DUF4373 - PFAM28P - GREMLIN Contacts

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DUF4373 - Domain of unknown function (DUF4373)

PFAM:	PF14297	Sequences: YFPHDVNARNDPKIKKLRAKYGLEGYGIYWKLLELLYENEGYYLEWDEDLILLFAARAKLGVDEEKVKEIINYCVELGLFDKELFEKDGILTSKGI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	96 (93)
Sequences:	5159 (4362)
Seq/√Len:	452.3
META:	0.952

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_E	66_K	2.935	1.00
18_R	31_K	2.762	1.00
28_I	70_I	2.561	1.00
21_Y	73_Y	2.484	1.00
15_K	59_K	2.426	1.00
4_H	30_W	2.339	1.00
23_L	31_K	2.236	1.00
20_K	73_Y	2.198	1.00
6_V	37_Y	2.195	1.00
23_L	27_G	2.169	1.00
7_N	38_E	2.093	1.00
4_H	34_E	1.988	1.00
8_A	30_W	1.908	1.00
82_K	86_E	1.859	1.00
68_K	72_N	1.854	1.00
10_N	38_E	1.641	1.00
21_Y	69_E	1.529	1.00
29_Y	33_L	1.527	1.00
26_Y	34_E	1.483	1.00
4_H	8_A	1.459	1.00
26_Y	31_K	1.449	1.00
47_D	50_L	1.359	1.00
17_L	74_C	1.348	1.00
29_Y	79_L	1.339	1.00
28_I	67_V	1.329	1.00
66_K	69_E	1.299	1.00
15_K	56_A	1.280	1.00
9_R	31_K	1.241	1.00
37_Y	42_Y	1.231	1.00
75_V	85_F	1.210	1.00
81_D	94_K	1.191	1.00
21_Y	70_I	1.173	1.00
83_E	87_K	1.166	1.00
73_Y	77_L	1.145	1.00
63_D	66_K	1.122	1.00
51_I	68_K	1.119	1.00
35_L	38_E	1.089	1.00
26_Y	30_W	1.086	1.00
2_F	34_E	1.061	1.00
43_Y	90_I	1.060	1.00
18_R	26_Y	1.047	1.00
12_P	35_L	1.043	1.00
74_C	80_F	1.041	1.00
71_I	75_V	1.038	1.00
49_D	77_L	1.036	1.00
35_L	39_N	1.032	1.00
51_I	55_A	1.027	1.00
64_E	68_K	1.020	1.00
21_Y	25_G	1.013	1.00
8_A	26_Y	1.008	1.00
73_Y	76_E	0.986	1.00
70_I	74_C	0.978	1.00
66_K	70_I	0.970	1.00
75_V	80_F	0.964	1.00
50_L	53_L	0.956	1.00
84_L	88_D	0.952	1.00
15_K	18_R	0.947	1.00
65_E	69_E	0.944	1.00
15_K	19_A	0.941	1.00
19_A	56_A	0.937	1.00
19_A	53_L	0.923	1.00
46_W	50_L	0.914	1.00
9_R	38_E	0.912	1.00
46_W	51_I	0.902	1.00
62_V	66_K	0.897	1.00
30_W	34_E	0.892	1.00
23_L	28_I	0.882	1.00
56_A	61_G	0.881	1.00
48_E	52_L	0.875	1.00
17_L	25_G	0.861	1.00
17_L	70_I	0.852	1.00
20_K	77_L	0.847	1.00
14_I	17_L	0.843	1.00
16_K	53_L	0.835	1.00
20_K	52_L	0.825	1.00
52_L	56_A	0.823	1.00
52_L	55_A	0.814	1.00
12_P	39_N	0.802	1.00
18_R	61_G	0.802	1.00
32_L	71_I	0.793	1.00
29_Y	74_C	0.780	1.00
14_I	26_Y	0.778	1.00
84_L	90_I	0.773	1.00
62_V	67_V	0.769	1.00
35_L	44_L	0.767	1.00
16_K	77_L	0.760	1.00
17_L	29_Y	0.755	1.00
10_N	59_K	0.753	1.00
74_C	79_L	0.752	1.00
18_R	23_L	0.747	1.00
14_I	29_Y	0.735	1.00
9_R	34_E	0.730	1.00
20_K	69_E	0.730	1.00
24_E	27_G	0.696	1.00
9_R	35_L	0.696	1.00
24_E	62_V	0.694	1.00
2_F	30_W	0.687	1.00
16_K	20_K	0.677	1.00
10_N	34_E	0.672	1.00
6_V	38_E	0.647	1.00
69_E	76_E	0.643	1.00
16_K	19_A	0.643	1.00
20_K	49_D	0.630	0.99
4_H	26_Y	0.622	0.99
5_D	8_A	0.622	0.99
16_K	49_D	0.614	0.99
27_G	31_K	0.603	0.99
69_E	73_Y	0.598	0.99
52_L	64_E	0.598	0.99
80_F	91_L	0.592	0.99
29_Y	80_F	0.590	0.99
48_E	76_E	0.588	0.99
49_D	52_L	0.586	0.99
53_L	56_A	0.580	0.99
89_G	92_T	0.571	0.99
45_E	48_E	0.566	0.99
45_E	90_I	0.563	0.99
13_K	79_L	0.561	0.99
13_K	95_G	0.560	0.99
18_R	56_A	0.558	0.99
36_L	40_E	0.552	0.98
31_K	60_L	0.551	0.98
50_L	54_F	0.550	0.98
49_D	53_L	0.549	0.98
67_V	70_I	0.544	0.98
49_D	76_E	0.543	0.98
83_E	92_T	0.539	0.98
8_A	34_E	0.536	0.98
23_L	60_L	0.535	0.98
30_W	33_L	0.520	0.98
78_G	81_D	0.520	0.98
19_A	61_G	0.519	0.98
13_K	33_L	0.512	0.98
82_K	88_D	0.511	0.98
23_L	26_Y	0.510	0.97
83_E	86_E	0.509	0.97
49_D	78_G	0.508	0.97
45_E	89_G	0.503	0.97
31_K	59_K	0.501	0.97
51_I	54_F	0.500	0.97

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
4y66A	1	0.7188	49.5	0.829	Contact Map
4ptaD	3	0.875	40	0.838	Contact Map
4pt7A	3	0.9375	38.2	0.84	Contact Map
1z7uA	2	0.8438	23.5	0.857	Contact Map
2xvcA	1	0.5833	18.2	0.863	Contact Map
2o03A	2	0.7917	18.2	0.863	Contact Map
4y66B	1	0.7083	18.2	0.863	Contact Map
1fc3A	3	0.9375	17.8	0.864	Contact Map
3r4kA	2	0.6771	16.9	0.866	Contact Map
2fu4A	2	0.8438	16.6	0.866	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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