DUF2846 - PFAM28P - GREMLIN Contacts

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DUF2846 - Protein of unknown function (DUF2846)

PFAM:	PF11008	Sequences: LAGCASVPMASPEQDAAAKPFPPPPPGKARVYVYRPSSFFGAALKPDVYLDGKVVGELAPGTYFYVDVPPGEHTISTESGEFEPGSLLFPGTNSLTLTAEAGKTYYVRQEIKMGPNLVFVGGAN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	124 (104)
Sequences:	4073 (3162)
Seq/√Len:	310.1
META:	0.905

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_D	73_H	3.939	1.00
29_A	99_A	3.430	1.00
100_E	103_K	3.143	1.00
30_R	65_Y	2.847	1.00
30_R	67_D	2.821	1.00
28_K	69_P	2.726	1.00
31_V	68_V	2.537	1.00
72_E	98_T	2.500	1.00
74_T	94_S	2.489	1.00
56_G	64_F	2.481	1.00
72_E	96_T	2.194	1.00
30_R	104_T	2.179	1.00
74_T	96_T	2.026	1.00
58_L	109_Q	1.929	1.00
27_G	101_A	1.796	1.00
49_Y	54_V	1.762	1.00
50_L	68_V	1.720	1.00
55_V	66_V	1.693	1.00
11_S	14_Q	1.655	1.00
68_V	73_H	1.619	1.00
75_I	107_V	1.512	1.00
39_F	42_A	1.506	1.00
14_Q	17_A	1.492	1.00
15_D	19_K	1.486	1.00
47_D	54_V	1.441	1.00
97_L	105_Y	1.412	1.00
15_D	18_A	1.390	1.00
29_A	105_Y	1.379	1.00
25_P	67_D	1.354	1.00
34_Y	108_R	1.351	1.00
36_P	108_R	1.346	1.00
47_D	57_E	1.299	1.00
39_F	61_G	1.208	1.00
76_S	94_S	1.177	1.00
95_L	107_V	1.174	1.00
31_V	75_I	1.172	1.00
25_P	28_K	1.163	1.00
70_P	101_A	1.140	1.00
28_K	67_D	1.129	1.00
50_L	75_I	1.128	1.00
99_A	105_Y	1.095	1.00
68_V	99_A	1.064	1.00
50_L	73_H	1.057	1.00
49_Y	76_S	1.042	1.00
42_A	60_P	1.035	1.00
33_V	66_V	1.025	1.00
33_V	75_I	1.001	1.00
69_P	73_H	0.999	1.00
7_V	10_A	0.999	1.00
41_G	44_L	0.990	1.00
48_V	58_L	0.986	1.00
35_R	41_G	0.981	1.00
50_L	55_V	0.972	1.00
52_G	76_S	0.961	1.00
77_T	109_Q	0.906	1.00
15_D	21_F	0.900	1.00
79_S	91_G	0.897	1.00
17_A	21_F	0.894	1.00
45_K	57_E	0.894	1.00
32_Y	63_Y	0.884	1.00
16_A	20_P	0.862	1.00
24_P	27_G	0.857	1.00
49_Y	78_E	0.849	1.00
21_F	106_Y	0.849	1.00
100_E	105_Y	0.849	1.00
12_P	16_A	0.848	1.00
27_G	102_G	0.830	1.00
24_P	30_R	0.799	1.00
18_A	32_Y	0.797	1.00
34_Y	107_V	0.797	1.00
58_L	77_T	0.794	1.00
14_Q	18_A	0.781	1.00
45_K	59_A	0.778	0.99
31_V	99_A	0.778	0.99
73_H	99_A	0.778	0.99
58_L	64_F	0.760	0.99
50_L	66_V	0.755	0.99
17_A	20_P	0.754	0.99
36_P	110_E	0.753	0.99
10_A	13_E	0.749	0.99
10_A	14_Q	0.746	0.99
52_G	74_T	0.741	0.99
81_E	84_P	0.741	0.99
18_A	21_F	0.737	0.99
39_F	60_P	0.730	0.99
32_Y	104_T	0.729	0.99
40_F	43_A	0.718	0.99
39_F	43_A	0.714	0.99
17_A	22_P	0.710	0.99
36_P	39_F	0.702	0.99
97_L	107_V	0.702	0.99
12_P	17_A	0.697	0.99
19_K	22_P	0.695	0.99
24_P	28_K	0.693	0.99
16_A	19_K	0.693	0.99
78_E	92_T	0.691	0.99
33_V	55_V	0.689	0.99
11_S	16_A	0.686	0.99
46_P	77_T	0.680	0.99
9_M	12_P	0.678	0.99
10_A	18_A	0.677	0.99
32_Y	65_Y	0.676	0.99
13_E	19_K	0.673	0.99
14_Q	20_P	0.660	0.98
49_Y	52_G	0.658	0.98
8_P	12_P	0.654	0.98
53_K	68_V	0.651	0.98
53_K	66_V	0.646	0.98
12_P	15_D	0.639	0.98
48_V	64_F	0.635	0.98
37_S	60_P	0.634	0.98
21_F	104_T	0.627	0.98
24_P	67_D	0.627	0.98
44_L	109_Q	0.621	0.98
16_A	21_F	0.610	0.97
9_M	14_Q	0.609	0.97
8_P	11_S	0.605	0.97
79_S	83_E	0.603	0.97
38_S	60_P	0.602	0.97
59_A	62_T	0.599	0.97
31_V	97_L	0.592	0.97
5_A	8_P	0.589	0.97
33_V	64_F	0.586	0.97
31_V	66_V	0.580	0.96
76_S	92_T	0.577	0.96
11_S	18_A	0.576	0.96
21_F	30_R	0.571	0.96
7_V	59_A	0.570	0.96
13_E	16_A	0.569	0.96
67_D	104_T	0.568	0.96
48_V	109_Q	0.568	0.96
45_K	58_L	0.566	0.96
46_P	58_L	0.565	0.96
63_Y	105_Y	0.565	0.96
38_S	41_G	0.562	0.96
34_Y	62_T	0.558	0.95
38_S	93_N	0.558	0.95
37_S	42_A	0.557	0.95
29_A	101_A	0.555	0.95
33_V	56_G	0.554	0.95
37_S	108_R	0.554	0.95
68_V	105_Y	0.551	0.95
48_V	77_T	0.546	0.95
79_S	111_I	0.544	0.95
33_V	50_L	0.543	0.95
13_E	17_A	0.540	0.95
21_F	32_Y	0.535	0.94
44_L	79_S	0.517	0.93
3_G	9_M	0.516	0.93
22_P	65_Y	0.514	0.93
15_D	62_T	0.510	0.93
9_M	59_A	0.505	0.92
2_A	5_A	0.504	0.92
98_T	105_Y	0.504	0.92
18_A	63_Y	0.503	0.92
54_V	57_E	0.500	0.92

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
1h8lA	1	0.8306	32.4	0.884	Contact Map
2uvfA	2	0.8145	29.8	0.886	Contact Map
2vzsA	1	0	28.9	0.887	Contact Map
3pe9A	1	0.7097	28.1	0.887	Contact Map
1uwyA	1	0.8387	26.1	0.889	Contact Map
1xpnA	1	0.871	25	0.89	Contact Map
3wnoA	2	0.9597	21.5	0.893	Contact Map
2vzpA	1	0.7339	19.8	0.895	Contact Map
3pddA	1	0.879	17.7	0.898	Contact Map
2wgnB	1	0.7823	15.2	0.9	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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