DUF3784 - PFAM28P - GREMLIN Contacts

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DUF3784 - Domain of unknown function (DUF3784)

PFAM:	PF12650	Sequences: IIIGLLFIILGILILKGKGAFLIAGYNTMSKEEKEKYDIKKLCRFMGKFLLILGIILLLGGLLSLFLSNWLIIAIILFIVILIGVVIYINKGNRFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	96 (93)
Sequences:	2787 (2420)
Seq/√Len:	250.9
META:	0.822

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_K	35_E	2.644	1.00
4_G	54_G	2.440	1.00
20_A	43_C	2.375	1.00
38_D	41_K	2.347	1.00
11_G	51_L	2.272	1.00
12_I	17_G	2.244	1.00
37_Y	42_L	2.241	1.00
8_I	54_G	2.220	1.00
77_L	81_I	2.132	1.00
15_L	48_K	2.115	1.00
24_A	27_N	2.051	1.00
30_S	33_E	1.918	1.00
87_I	91_K	1.773	1.00
24_A	28_T	1.751	1.00
21_F	34_K	1.719	1.00
72_I	76_I	1.719	1.00
26_Y	39_I	1.710	1.00
2_I	6_L	1.698	1.00
4_G	58_L	1.682	1.00
9_I	13_L	1.625	1.00
74_A	78_F	1.538	1.00
47_G	51_L	1.530	1.00
56_I	60_G	1.519	1.00
13_L	19_G	1.473	1.00
33_E	36_K	1.469	1.00
75_I	78_F	1.458	1.00
43_C	47_G	1.398	1.00
32_E	35_E	1.339	1.00
74_A	77_L	1.311	1.00
26_Y	34_K	1.285	1.00
11_G	54_G	1.278	1.00
25_G	28_T	1.265	1.00
85_V	89_I	1.231	1.00
63_L	70_W	1.218	1.00
87_I	90_N	1.194	1.00
90_N	93_N	1.175	1.00
75_I	79_I	1.166	1.00
3_I	7_F	1.148	1.00
11_G	15_L	1.145	1.00
15_L	51_L	1.135	1.00
67_L	70_W	1.131	1.00
63_L	68_S	1.125	1.00
31_K	34_K	1.114	1.00
84_G	88_Y	1.097	1.00
23_I	46_M	1.091	1.00
78_F	81_I	1.075	1.00
91_K	94_R	1.045	1.00
80_V	84_G	1.035	1.00
39_I	43_C	1.034	1.00
78_F	82_L	1.024	1.00
12_I	16_K	0.995	1.00
14_I	43_C	0.989	1.00
20_A	39_I	0.969	1.00
23_I	42_L	0.965	1.00
81_I	85_V	0.958	1.00
72_I	75_I	0.956	1.00
16_K	40_K	0.955	1.00
49_F	53_L	0.947	1.00
64_S	67_L	0.944	1.00
64_S	69_N	0.937	1.00
52_I	56_I	0.921	1.00
17_G	47_G	0.919	1.00
88_Y	91_K	0.915	1.00
51_L	55_I	0.897	1.00
71_L	75_I	0.871	1.00
14_I	20_A	0.862	0.99
26_Y	29_M	0.847	0.99
64_S	70_W	0.828	0.99
14_I	46_M	0.824	0.99
48_K	51_L	0.809	0.99
86_V	90_N	0.801	0.99
42_L	46_M	0.801	0.99
23_I	43_C	0.800	0.99
48_K	52_I	0.780	0.99
18_K	43_C	0.769	0.99
58_L	61_G	0.767	0.99
82_L	85_V	0.761	0.99
6_L	54_G	0.756	0.99
81_I	84_G	0.756	0.99
88_Y	92_G	0.749	0.99
90_N	94_R	0.743	0.98
4_G	11_G	0.736	0.98
17_G	20_A	0.732	0.98
11_G	14_I	0.728	0.98
82_L	86_V	0.724	0.98
20_A	34_K	0.719	0.98
89_I	92_G	0.697	0.98
37_Y	41_K	0.694	0.98
41_K	45_F	0.685	0.97
16_K	48_K	0.679	0.97
64_S	68_S	0.672	0.97
16_K	20_A	0.667	0.97
53_L	61_G	0.661	0.97
46_M	50_L	0.661	0.97
77_L	88_Y	0.661	0.97
81_I	88_Y	0.658	0.97
8_I	51_L	0.654	0.97
73_I	79_I	0.648	0.96
84_G	87_I	0.647	0.96
10_L	13_L	0.644	0.96
74_A	85_V	0.642	0.96
76_I	81_I	0.639	0.96
85_V	90_N	0.638	0.96
85_V	88_Y	0.634	0.96
15_L	44_R	0.626	0.96
29_M	37_Y	0.625	0.96
45_F	48_K	0.619	0.95
86_V	92_G	0.618	0.95
37_Y	43_C	0.615	0.95
72_I	83_I	0.609	0.95
52_I	55_I	0.600	0.94
7_F	46_M	0.591	0.94
49_F	85_V	0.586	0.94
81_I	86_V	0.583	0.94
29_M	33_E	0.579	0.93
49_F	88_Y	0.574	0.93
71_L	78_F	0.573	0.93
65_L	69_N	0.572	0.93
88_Y	94_R	0.571	0.93
4_G	61_G	0.559	0.92
84_G	92_G	0.553	0.92
57_L	60_G	0.551	0.92
77_L	80_V	0.542	0.91
15_L	47_G	0.542	0.91
15_L	19_G	0.537	0.90
81_I	87_I	0.535	0.90
4_G	57_L	0.533	0.90
4_G	7_F	0.523	0.89
46_M	49_F	0.523	0.89
55_I	62_L	0.518	0.89
7_F	53_L	0.517	0.89
15_L	50_L	0.517	0.89
26_Y	43_C	0.516	0.89
29_M	47_G	0.514	0.88
27_N	34_K	0.512	0.88
63_L	67_L	0.511	0.88
57_L	77_L	0.509	0.88
14_I	50_L	0.509	0.88
9_I	36_K	0.501	0.87
21_F	24_A	0.500	0.87

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
3pjzA	2	0.625	14.5	0.852	Contact Map
2akhX	1	0.7188	9.2	0.864	Contact Map
2xq2A	2	0.8542	8.8	0.866	Contact Map
3j45G	1	0.6667	7.9	0.869	Contact Map
3dinE	1	0.6771	6.9	0.872	Contact Map
2mkvA	1	0.375	6.5	0.873	Contact Map
4a2nB	1	0.9583	6.3	0.875	Contact Map
2wjnH	1	0.4062	6.1	0.875	Contact Map
4ev6A	3	0.9479	5.6	0.878	Contact Map
2mofA	1	0.2708	5.4	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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