DUF1987 - PFAM28P - GREMLIN Contacts

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DUF1987 - Domain of unknown function (DUF1987)

PFAM:	PF09345	Sequences: PEVIFDPETGILEISGRSIPENAAEFYEPVLDWLDEYLKNPNEKTTVNFKLEYFNTSSSKCLLDILKKLEEIHKKGKKVKVNWYYEEDDEDMLEAGEDF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	99 (99)
Sequences:	10474 (7564)
Seq/√Len:	760.2
META:	0.959

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_N	82_N	3.944	1.00
35_D	68_K	3.376	1.00
46_T	82_N	2.878	1.00
44_K	78_K	2.730	1.00
18_S	27_Y	2.411	1.00
13_E	48_N	2.372	1.00
38_L	72_I	2.299	1.00
6_D	9_T	2.226	1.00
17_R	52_E	2.189	1.00
15_S	50_K	2.146	1.00
85_Y	93_L	2.140	1.00
54_F	95_A	2.134	1.00
5_F	12_L	1.946	1.00
2_E	15_S	1.897	1.00
50_K	84_Y	1.879	1.00
44_K	80_K	1.824	1.00
48_N	84_Y	1.786	1.00
18_S	58_S	1.731	1.00
11_I	48_N	1.710	1.00
37_Y	45_T	1.690	1.00
28_E	32_D	1.679	1.00
93_L	97_E	1.636	1.00
2_E	13_E	1.606	1.00
46_T	80_K	1.482	1.00
41_P	45_T	1.478	1.00
11_I	46_T	1.445	1.00
24_A	61_C	1.377	1.00
54_F	59_S	1.364	1.00
4_I	13_E	1.331	1.00
3_V	30_V	1.261	1.00
61_C	64_D	1.217	1.00
23_A	57_S	1.208	1.00
10_G	37_Y	1.207	1.00
32_D	36_E	1.207	1.00
5_F	30_V	1.205	1.00
60_K	64_D	1.181	1.00
12_L	47_V	1.176	1.00
34_L	65_I	1.160	1.00
70_E	73_H	1.147	1.00
49_F	66_L	1.140	1.00
22_N	25_E	1.127	1.00
47_V	69_L	1.082	1.00
31_L	61_C	1.042	1.00
43_E	77_K	1.032	1.00
51_L	62_L	1.008	1.00
36_E	39_K	0.997	1.00
7_P	33_W	0.988	1.00
5_F	14_I	0.980	1.00
34_L	69_L	0.952	1.00
94_E	97_E	0.946	1.00
13_E	50_K	0.945	1.00
67_K	71_E	0.920	1.00
37_Y	41_P	0.910	1.00
24_A	28_E	0.901	1.00
6_D	11_I	0.887	1.00
54_F	62_L	0.887	1.00
25_E	28_E	0.864	1.00
7_P	42_N	0.862	1.00
12_L	45_T	0.860	1.00
24_A	64_D	0.857	1.00
54_F	58_S	0.855	1.00
19_I	61_C	0.851	1.00
10_G	43_E	0.847	1.00
41_P	77_K	0.844	1.00
38_L	68_K	0.834	1.00
56_T	95_A	0.828	1.00
91_D	95_A	0.825	1.00
7_P	40_N	0.800	1.00
69_L	79_V	0.792	1.00
95_A	99_F	0.792	1.00
89_D	92_M	0.785	1.00
70_E	74_K	0.783	1.00
55_N	58_S	0.775	1.00
68_K	71_E	0.774	1.00
26_F	30_V	0.774	1.00
23_A	27_Y	0.764	1.00
72_I	77_K	0.762	1.00
73_H	78_K	0.756	1.00
49_F	62_L	0.756	1.00
63_L	67_K	0.753	1.00
32_D	35_D	0.746	1.00
31_L	35_D	0.737	1.00
68_K	72_I	0.724	1.00
27_Y	58_S	0.713	1.00
85_Y	96_G	0.709	1.00
51_L	58_S	0.698	1.00
70_E	79_V	0.694	1.00
31_L	65_I	0.690	1.00
53_Y	56_T	0.687	1.00
31_L	68_K	0.683	1.00
4_I	7_P	0.678	1.00
20_P	58_S	0.677	1.00
56_T	91_D	0.675	1.00
42_N	77_K	0.670	1.00
73_H	76_G	0.670	1.00
5_F	33_W	0.663	1.00
23_A	61_C	0.662	1.00
45_T	72_I	0.656	1.00
14_I	49_F	0.655	1.00
42_N	45_T	0.653	1.00
45_T	77_K	0.648	1.00
60_K	63_L	0.647	1.00
72_I	75_K	0.642	1.00
33_W	37_Y	0.641	1.00
66_L	81_V	0.641	1.00
18_S	51_L	0.631	1.00
29_P	32_D	0.630	1.00
56_T	59_S	0.629	1.00
92_M	96_G	0.626	1.00
10_G	45_T	0.622	1.00
21_E	56_T	0.616	1.00
59_S	63_L	0.609	1.00
62_L	66_L	0.605	1.00
64_D	67_K	0.600	1.00
34_L	68_K	0.599	1.00
20_P	23_A	0.594	1.00
20_P	57_S	0.594	1.00
21_E	55_N	0.586	1.00
10_G	42_N	0.583	1.00
41_P	44_K	0.573	1.00
30_V	65_I	0.572	1.00
14_I	47_V	0.572	1.00
41_P	72_I	0.570	1.00
57_S	60_K	0.565	1.00
95_A	98_D	0.564	1.00
86_E	89_D	0.559	1.00
63_L	99_F	0.559	1.00
12_L	37_Y	0.553	1.00
4_I	9_T	0.551	1.00
38_L	75_K	0.550	1.00
3_V	14_I	0.549	1.00
71_E	74_K	0.546	1.00
55_N	60_K	0.545	1.00
17_R	90_E	0.539	1.00
94_E	98_D	0.537	1.00
12_L	34_L	0.537	1.00
51_L	54_F	0.536	1.00
33_W	47_V	0.535	1.00
30_V	33_W	0.534	1.00
12_L	33_W	0.532	1.00
21_E	57_S	0.528	1.00
77_K	80_K	0.524	1.00
5_F	37_Y	0.522	1.00
93_L	96_G	0.517	1.00
59_S	95_A	0.514	1.00
19_I	23_A	0.512	1.00
64_D	68_K	0.506	1.00
49_F	96_G	0.500	1.00

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
4dghA	4	0.9091	26.7	0.874	Contact Map
3eikA	2	0.404	19.7	0.882	Contact Map
3mcbB	1	0.3434	17.3	0.885	Contact Map
3lloA	1	0.8485	17.3	0.885	Contact Map
4b0aA	1	0.404	17	0.885	Contact Map
1ytbA	1	0.404	16.9	0.885	Contact Map
1rm1A	1	0.404	13.9	0.89	Contact Map
2o8rA	2	0.9394	10.5	0.895	Contact Map
1aisA	1	0.3737	10.3	0.896	Contact Map
4dgfA	1	0.9091	9.7	0.897	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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