DUF4230 - PFAM28P - GREMLIN Contacts

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DUF4230 - Protein of unknown function (DUF4230)

PFAM:	PF14014	Sequences: EQIRDLSELETVEYTFEKVVTYEDSKDFLGGKRLLLVAHGTVKAGVDLSKLKPEDVEVDGDVTITLPPPEILSVELDEDRTRVYDRQTGLLNRFDPEDETELRQEAEEQIRKAALESGLLEQAEENARALLESLLRSLGFKEVTV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	145 (141)
Sequences:	10862 (7576)
Seq/√Len:	638.0
META:	0.883

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_K	70_E	3.114	1.00
68_P	124_E	2.361	1.00
69_P	124_E	2.336	1.00
132_E	136_R	2.322	1.00
10_E	43_K	2.101	1.00
6_L	10_E	2.092	1.00
128_R	132_E	2.040	1.00
124_E	128_R	2.030	1.00
43_K	73_S	2.010	1.00
36_L	81_T	1.990	1.00
121_E	125_E	1.969	1.00
111_R	115_L	1.956	1.00
45_G	72_L	1.931	1.00
107_E	111_R	1.925	1.00
47_D	50_K	1.893	1.00
77_D	80_R	1.863	1.00
109_Q	112_K	1.862	1.00
46_V	127_A	1.760	1.00
37_V	82_R	1.729	1.00
108_E	112_K	1.718	1.00
41_T	75_E	1.710	1.00
37_V	84_Y	1.704	1.00
53_P	56_V	1.663	1.00
39_H	80_R	1.634	1.00
44_A	119_L	1.595	1.00
101_E	104_Q	1.591	1.00
13_E	41_T	1.588	1.00
23_E	31_G	1.565	1.00
100_T	104_Q	1.551	1.00
52_K	55_D	1.549	1.00
98_D	102_L	1.524	1.00
103_R	107_E	1.517	1.00
105_E	108_E	1.506	1.00
40_G	110_I	1.493	1.00
23_E	33_R	1.485	1.00
27_D	30_G	1.470	1.00
122_Q	125_E	1.442	1.00
56_V	59_D	1.417	1.00
101_E	105_E	1.415	1.00
125_E	128_R	1.401	1.00
56_V	60_G	1.370	1.00
44_A	123_A	1.367	1.00
47_D	70_E	1.348	1.00
24_D	32_K	1.344	1.00
105_E	109_Q	1.342	1.00
35_L	84_Y	1.338	1.00
57_E	63_T	1.328	1.00
118_G	121_E	1.321	1.00
99_E	103_R	1.309	1.00
125_E	129_A	1.276	1.00
15_T	41_T	1.275	1.00
121_E	124_E	1.273	1.00
61_D	141_K	1.254	1.00
10_E	72_L	1.227	1.00
74_V	111_R	1.215	1.00
13_E	43_K	1.202	1.00
129_A	133_S	1.201	1.00
17_E	39_H	1.194	1.00
42_V	71_I	1.186	1.00
57_E	65_T	1.184	1.00
112_K	116_E	1.175	1.00
4_R	13_E	1.125	1.00
12_V	44_A	1.098	1.00
104_Q	108_E	1.092	1.00
69_P	120_L	1.088	1.00
8_E	43_K	1.080	1.00
11_T	45_G	1.074	1.00
104_Q	107_E	1.069	1.00
115_L	120_L	1.047	1.00
95_D	98_D	1.045	1.00
129_A	132_E	1.031	1.00
14_Y	119_L	1.025	1.00
86_R	99_E	1.012	1.00
7_S	130_L	1.011	1.00
8_E	70_E	0.996	1.00
78_E	107_E	0.980	1.00
115_L	118_G	0.967	1.00
126_N	130_L	0.965	1.00
19_V	84_Y	0.960	1.00
108_E	111_R	0.954	1.00
51_L	55_D	0.950	1.00
42_V	74_V	0.931	1.00
97_E	101_E	0.931	1.00
19_V	35_L	0.931	1.00
36_L	103_R	0.919	1.00
15_T	39_H	0.895	1.00
56_V	61_D	0.892	1.00
7_S	49_S	0.892	1.00
32_K	86_R	0.888	1.00
64_I	135_L	0.884	1.00
48_L	51_L	0.882	1.00
41_T	73_S	0.881	1.00
72_L	75_E	0.877	1.00
58_V	62_V	0.873	1.00
11_T	127_A	0.870	1.00
99_E	102_L	0.867	1.00
44_A	120_L	0.864	1.00
43_K	75_E	0.861	1.00
44_A	71_I	0.860	1.00
118_G	122_Q	0.859	1.00
109_Q	113_A	0.859	1.00
33_R	87_Q	0.857	1.00
32_K	98_D	0.854	1.00
25_S	31_G	0.851	1.00
78_E	103_R	0.850	1.00
44_A	118_G	0.848	1.00
120_L	124_E	0.848	1.00
26_K	30_G	0.843	1.00
5_D	126_N	0.840	1.00
17_E	37_V	0.829	1.00
18_K	109_Q	0.821	1.00
21_T	33_R	0.818	1.00
42_V	114_A	0.813	1.00
41_T	77_D	0.812	1.00
21_T	35_L	0.807	1.00
98_D	103_R	0.804	1.00
100_T	103_R	0.802	1.00
136_R	141_K	0.801	1.00
10_E	13_E	0.800	1.00
126_N	129_A	0.799	1.00
135_L	140_F	0.798	1.00
75_E	107_E	0.796	1.00
50_K	67_P	0.795	1.00
59_D	63_T	0.795	1.00
52_K	65_T	0.783	1.00
12_V	122_Q	0.783	1.00
113_A	116_E	0.780	1.00
55_D	58_V	0.780	1.00
51_L	54_E	0.773	1.00
46_V	69_P	0.773	1.00
12_V	119_L	0.762	1.00
130_L	133_S	0.758	1.00
19_V	37_V	0.750	1.00
33_R	85_D	0.748	1.00
38_A	110_I	0.742	1.00
89_G	93_R	0.740	1.00
40_G	106_A	0.740	1.00
38_A	76_L	0.737	1.00
55_D	65_T	0.735	1.00
98_D	101_E	0.732	1.00
58_V	61_D	0.729	1.00
8_E	45_G	0.722	1.00
79_D	104_Q	0.719	1.00
38_A	106_A	0.718	1.00
5_D	129_A	0.717	1.00
54_E	58_V	0.710	1.00
62_V	135_L	0.708	1.00
112_K	115_L	0.707	1.00
8_E	47_D	0.706	1.00
44_A	69_P	0.705	1.00
44_A	114_A	0.701	1.00
8_E	72_L	0.698	1.00
75_E	78_E	0.696	1.00
9_L	48_L	0.693	1.00
4_R	15_T	0.685	1.00
106_A	110_I	0.677	1.00
6_L	13_E	0.671	1.00
131_L	135_L	0.671	1.00
35_L	85_D	0.669	1.00
11_T	126_N	0.664	1.00
5_D	122_Q	0.658	1.00
24_D	101_E	0.658	1.00
8_E	13_E	0.657	1.00
133_S	137_S	0.657	1.00
122_Q	126_N	0.656	1.00
130_L	134_L	0.652	1.00
66_L	127_A	0.646	1.00
102_L	106_A	0.645	1.00
53_P	58_V	0.641	1.00
9_L	130_L	0.639	1.00
66_L	131_L	0.632	1.00
88_T	92_N	0.629	1.00
91_L	94_F	0.628	1.00
18_K	113_A	0.627	1.00
16_F	42_V	0.626	1.00
43_K	72_L	0.616	1.00
7_S	11_T	0.614	1.00
114_A	119_L	0.614	1.00
40_G	76_L	0.612	1.00
12_V	15_T	0.607	1.00
18_K	38_A	0.603	1.00
83_V	86_R	0.599	1.00
22_Y	102_L	0.598	1.00
106_A	109_Q	0.597	1.00
39_H	81_T	0.588	1.00
16_F	117_S	0.583	1.00
88_T	91_L	0.573	1.00
32_K	92_N	0.566	1.00
133_S	136_R	0.564	1.00
14_Y	44_A	0.564	1.00
74_V	77_D	0.561	1.00
94_F	102_L	0.560	1.00
22_Y	105_E	0.557	1.00
20_V	38_A	0.555	1.00
103_R	106_A	0.554	1.00
136_R	142_E	0.547	1.00
94_F	98_D	0.538	0.99
64_I	131_L	0.535	0.99
35_L	39_H	0.535	0.99
57_E	61_D	0.534	0.99
58_V	140_F	0.530	0.99
113_A	117_S	0.524	0.99
18_K	21_T	0.522	0.99
83_V	100_T	0.520	0.99
53_P	57_E	0.518	0.99
42_V	45_G	0.514	0.99
38_A	81_T	0.512	0.99
18_K	110_I	0.511	0.99
36_L	83_V	0.510	0.99
76_L	107_E	0.507	0.99
102_L	107_E	0.501	0.99
13_E	122_Q	0.500	0.99

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
2jvfA	1	0.5172	9.1	0.907	Contact Map
3h4zA	1	0.8483	8.8	0.908	Contact Map
2ck3A	1	0.9241	6.8	0.912	Contact Map
3gkuA	2	0.5379	6.7	0.912	Contact Map
3uv1A	2	0.8207	6.2	0.914	Contact Map
1usuB	1	0.8	6	0.915	Contact Map
1qysA	1	0.5034	5.7	0.915	Contact Map
3iibA	2	0.3793	4.7	0.919	Contact Map
4gfqA	1	0.8828	4.2	0.921	Contact Map
2gljA	6	0.4	4.1	0.921	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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