
89_T	98_T	2.042	1.00
4_A	69_G	1.908	1.00
13_Y	96_F	1.846	1.00
66_Q	73_I	1.818	1.00
14_E	60_D	1.801	1.00
6_T	94_G	1.773	1.00
63_T	76_T	1.673	1.00
10_K	14_E	1.670	1.00
7_N	65_R	1.643	1.00
74_Y	89_T	1.605	1.00
92_I	97_F	1.574	1.00
30_C	44_C	1.564	1.00
35_N	38_G	1.546	1.00
7_N	74_Y	1.513	1.00
63_T	74_Y	1.459	1.00
16_F	98_T	1.442	1.00
90_L	99_L	1.434	1.00
15_E	19_E	1.432	1.00
7_N	72_S	1.399	0.99
47_L	50_S	1.361	0.99
46_S	50_S	1.315	0.99
26_K	49_A	1.292	0.99
13_Y	89_T	1.268	0.99
89_T	96_F	1.258	0.99
13_Y	16_F	1.250	0.99
34_P	37_L	1.180	0.98
42_S	45_K	1.176	0.98
16_F	74_Y	1.167	0.98
17_A	21_L	1.124	0.98
19_E	52_G	1.103	0.97
4_A	7_N	1.072	0.97
58_L	62_N	1.064	0.97
15_E	95_N	1.056	0.96
42_S	91_G	1.041	0.96
66_Q	69_G	1.031	0.96
75_T	79_G	1.001	0.95
25_L	28_E	0.994	0.95
68_Y	71_F	0.984	0.95
16_F	63_T	0.976	0.94
75_T	88_V	0.946	0.93
43_N	46_S	0.945	0.93
7_N	63_T	0.918	0.92
17_A	28_E	0.901	0.92
28_E	53_P	0.871	0.90
88_V	96_F	0.869	0.90
17_A	65_R	0.866	0.90
44_C	47_L	0.863	0.90
12_D	15_E	0.850	0.89
63_T	96_F	0.811	0.87
45_K	49_A	0.798	0.86
11_E	24_Y	0.787	0.85
41_Q	45_K	0.780	0.85
22_T	67_N	0.778	0.84
10_K	65_R	0.764	0.83
62_N	73_I	0.746	0.82
74_Y	78_L	0.741	0.81
2_A	57_S	0.737	0.81
10_K	61_N	0.737	0.81
51_G	56_E	0.732	0.81
74_Y	88_V	0.727	0.80
5_L	42_S	0.723	0.80
77_E	85_Y	0.721	0.80
40_L	43_N	0.705	0.78
53_P	56_E	0.699	0.77
12_D	38_G	0.693	0.77
9_S	67_N	0.689	0.76
2_A	23_E	0.685	0.76
8_P	91_G	0.681	0.76
42_S	50_S	0.674	0.75
3_L	69_G	0.673	0.75
51_G	79_G	0.671	0.75
51_G	54_L	0.660	0.73
65_R	73_I	0.658	0.73
14_E	17_A	0.656	0.73
80_G	88_V	0.656	0.73
25_L	48_V	0.650	0.72
10_K	60_D	0.650	0.72
29_L	58_L	0.648	0.72
67_N	72_S	0.645	0.72
4_A	67_N	0.642	0.71
30_C	34_P	0.641	0.71
88_V	100_D	0.639	0.71
4_A	34_P	0.632	0.70
20_Q	24_Y	0.632	0.70
75_T	81_E	0.624	0.69
12_D	31_E	0.624	0.69
27_E	100_D	0.621	0.69
24_Y	27_E	0.614	0.68
17_A	72_S	0.613	0.68
20_Q	57_S	0.608	0.67
26_K	46_S	0.607	0.67
29_L	33_T	0.602	0.66
31_E	60_D	0.599	0.66
7_N	89_T	0.599	0.66
7_N	17_A	0.594	0.65
90_L	96_F	0.594	0.65
13_Y	93_F	0.591	0.65
94_G	99_L	0.591	0.65
21_L	78_L	0.583	0.64
70_L	98_T	0.581	0.64
24_Y	49_A	0.578	0.63
80_G	97_F	0.578	0.63
77_E	92_I	0.576	0.63
87_V	94_G	0.575	0.63
19_E	32_K	0.570	0.62
5_L	21_L	0.561	0.61
70_L	73_I	0.559	0.61
25_L	95_N	0.558	0.61
22_T	77_E	0.556	0.60
13_Y	56_E	0.556	0.60
13_Y	88_V	0.554	0.60
68_Y	73_I	0.554	0.60
5_L	67_N	0.548	0.59
65_R	96_F	0.547	0.59
63_T	88_V	0.545	0.59
23_E	40_L	0.544	0.59
36_I	71_F	0.539	0.58
15_E	86_K	0.539	0.58
46_S	70_L	0.533	0.57
32_K	100_D	0.532	0.57
11_E	31_E	0.532	0.57
20_Q	60_D	0.532	0.57
25_L	58_L	0.529	0.57
17_A	27_E	0.529	0.57
9_S	81_E	0.523	0.56
28_E	34_P	0.519	0.55
61_N	64_E	0.517	0.55
4_A	75_T	0.517	0.55
42_S	90_L	0.515	0.55
55_I	73_I	0.506	0.53
71_F	90_L	0.500	0.52

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
2rp4A	4	0.5446	11	0.894	Contact Map
1h6qA	1	0.8416	7.2	0.903	Contact Map
1wixA	1	0.4356	6.7	0.904	Contact Map
1yz1A	1	0.8416	5.8	0.907	Contact Map
1txjA	1	0.8416	5.1	0.909	Contact Map
1lshA	1	0.9307	4.6	0.911	Contact Map
2kg4A	1	0.4257	3.9	0.914	Contact Map
4cgyA	1	0.7129	3.8	0.915	Contact Map
2iueA	1	0.4554	3.6	0.916	Contact Map
1wy6A	1	0.6634	3.6	0.916	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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