DUF4304 - PFAM28P - GREMLIN Contacts

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DUF4304 - Domain of unknown function (DUF4304)

PFAM:	PF14137	Sequences: IAPLLKPLGFKKSGRTFYRESDDLIQVINFQKSRWNTADGGSFTVNLGVYSPELAEWGGKPPPKKPKEYDCHIRARLGSLLPGGESDKWWDLDDDTDLEELAEEVAEALEEYALPWF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	117 (114)
Sequences:	3256 (2835)
Seq/√Len:	265.5
META:	0.911

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
68_E	74_R	3.415	1.00
19_R	26_Q	3.403	1.00
44_T	89_W	3.363	1.00
31_Q	46_N	3.318	1.00
16_T	29_N	3.156	1.00
107_E	111_E	2.362	1.00
48_G	71_C	2.283	1.00
46_N	76_R	2.215	1.00
29_N	46_N	2.196	1.00
3_P	7_P	2.045	1.00
47_L	113_A	1.935	1.00
50_Y	55_A	1.930	1.00
20_E	52_P	1.907	1.00
31_Q	76_R	1.829	1.00
6_K	12_K	1.785	1.00
73_I	116_W	1.671	1.00
44_T	87_D	1.644	1.00
106_A	110_E	1.596	1.00
32_K	41_G	1.585	1.00
44_T	76_R	1.550	1.00
42_S	91_D	1.549	1.00
10_F	26_Q	1.456	1.00
17_F	30_F	1.447	1.00
4_L	8_L	1.439	1.00
21_S	26_Q	1.423	1.00
96_T	101_L	1.410	1.00
54_L	72_H	1.406	1.00
99_E	103_E	1.376	1.00
27_V	71_C	1.360	1.00
77_L	113_A	1.350	1.00
33_S	36_N	1.339	1.00
18_Y	66_P	1.326	1.00
5_L	28_I	1.325	1.00
24_L	51_S	1.324	1.00
90_W	108_A	1.268	1.00
2_A	12_K	1.267	1.00
27_V	48_G	1.260	1.00
102_A	106_A	1.260	1.00
29_N	68_E	1.227	1.00
57_W	60_K	1.222	1.00
35_W	42_S	1.197	1.00
71_C	74_R	1.197	1.00
43_F	105_V	1.183	1.00
15_R	32_K	1.164	1.00
78_G	88_K	1.151	1.00
33_S	42_S	1.147	1.00
78_G	87_D	1.145	1.00
3_P	43_F	1.137	1.00
13_S	65_K	1.130	1.00
18_Y	25_I	1.123	1.00
28_I	109_L	1.098	1.00
30_F	43_F	1.082	1.00
8_L	110_E	1.080	1.00
104_E	108_A	1.067	1.00
44_T	78_G	1.051	1.00
4_L	7_P	1.049	1.00
67_K	70_D	1.040	1.00
81_L	108_A	1.017	1.00
110_E	113_A	1.010	1.00
108_A	112_Y	1.002	1.00
93_D	96_T	0.965	1.00
45_V	77_L	0.953	1.00
58_G	62_P	0.932	1.00
2_A	17_F	0.930	1.00
76_R	87_D	0.926	1.00
28_I	45_V	0.923	1.00
25_I	52_P	0.917	1.00
40_G	91_D	0.909	1.00
103_E	107_E	0.908	1.00
44_T	80_L	0.895	1.00
26_Q	49_V	0.893	1.00
18_Y	27_V	0.891	1.00
47_L	77_L	0.890	1.00
21_S	24_L	0.890	1.00
68_E	71_C	0.879	1.00
13_S	18_Y	0.878	1.00
36_N	41_G	0.875	1.00
97_D	100_E	0.873	1.00
63_P	67_K	0.869	1.00
24_L	49_V	0.861	1.00
66_P	70_D	0.856	1.00
2_A	6_K	0.848	1.00
10_F	19_R	0.844	1.00
18_Y	65_K	0.827	0.99
36_N	40_G	0.819	0.99
32_K	36_N	0.816	0.99
50_Y	72_H	0.816	0.99
97_D	101_L	0.806	0.99
101_L	105_V	0.805	0.99
51_S	72_H	0.800	0.99
34_R	42_S	0.799	0.99
50_Y	71_C	0.795	0.99
58_G	61_P	0.793	0.99
89_W	104_E	0.791	0.99
66_P	71_C	0.787	0.99
12_K	17_F	0.786	0.99
82_P	112_Y	0.785	0.99
23_D	53_E	0.778	0.99
100_E	104_E	0.771	0.99
53_E	56_E	0.761	0.99
109_L	114_L	0.753	0.99
105_V	108_A	0.747	0.99
51_S	54_L	0.731	0.99
16_T	27_V	0.731	0.99
85_E	88_K	0.730	0.99
75_A	79_S	0.718	0.98
33_S	44_T	0.712	0.98
35_W	40_G	0.700	0.98
78_G	82_P	0.694	0.98
44_T	90_W	0.690	0.98
77_L	90_W	0.684	0.98
33_S	39_D	0.672	0.98
4_L	106_A	0.671	0.97
109_L	113_A	0.669	0.97
2_A	15_R	0.669	0.97
4_L	110_E	0.665	0.97
81_L	84_G	0.665	0.97
55_A	65_K	0.659	0.97
52_P	55_A	0.653	0.97
98_L	102_A	0.642	0.97
37_T	40_G	0.633	0.96
31_Q	44_T	0.628	0.96
56_E	61_P	0.625	0.96
99_E	107_E	0.618	0.96
25_I	55_A	0.616	0.96
47_L	80_L	0.615	0.96
40_G	93_D	0.614	0.96
107_E	110_E	0.613	0.96
25_I	50_Y	0.612	0.96
50_Y	54_L	0.611	0.96
50_Y	66_P	0.608	0.96
78_G	81_L	0.607	0.96
59_G	62_P	0.602	0.95
30_F	45_V	0.599	0.95
83_G	88_K	0.594	0.95
13_S	17_F	0.592	0.95
61_P	65_K	0.589	0.95
103_E	110_E	0.587	0.95
81_L	112_Y	0.584	0.94
94_D	101_L	0.584	0.94
55_A	72_H	0.582	0.94
13_S	64_K	0.581	0.94
38_A	41_G	0.574	0.94
36_N	39_D	0.573	0.94
12_K	15_R	0.572	0.94
79_S	85_E	0.570	0.94
11_K	20_E	0.564	0.93
17_F	101_L	0.561	0.93
49_V	73_I	0.560	0.93
44_T	77_L	0.557	0.93
29_N	76_R	0.548	0.92
113_A	116_W	0.548	0.92
99_E	110_E	0.546	0.92
32_K	51_S	0.537	0.92
80_L	112_Y	0.530	0.91
81_L	85_E	0.526	0.91
88_K	104_E	0.525	0.91
112_Y	115_P	0.518	0.90
26_Q	51_S	0.518	0.90
98_L	101_L	0.516	0.90
35_W	91_D	0.514	0.90
36_N	42_S	0.513	0.90
24_L	73_I	0.512	0.90
67_K	71_C	0.510	0.89
57_W	61_P	0.507	0.89
31_Q	89_W	0.504	0.89
48_G	54_L	0.504	0.89
52_P	91_D	0.504	0.89
93_D	101_L	0.504	0.89
78_G	90_W	0.503	0.89
50_Y	77_L	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
2ofkA	1	0.3333	16	0.876	Contact Map
1gm6A	1	0.2479	5.4	0.899	Contact Map
1y8cA	1	0.3333	4.4	0.903	Contact Map
3ui3A	2	0.5983	3.3	0.909	Contact Map
3dp7A	2	0.265	3.2	0.91	Contact Map
3h2bA	2	0.2735	3.1	0.911	Contact Map
4wxhA	2	0.2991	3.1	0.911	Contact Map
2a2pA	1	0.4103	3	0.911	Contact Map
4crwA	1	0.3333	2.8	0.913	Contact Map
4pv6C	3	0.3077	2.7	0.913	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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