DUF751 - PFAM28P - GREMLIN Contacts

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DUF751 - Protein of unknown function (DUF751)

PFAM:	PF05421	Sequences: FWNNVSRYPRFFISSLLGLILVILEPLKNLLKNPKTAIALIGALIGGFIFLYFTLRAMLG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (60)
Sequences:	818 (502)
Seq/√Len:	64.8
META:	0.744

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_F	54_T	3.723	1.00
33_N	36_T	3.456	1.00
4_N	7_R	2.554	1.00
12_F	16_L	2.363	1.00
54_T	59_L	1.985	1.00
34_P	41_I	1.959	1.00
41_I	45_I	1.914	1.00
22_V	26_P	1.872	1.00
9_P	12_F	1.821	1.00
5_V	11_F	1.774	1.00
20_I	24_L	1.364	0.97
56_R	59_L	1.352	0.97
6_S	9_P	1.343	0.97
33_N	59_L	1.326	0.97
7_R	11_F	1.301	0.96
19_L	23_I	1.292	0.96
22_V	28_K	1.251	0.95
11_F	15_S	1.190	0.94
1_F	4_N	1.190	0.94
20_I	26_P	1.174	0.94
4_N	10_R	1.149	0.93
10_R	13_I	1.144	0.93
48_F	53_F	1.132	0.92
49_I	53_F	1.118	0.92
12_F	15_S	1.100	0.91
31_L	40_L	1.088	0.91
3_N	7_R	1.078	0.90
27_L	40_L	1.059	0.90
34_P	37_A	1.058	0.90
3_N	6_S	1.051	0.89
46_G	49_I	1.045	0.89
4_N	14_S	1.027	0.88
44_L	50_F	1.023	0.88
34_P	38_I	1.011	0.87
11_F	14_S	0.979	0.86
53_F	57_A	0.972	0.85
51_L	55_L	0.970	0.85
5_V	9_P	0.925	0.82
36_T	41_I	0.922	0.82
4_N	11_F	0.888	0.79
24_L	45_I	0.873	0.78
10_R	15_S	0.870	0.78
26_P	32_K	0.860	0.77
15_S	19_L	0.848	0.76
19_L	22_V	0.820	0.74
31_L	60_G	0.809	0.73
48_F	51_L	0.794	0.71
8_Y	28_K	0.789	0.71
14_S	21_L	0.785	0.70
4_N	13_I	0.779	0.70
8_Y	27_L	0.776	0.70
32_K	40_L	0.763	0.68
21_L	25_E	0.758	0.68
14_S	17_L	0.752	0.67
8_Y	60_G	0.728	0.65
38_I	41_I	0.703	0.62
42_G	45_I	0.698	0.61
6_S	12_F	0.696	0.61
7_R	14_S	0.694	0.61
48_F	52_Y	0.690	0.61
35_K	39_A	0.678	0.59
55_L	59_L	0.677	0.59
8_Y	11_F	0.676	0.59
10_R	31_L	0.675	0.59
33_N	44_L	0.665	0.58
17_L	47_G	0.634	0.54
16_L	21_L	0.631	0.54
2_W	19_L	0.628	0.53
43_A	50_F	0.618	0.52
15_S	22_V	0.609	0.51
52_Y	60_G	0.606	0.51
9_P	13_I	0.597	0.50
24_L	28_K	0.585	0.48
22_V	42_G	0.583	0.48
7_R	12_F	0.573	0.47
1_F	8_Y	0.572	0.47
19_L	26_P	0.561	0.46
29_N	33_N	0.561	0.46
50_F	56_R	0.557	0.45
28_K	31_L	0.554	0.45
41_I	55_L	0.551	0.44
21_L	30_L	0.551	0.44
17_L	37_A	0.549	0.44
6_S	10_R	0.547	0.44
23_I	43_A	0.544	0.44
43_A	46_G	0.528	0.42
35_K	42_G	0.527	0.42
36_T	40_L	0.524	0.41
22_V	25_E	0.509	0.40
3_N	34_P	0.500	0.39

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
4g1uA	2	0.9333	9.4	0.867	Contact Map
2nq2A	2	0.9667	8.7	0.87	Contact Map
2qi9A	2	0.9667	7.7	0.873	Contact Map
2zy9A	2	0.8833	2.8	0.898	Contact Map
2js7A	1	0.3333	2.6	0.899	Contact Map
3ar4A	1	1	2.5	0.9	Contact Map
1nmbN	1	0	2.4	0.9	Contact Map
1zauA	1	0.3333	2.2	0.902	Contact Map
2kogA	1	0.4667	2.2	0.903	Contact Map
3tiaA	3	0	2.2	0.903	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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