DUF4376 - PFAM28P - GREMLIN Contacts

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DUF4376 - Domain of unknown function (DUF4376)

PFAM:	PF14301	Sequences: WAEIKAARDRAETGGFTVNGKTFDTDRESQARITGAVLAAQAAPAAGTPTWKTADNTFVTLTAAQLIALAAAVAAHVQACFAAERALKAAIEAATTIEEVEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	102 (99)
Sequences:	3306 (2795)
Seq/√Len:	280.9
META:	0.838

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_A	11_A	3.890	1.00
62_T	65_Q	3.671	1.00
26_D	29_S	2.965	1.00
96_T	99_E	2.554	1.00
83_A	87_L	2.248	1.00
7_A	10_R	2.182	1.00
87_L	90_A	2.101	1.00
15_G	25_T	1.950	1.00
39_A	74_A	1.947	1.00
87_L	94_A	1.946	1.00
53_T	57_T	1.938	1.00
83_A	86_A	1.906	1.00
52_K	58_F	1.787	1.00
76_H	80_C	1.638	1.00
52_K	84_E	1.574	1.00
78_Q	82_A	1.573	1.00
5_K	88_K	1.561	1.00
34_T	38_L	1.555	1.00
53_T	59_V	1.541	1.00
6_A	10_R	1.500	1.00
52_K	85_R	1.462	1.00
17_T	22_T	1.460	1.00
50_T	60_T	1.415	1.00
24_D	29_S	1.320	1.00
85_R	89_A	1.316	1.00
36_A	51_W	1.306	1.00
23_F	69_L	1.269	1.00
52_K	81_F	1.235	1.00
63_A	67_I	1.235	1.00
97_I	100_V	1.228	1.00
41_Q	67_I	1.223	1.00
84_E	88_K	1.209	1.00
4_I	91_I	1.208	1.00
44_P	47_G	1.207	1.00
11_A	14_G	1.206	1.00
37_V	41_Q	1.201	1.00
25_T	73_V	1.195	1.00
16_F	76_H	1.171	1.00
37_V	67_I	1.157	1.00
42_A	71_A	1.123	1.00
94_A	100_V	1.114	1.00
4_I	84_E	1.077	1.00
5_K	9_D	1.072	1.00
37_V	70_A	1.060	1.00
30_Q	77_V	1.058	1.00
27_R	31_A	1.053	1.00
24_D	56_N	1.053	1.00
24_D	54_A	1.047	1.00
21_K	53_T	1.041	1.00
11_A	80_C	1.037	1.00
79_A	83_A	1.030	1.00
21_K	57_T	1.030	1.00
75_A	79_A	1.002	1.00
40_A	66_L	0.999	1.00
40_A	67_I	0.998	1.00
9_D	12_E	0.994	1.00
15_G	76_H	0.987	1.00
18_V	69_L	0.971	1.00
9_D	13_T	0.958	1.00
61_L	65_Q	0.949	1.00
64_A	67_I	0.943	1.00
95_T	99_E	0.928	1.00
43_A	47_G	0.912	1.00
68_A	72_A	0.910	1.00
12_E	80_C	0.905	1.00
43_A	46_A	0.903	1.00
12_E	32_R	0.898	1.00
16_F	73_V	0.894	1.00
8_R	84_E	0.880	1.00
40_A	63_A	0.872	1.00
4_I	7_A	0.865	1.00
18_V	65_Q	0.850	1.00
38_L	41_Q	0.849	1.00
37_V	42_A	0.834	1.00
65_Q	68_A	0.827	1.00
21_K	59_V	0.801	0.99
22_T	54_A	0.798	0.99
19_N	65_Q	0.798	0.99
2_A	6_A	0.793	0.99
18_V	72_A	0.792	0.99
23_F	61_L	0.788	0.99
21_K	55_D	0.784	0.99
85_R	88_K	0.780	0.99
36_A	66_L	0.771	0.99
40_A	43_A	0.765	0.99
81_F	85_R	0.747	0.99
32_R	35_G	0.741	0.99
89_A	93_A	0.732	0.99
32_R	77_V	0.727	0.99
33_I	73_V	0.727	0.99
27_R	32_R	0.714	0.99
88_K	92_E	0.713	0.99
23_F	53_T	0.713	0.99
11_A	83_A	0.712	0.99
50_T	58_F	0.712	0.99
29_S	32_R	0.702	0.98
4_I	88_K	0.700	0.98
90_A	94_A	0.698	0.98
91_I	100_V	0.695	0.98
30_Q	35_G	0.673	0.98
64_A	68_A	0.668	0.98
86_A	90_A	0.668	0.98
47_G	60_T	0.667	0.98
70_A	74_A	0.662	0.98
32_R	81_F	0.659	0.98
28_E	31_A	0.658	0.98
44_P	64_A	0.653	0.98
37_V	66_L	0.648	0.97
82_A	86_A	0.643	0.97
3_E	6_A	0.643	0.97
13_T	30_Q	0.643	0.97
36_A	74_A	0.639	0.97
49_P	60_T	0.634	0.97
39_A	71_A	0.629	0.97
8_R	12_E	0.627	0.97
25_T	76_H	0.619	0.97
38_L	42_A	0.613	0.96
12_E	77_V	0.613	0.96
44_P	48_T	0.612	0.96
31_A	34_T	0.608	0.96
16_F	25_T	0.606	0.96
79_A	82_A	0.604	0.96
89_A	92_E	0.597	0.96
6_A	9_D	0.595	0.96
13_T	27_R	0.588	0.95
49_P	82_A	0.586	0.95
2_A	5_K	0.583	0.95
22_T	55_D	0.581	0.95
4_I	87_L	0.579	0.95
29_S	51_W	0.574	0.95
50_T	82_A	0.573	0.95
33_I	70_A	0.573	0.95
36_A	78_Q	0.571	0.95
56_N	88_K	0.569	0.95
14_G	76_H	0.565	0.94
30_Q	34_T	0.565	0.94
35_G	77_V	0.564	0.94
35_G	70_A	0.560	0.94
58_F	85_R	0.541	0.93
76_H	79_A	0.535	0.93
49_P	85_R	0.533	0.92
73_V	77_V	0.524	0.92
52_K	56_N	0.523	0.92
67_I	70_A	0.521	0.92
80_C	83_A	0.516	0.91
83_A	94_A	0.511	0.91
42_A	67_I	0.509	0.91
72_A	75_A	0.500	0.90

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
4glwA	2	0.5	16.9	0.863	Contact Map
3uq8A	1	0.5588	11.7	0.873	Contact Map
1zauA	1	0.5098	10.8	0.875	Contact Map
4lh6A	1	0.549	7.8	0.882	Contact Map
1kq3A	5	0.7451	7.5	0.883	Contact Map
3jslA	2	0.4902	6.6	0.886	Contact Map
1b04A	1	0.5098	5.2	0.891	Contact Map
3uhjA	5	0.7255	5	0.893	Contact Map
2xb0X	1	0.7451	4.7	0.894	Contact Map
1jq5A	5	0.7353	4.4	0.896	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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