DUF4248 - PFAM28P - GREMLIN Contacts

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DUF4248 - Domain of unknown function (DUF4248)

PFAM:	PF14053	Sequences: KIRSYGKSELAQLYFPDLTPKSAVRKLRRWIKRNPELKEELEALGYRKRQRTFTPRQVRLIVEYLGEP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	68 (67)
Sequences:	1477 (1130)
Seq/√Len:	138.1
META:	0.869

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_L	60_L	2.387	1.00
7_K	24_V	2.192	1.00
21_K	25_R	2.176	1.00
32_K	38_K	2.134	1.00
54_T	57_Q	1.936	1.00
38_K	42_E	1.848	1.00
44_L	57_Q	1.833	1.00
15_F	26_K	1.832	1.00
50_Q	57_Q	1.745	1.00
36_E	64_Y	1.684	1.00
6_G	9_E	1.623	1.00
18_L	26_K	1.599	1.00
34_N	64_Y	1.594	1.00
15_F	30_W	1.536	1.00
12_Q	20_P	1.499	1.00
19_T	22_S	1.470	1.00
40_E	43_A	1.451	1.00
8_S	12_Q	1.451	1.00
24_V	28_R	1.450	1.00
39_E	43_A	1.439	1.00
2_I	5_Y	1.372	1.00
40_E	63_E	1.317	1.00
26_K	30_W	1.267	1.00
40_E	60_L	1.252	1.00
13_L	62_V	1.228	1.00
8_S	51_R	1.217	1.00
15_F	18_L	1.210	1.00
59_R	63_E	1.203	1.00
28_R	32_K	1.181	1.00
22_S	26_K	1.181	1.00
10_L	61_I	1.154	0.99
18_L	22_S	1.154	0.99
4_S	55_P	1.138	0.99
16_P	23_A	1.126	0.99
35_P	38_K	1.117	0.99
40_E	64_Y	1.116	0.99
39_E	42_E	1.067	0.99
8_S	20_P	1.052	0.99
29_R	33_R	1.035	0.99
31_I	38_K	1.030	0.99
10_L	58_V	1.019	0.99
24_V	51_R	1.014	0.98
56_R	59_R	1.011	0.98
55_P	66_G	0.990	0.98
27_L	31_I	0.987	0.98
7_K	53_F	0.952	0.98
3_R	9_E	0.944	0.98
46_Y	53_F	0.932	0.97
36_E	40_E	0.926	0.97
40_E	44_L	0.901	0.97
56_R	63_E	0.895	0.97
8_S	24_V	0.882	0.96
37_L	60_L	0.849	0.95
5_Y	13_L	0.827	0.95
10_L	14_Y	0.806	0.94
7_K	46_Y	0.801	0.94
5_Y	58_V	0.798	0.94
26_K	52_T	0.780	0.93
41_L	46_Y	0.773	0.93
47_R	50_Q	0.771	0.93
62_V	67_E	0.759	0.92
50_Q	62_V	0.756	0.92
18_L	33_R	0.749	0.91
26_K	29_R	0.737	0.91
7_K	28_R	0.730	0.90
20_P	23_A	0.719	0.90
41_L	45_G	0.703	0.89
17_D	35_P	0.686	0.87
57_Q	60_L	0.681	0.87
30_W	67_E	0.677	0.87
9_E	13_L	0.646	0.84
28_R	53_F	0.643	0.84
14_Y	68_P	0.637	0.83
37_L	65_L	0.635	0.83
36_E	39_E	0.604	0.80
35_P	64_Y	0.601	0.80
34_N	37_L	0.587	0.78
25_R	28_R	0.584	0.78
5_Y	59_R	0.580	0.77
46_Y	66_G	0.576	0.77
15_F	52_T	0.564	0.75
39_E	63_E	0.562	0.75
60_L	64_Y	0.561	0.75
32_K	48_K	0.556	0.74
22_S	25_R	0.547	0.73
31_I	37_L	0.535	0.71
24_V	53_F	0.527	0.70
25_R	29_R	0.526	0.70
49_R	57_Q	0.526	0.70
11_A	28_R	0.525	0.70
4_S	52_T	0.525	0.70
4_S	54_T	0.520	0.69
29_R	32_K	0.520	0.69
17_D	38_K	0.518	0.69
45_G	66_G	0.515	0.69
30_W	34_N	0.510	0.68
60_L	63_E	0.508	0.67
6_G	11_A	0.506	0.67
7_K	51_R	0.505	0.67
61_I	64_Y	0.500	0.66

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
1q06A	2	0.7941	32	0.857	Contact Map
2vz4A	2	0.8088	23.2	0.867	Contact Map
3whpA	1	0	23.1	0.867	Contact Map
1r8dA	2	0.8235	22.9	0.867	Contact Map
3qaoA	2	0.8382	21.9	0.868	Contact Map
4r4eB	2	0.8382	21.4	0.869	Contact Map
4r24B	2	0.8382	19.1	0.872	Contact Map
1r8eA	2	0.7794	19.1	0.872	Contact Map
2jmlA	1	0.8676	17.2	0.875	Contact Map
3gp4A	4	0.8088	15	0.878	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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