DUF2304 - PFAM28P - GREMLIN Contacts

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DUF2304 - Uncharacterized conserved protein (DUF2304)

PFAM:	PF10066	Sequences: IIQILLIILSLLLLLLVLELVRRRRLRERYALLWLLVALVLLVLALFPDLLDWLARLLGIGRPPDLLFYLAILFLLLLLLHLSVRISRLERQITRLAQELALLEAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	106 (104)
Sequences:	14237 (10680)
Seq/√Len:	1047.2
META:	0.931

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_R	65_D	3.008	1.00
53_W	57_L	2.856	1.00
75_L	79_L	2.729	1.00
99_E	104_E	2.720	1.00
99_E	103_L	2.664	1.00
89_L	93_I	2.363	1.00
47_F	50_L	2.301	1.00
19_E	23_R	2.074	1.00
43_V	50_L	2.020	1.00
7_I	46_L	1.988	1.00
82_L	86_I	1.870	1.00
55_A	66_L	1.790	1.00
95_R	99_E	1.750	1.00
52_D	56_R	1.737	1.00
94_T	98_Q	1.726	1.00
49_D	52_D	1.724	1.00
100_L	103_L	1.692	1.00
10_S	45_A	1.684	1.00
71_A	75_L	1.656	1.00
88_R	92_Q	1.641	1.00
68_F	72_I	1.636	1.00
21_V	31_A	1.633	1.00
93_I	97_A	1.587	1.00
52_D	63_P	1.568	1.00
19_E	22_R	1.528	1.00
15_L	19_E	1.485	1.00
65_D	68_F	1.478	1.00
53_W	56_R	1.469	1.00
86_I	89_L	1.421	1.00
10_S	42_L	1.385	1.00
79_L	82_L	1.378	1.00
41_L	45_A	1.343	1.00
20_L	80_L	1.305	1.00
72_I	75_L	1.278	1.00
50_L	53_W	1.271	1.00
20_L	25_R	1.268	1.00
89_L	92_Q	1.254	1.00
55_A	60_I	1.235	1.00
85_R	90_E	1.229	1.00
60_I	64_P	1.203	1.00
12_L	16_L	1.198	1.00
44_L	51_L	1.170	1.00
10_S	38_A	1.163	1.00
93_I	96_L	1.160	1.00
4_I	8_I	1.146	1.00
96_L	100_L	1.142	1.00
60_I	69_Y	1.108	1.00
7_I	42_L	1.104	1.00
14_L	35_L	1.096	1.00
77_L	81_H	1.077	1.00
34_W	83_S	1.070	1.00
64_P	69_Y	1.068	1.00
60_I	66_L	1.035	1.00
85_R	88_R	1.030	1.00
16_L	20_L	1.026	1.00
64_P	68_F	0.986	1.00
91_R	95_R	0.969	1.00
65_D	69_Y	0.962	1.00
34_W	80_L	0.939	1.00
49_D	53_W	0.924	1.00
14_L	38_A	0.911	1.00
17_V	38_A	0.897	1.00
27_R	91_R	0.891	1.00
78_L	82_L	0.875	1.00
6_L	45_A	0.874	1.00
60_I	65_D	0.873	1.00
81_H	85_R	0.868	1.00
93_I	100_L	0.855	1.00
91_R	94_T	0.851	1.00
48_P	52_D	0.847	1.00
35_L	39_L	0.842	1.00
98_Q	101_A	0.839	1.00
90_E	94_T	0.829	1.00
28_E	31_A	0.825	1.00
20_L	84_V	0.821	1.00
71_A	76_L	0.820	1.00
51_L	63_P	0.818	1.00
30_Y	87_S	0.815	1.00
36_L	40_V	0.815	1.00
17_V	26_L	0.793	1.00
97_A	100_L	0.790	1.00
11_L	15_L	0.787	1.00
3_Q	48_P	0.783	1.00
78_L	81_H	0.771	1.00
8_I	12_L	0.758	1.00
100_L	104_E	0.756	1.00
44_L	50_L	0.751	1.00
87_S	90_E	0.741	1.00
17_V	31_A	0.740	1.00
17_V	34_W	0.739	1.00
21_V	28_E	0.728	1.00
73_L	77_L	0.723	1.00
55_A	63_P	0.721	1.00
44_L	48_P	0.718	1.00
31_A	35_L	0.716	1.00
20_L	24_R	0.716	1.00
12_L	15_L	0.712	1.00
43_V	47_F	0.703	1.00
18_L	35_L	0.695	1.00
13_L	38_A	0.691	1.00
2_I	60_I	0.687	1.00
30_Y	33_L	0.685	1.00
51_L	67_L	0.684	1.00
7_I	45_A	0.684	1.00
85_R	89_L	0.679	1.00
17_V	21_V	0.679	1.00
52_D	55_A	0.670	1.00
70_L	74_F	0.662	1.00
71_A	78_L	0.661	1.00
38_A	80_L	0.660	1.00
39_L	43_V	0.659	1.00
25_R	88_R	0.656	1.00
30_Y	85_R	0.653	1.00
20_L	23_R	0.647	1.00
2_I	6_L	0.646	1.00
37_V	74_F	0.642	1.00
7_I	10_S	0.641	1.00
30_Y	82_L	0.636	1.00
10_S	41_L	0.622	1.00
27_R	30_Y	0.616	1.00
52_D	64_P	0.610	1.00
51_L	55_A	0.608	1.00
32_L	36_L	0.606	1.00
26_L	84_V	0.606	1.00
93_I	103_L	0.604	1.00
6_L	64_P	0.593	1.00
34_W	84_V	0.588	1.00
41_L	73_L	0.586	1.00
89_L	100_L	0.584	1.00
26_L	30_Y	0.582	1.00
64_P	67_L	0.574	1.00
58_L	66_L	0.567	1.00
16_L	80_L	0.563	1.00
81_H	84_V	0.561	1.00
26_L	31_A	0.558	1.00
61_G	64_P	0.553	1.00
6_L	9_L	0.550	1.00
102_L	105_A	0.548	1.00
61_G	65_D	0.544	1.00
33_L	37_V	0.544	1.00
67_L	71_A	0.538	1.00
56_R	61_G	0.532	1.00
27_R	90_E	0.532	1.00
17_V	80_L	0.531	1.00
3_Q	6_L	0.527	1.00
94_T	97_A	0.524	1.00
24_R	27_R	0.521	1.00
37_V	41_L	0.521	1.00
97_A	101_A	0.517	1.00
33_L	78_L	0.516	1.00
88_R	91_R	0.512	1.00
66_L	69_Y	0.508	1.00
55_A	58_L	0.505	1.00
30_Y	81_H	0.502	1.00
90_E	93_I	0.500	1.00
69_Y	73_L	0.500	1.00

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
3ra3B	1	0.1981	28	0.838	Contact Map
2wq1A	3	0.2075	13.3	0.861	Contact Map
3w92A	3	0.1981	12.4	0.862	Contact Map
3c3gA	2	0.1226	9.6	0.869	Contact Map
2r2vA	3	0.217	9	0.871	Contact Map
1kd8A	1	0.2075	7.5	0.875	Contact Map
4hjbC	3	0.1981	6.8	0.878	Contact Map
2hy6A	3	0.1981	6.6	0.879	Contact Map
4tl1A	2	0.1981	6.6	0.879	Contact Map
3c3fA	3	0.1604	6.5	0.879	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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