DUF310 - PFAM28P - GREMLIN Contacts

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DUF310 - Protein of unknown function (DUF310)

PFAM:	PF03750	Sequences: DKDPELLVEKAEKIAKELAKKKLTTSQIRKFYDEVKRIENKVKRGKEEEFEEILPELKMLKPKLAYAAGRKLVVKEFVEFLDEAIDQVKDSKEDFKNFVDFFEAIVAYHKYYGGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	115 (109)
Sequences:	3333 (2812)
Seq/√Len:	269.4
META:	0.906

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
61_K	86_D	3.909	1.00
89_K	94_D	2.360	1.00
61_K	82_D	2.318	1.00
35_V	99_V	2.243	1.00
23_L	74_V	2.236	1.00
35_V	98_F	2.209	1.00
68_A	75_K	2.176	1.00
25_T	110_K	2.159	1.00
41_K	56_E	2.052	1.00
75_K	79_E	2.047	1.00
34_E	56_E	2.019	1.00
39_E	96_K	2.010	1.00
68_A	78_V	1.974	1.00
32_Y	36_K	1.867	1.00
78_V	82_D	1.851	1.00
59_M	63_K	1.846	1.00
36_K	39_E	1.808	1.00
12_E	112_Y	1.720	1.00
27_Q	67_A	1.719	1.00
30_K	67_A	1.717	1.00
34_E	63_K	1.710	1.00
12_E	16_K	1.679	1.00
36_K	99_V	1.668	1.00
31_F	64_L	1.646	1.00
80_F	101_F	1.552	1.00
35_V	102_F	1.544	1.00
90_D	94_D	1.505	1.00
11_A	15_A	1.453	1.00
34_E	37_R	1.423	1.00
15_A	18_L	1.392	1.00
94_D	97_N	1.391	1.00
57_L	88_V	1.387	1.00
39_E	99_V	1.345	1.00
9_E	13_K	1.300	1.00
57_L	85_I	1.287	1.00
83_E	86_D	1.270	1.00
10_K	13_K	1.268	1.00
16_K	20_K	1.260	1.00
35_V	60_L	1.234	1.00
91_S	94_D	1.206	1.00
11_A	14_I	1.203	1.00
39_E	43_K	1.195	1.00
38_I	53_I	1.177	1.00
51_E	54_L	1.129	1.00
65_A	82_D	1.112	1.00
73_V	77_F	1.106	1.00
84_A	98_F	1.104	1.00
42_V	57_L	1.094	1.00
84_A	101_F	1.091	1.00
27_Q	30_K	1.086	1.00
98_F	102_F	1.052	1.00
59_M	100_D	1.050	1.00
64_L	81_L	1.030	1.00
14_I	18_L	1.021	1.00
31_F	67_A	1.010	1.00
45_G	48_E	1.004	1.00
82_D	86_D	0.997	1.00
7_L	15_A	0.984	1.00
15_A	105_I	0.972	1.00
37_R	41_K	0.971	1.00
77_F	81_L	0.969	1.00
66_Y	70_R	0.964	1.00
81_L	85_I	0.960	1.00
64_L	78_V	0.944	1.00
57_L	95_F	0.933	1.00
109_H	114_G	0.930	1.00
6_L	10_K	0.928	1.00
42_V	53_I	0.924	1.00
16_K	112_Y	0.913	1.00
23_L	106_V	0.912	1.00
32_Y	103_E	0.910	1.00
97_N	100_D	0.898	1.00
11_A	104_A	0.896	1.00
32_Y	102_F	0.891	1.00
93_E	97_N	0.870	1.00
100_D	103_E	0.869	1.00
65_A	69_G	0.854	1.00
12_E	15_A	0.853	1.00
59_M	62_P	0.844	1.00
54_L	58_K	0.840	1.00
62_P	107_A	0.839	1.00
17_E	76_E	0.838	1.00
15_A	19_A	0.833	0.99
72_L	75_K	0.832	0.99
63_K	103_E	0.809	0.99
64_L	102_F	0.799	0.99
6_L	9_E	0.797	0.99
9_E	12_E	0.793	0.99
42_V	95_F	0.788	0.99
7_L	14_I	0.779	0.99
6_L	15_A	0.757	0.99
17_E	20_K	0.753	0.99
17_E	21_K	0.753	0.99
102_F	106_V	0.749	0.99
38_I	56_E	0.739	0.99
45_G	49_E	0.722	0.99
87_Q	90_D	0.721	0.99
28_I	106_V	0.720	0.98
75_K	78_V	0.716	0.98
69_G	74_V	0.714	0.98
84_A	87_Q	0.702	0.98
32_Y	106_V	0.700	0.98
88_V	98_F	0.688	0.98
68_A	74_V	0.685	0.98
11_A	18_L	0.682	0.98
74_V	77_F	0.681	0.98
8_V	12_E	0.676	0.98
38_I	57_L	0.675	0.98
7_L	11_A	0.671	0.98
41_K	53_I	0.669	0.98
58_K	62_P	0.666	0.97
105_I	109_H	0.666	0.97
13_K	16_K	0.661	0.97
24_T	72_L	0.660	0.97
96_K	100_D	0.657	0.97
23_L	73_V	0.654	0.97
37_R	56_E	0.649	0.97
64_L	84_A	0.646	0.97
54_L	90_D	0.636	0.97
32_Y	62_P	0.635	0.97
111_Y	114_G	0.634	0.97
58_K	61_K	0.634	0.97
80_F	84_A	0.633	0.97
80_F	105_I	0.633	0.97
58_K	89_K	0.625	0.96
31_F	81_L	0.625	0.96
22_K	76_E	0.622	0.96
26_S	66_Y	0.621	0.96
13_K	17_E	0.618	0.96
85_I	88_V	0.618	0.96
10_K	15_A	0.615	0.96
106_V	109_H	0.615	0.96
76_E	79_E	0.606	0.96
34_E	60_L	0.603	0.96
55_P	100_D	0.602	0.95
21_K	76_E	0.602	0.95
30_K	63_K	0.601	0.95
23_L	77_F	0.593	0.95
18_L	22_K	0.581	0.95
100_D	107_A	0.571	0.94
26_S	30_K	0.560	0.93
69_G	111_Y	0.560	0.93
30_K	34_E	0.556	0.93
35_V	95_F	0.549	0.93
79_E	83_E	0.548	0.93
46_K	49_E	0.544	0.92
33_D	37_R	0.544	0.92
14_I	17_E	0.543	0.92
44_R	47_E	0.541	0.92
50_F	54_L	0.534	0.92
9_E	17_E	0.529	0.91
67_A	70_R	0.527	0.91
8_V	15_A	0.527	0.91
61_K	108_Y	0.525	0.91
64_L	85_I	0.523	0.91
7_L	10_K	0.522	0.91
37_R	40_N	0.520	0.91
8_V	18_L	0.513	0.90
83_E	87_Q	0.511	0.90
99_V	103_E	0.505	0.89
40_N	43_K	0.501	0.89
61_K	85_I	0.501	0.89
101_F	105_I	0.501	0.89
15_A	21_K	0.500	0.89

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
4cekA	1	0.5304	7.7	0.909	Contact Map
1x4pA	1	0.4696	7.2	0.91	Contact Map
1dquA	4	0.8783	6.5	0.912	Contact Map
3qmlC	1	0.8087	5.6	0.915	Contact Map
4fp9B	2	0.8783	4.9	0.917	Contact Map
3ghgA	2	0.7913	4.7	0.918	Contact Map
1m9iA	1	0.9565	4.7	0.918	Contact Map
3u0rA	1	0.8696	4.2	0.92	Contact Map
2dt7A	1	0.2783	4	0.921	Contact Map
3a4uB	1	0.5304	3.7	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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