DUF3465 - PFAM28P - GREMLIN Contacts

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DUF3465 - Protein of unknown function (DUF3465)

PFAM:	PF11948	Sequences: AVLLSAASAPAAADDAAAALARAFANRRSDVQVEGEGTVTRLLPDDNDGSRHQRFILRLASGQTLLVAHNIDLAPRIPGLRVGDTVEFYGEYEWNEKGGVIHWTHHDPQGRHEGGWLKHNGRTYQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	125 (112)
Sequences:	2727 (1931)
Seq/√Len:	182.4
META:	0.914

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
118_K	123_T	4.681	1.00
35_G	88_F	3.581	1.00
32_Q	89_Y	3.146	1.00
34_E	89_Y	2.483	1.00
84_D	119_H	2.482	1.00
40_T	58_R	2.470	1.00
87_E	118_K	2.371	1.00
68_A	100_V	2.300	1.00
23_A	31_V	2.202	1.00
34_E	87_E	2.174	1.00
32_Q	112_H	2.113	1.00
45_D	76_R	2.093	1.00
95_N	100_V	2.060	1.00
47_N	51_R	2.054	1.00
93_E	100_V	2.031	1.00
21_A	25_A	1.944	1.00
67_V	101_I	1.851	1.00
21_A	63_Q	1.842	1.00
57_L	117_L	1.782	1.00
36_E	87_E	1.706	1.00
88_F	117_L	1.639	1.00
32_Q	91_E	1.636	1.00
24_F	63_Q	1.630	1.00
73_L	108_P	1.625	1.00
77_I	119_H	1.620	1.00
30_D	91_E	1.604	1.00
110_G	114_G	1.601	1.00
36_E	85_T	1.598	1.00
89_Y	113_E	1.576	1.00
59_L	62_G	1.513	1.00
32_Q	113_E	1.428	1.00
38_T	58_R	1.424	1.00
42_L	82_V	1.422	1.00
22_R	26_N	1.408	1.00
55_F	86_V	1.357	1.00
55_F	80_L	1.349	1.00
51_R	71_I	1.340	1.00
52_H	102_H	1.332	1.00
44_P	54_R	1.329	1.00
51_R	72_D	1.324	1.00
20_L	33_V	1.261	1.00
65_L	101_I	1.211	1.00
79_G	119_H	1.211	1.00
57_L	88_F	1.209	1.00
33_V	101_I	1.199	1.00
77_I	80_L	1.148	1.00
69_H	104_T	1.127	1.00
22_R	28_R	1.107	1.00
30_D	93_E	1.106	1.00
69_H	74_A	1.083	1.00
41_R	82_V	1.076	1.00
35_G	101_I	1.075	1.00
20_L	63_Q	1.022	1.00
92_Y	99_G	1.001	0.99
27_R	94_W	0.989	0.99
32_Q	114_G	0.962	0.99
79_G	124_Y	0.929	0.99
35_G	57_L	0.919	0.99
42_L	78_P	0.917	0.99
24_F	92_Y	0.912	0.99
35_G	117_L	0.908	0.99
28_R	31_V	0.907	0.99
55_F	67_V	0.902	0.99
91_E	112_H	0.882	0.99
54_R	66_L	0.866	0.98
56_I	97_K	0.858	0.98
39_V	80_L	0.843	0.98
38_T	85_T	0.842	0.98
22_R	25_A	0.836	0.98
114_G	125_Q	0.833	0.98
102_H	105_H	0.831	0.98
20_L	24_F	0.831	0.98
59_L	63_Q	0.814	0.98
39_V	84_D	0.812	0.97
57_L	86_V	0.806	0.97
14_D	17_A	0.796	0.97
72_D	103_W	0.793	0.97
67_V	88_F	0.792	0.97
57_L	67_V	0.789	0.97
14_D	19_A	0.752	0.96
119_H	124_Y	0.751	0.96
47_N	50_S	0.750	0.96
50_S	97_K	0.744	0.96
106_H	114_G	0.739	0.96
70_N	102_H	0.704	0.94
41_R	56_I	0.704	0.94
52_H	103_W	0.702	0.94
60_A	63_Q	0.697	0.94
15_D	19_A	0.690	0.94
19_A	31_V	0.689	0.94
46_D	49_G	0.687	0.94
29_S	93_E	0.687	0.94
85_T	120_N	0.685	0.93
75_P	122_R	0.684	0.93
103_W	108_P	0.679	0.93
43_L	46_D	0.678	0.93
52_H	70_N	0.673	0.93
46_D	53_Q	0.668	0.93
116_W	119_H	0.667	0.93
89_Y	114_G	0.649	0.91
46_D	54_R	0.648	0.91
94_W	99_G	0.647	0.91
42_L	54_R	0.646	0.91
49_G	103_W	0.646	0.91
56_I	64_T	0.644	0.91
34_E	38_T	0.643	0.91
20_L	31_V	0.643	0.91
15_D	60_A	0.640	0.91
40_T	82_V	0.633	0.90
50_S	73_L	0.631	0.90
109_Q	113_E	0.626	0.90
21_A	61_S	0.623	0.90
106_H	125_Q	0.623	0.90
46_D	51_R	0.622	0.90
88_F	101_I	0.615	0.89
13_A	17_A	0.614	0.89
77_I	117_L	0.613	0.89
34_E	113_E	0.613	0.89
46_D	66_L	0.611	0.89
52_H	105_H	0.608	0.89
51_R	68_A	0.607	0.89
56_I	95_N	0.606	0.88
20_L	88_F	0.600	0.88
78_P	124_Y	0.599	0.88
87_E	123_T	0.597	0.88
31_V	94_W	0.593	0.87
107_D	111_R	0.590	0.87
78_P	122_R	0.590	0.87
60_A	78_P	0.585	0.87
19_A	23_A	0.584	0.87
19_A	22_R	0.577	0.86
67_V	94_W	0.576	0.86
54_R	95_N	0.574	0.86
69_H	77_I	0.573	0.86
60_A	85_T	0.572	0.85
16_A	82_V	0.570	0.85
118_K	121_G	0.568	0.85
73_L	97_K	0.567	0.85
67_V	104_T	0.564	0.85
67_V	70_N	0.560	0.84
120_N	124_Y	0.555	0.84
94_W	98_G	0.547	0.83
36_E	40_T	0.540	0.82
84_D	120_N	0.539	0.82
49_G	54_R	0.533	0.81
106_H	111_R	0.532	0.81
21_A	58_R	0.529	0.81
24_F	27_R	0.528	0.81
68_A	93_E	0.527	0.81
95_N	99_G	0.523	0.80
58_R	61_S	0.522	0.80
96_E	120_N	0.521	0.80
46_D	103_W	0.521	0.80
13_A	16_A	0.520	0.80
70_N	73_L	0.519	0.80
19_A	38_T	0.519	0.80
52_H	64_T	0.518	0.79
43_L	53_Q	0.515	0.79
41_R	97_K	0.515	0.79
26_N	111_R	0.512	0.79
35_G	61_S	0.509	0.78
23_A	27_R	0.509	0.78
21_A	24_F	0.505	0.78
35_G	65_L	0.503	0.77
19_A	28_R	0.501	0.77
54_R	68_A	0.501	0.77
23_A	94_W	0.500	0.77
86_V	119_H	0.500	0.77

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
1nnxA	1	0.68	79.5	0.901	Contact Map
2dgyA	1	0.784	69.9	0.908	Contact Map
4mnoA	1	0.68	62.6	0.912	Contact Map
1ah9A	1	0.56	59.5	0.914	Contact Map
3wbkC	1	0.008	57.5	0.915	Contact Map
1jt8A	1	0.784	56.1	0.916	Contact Map
4ql5A	4	0.536	55.3	0.916	Contact Map
1hr0W	1	0.56	49.5	0.919	Contact Map
3i4oA	1	0.536	34.2	0.926	Contact Map
3j80i	1	0.672	30.2	0.928	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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