DUF2098 - PFAM28P - GREMLIN Contacts

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DUF2098 - Uncharacterized protein conserved in archaea (DUF2098)

PFAM:	PF09871	Sequences: EIKVGSRVRYPRTGTVGKVLDIKKEEDGEVWALLDSTGLYYRIDTLEPADESEKKEKKKEDREEDLEEIKEREKEFEEELDEAKNSDQSCEGGG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	94 (92)
Sequences:	604 (419)
Seq/√Len:	43.6
META:	0.897

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_A	43_I	3.739	1.00
9_R	14_G	2.806	1.00
23_K	26_E	2.694	1.00
81_D	84_K	2.358	1.00
88_Q	91_E	2.305	1.00
70_K	74_K	2.007	0.99
11_P	47_E	1.883	0.99
32_A	46_L	1.864	0.99
23_K	40_Y	1.840	0.99
31_W	47_E	1.777	0.98
91_E	94_G	1.774	0.98
79_E	84_K	1.749	0.98
12_R	33_L	1.697	0.98
13_T	17_G	1.689	0.97
58_K	61_D	1.650	0.97
78_E	81_D	1.630	0.97
42_R	45_T	1.582	0.96
7_R	48_P	1.580	0.96
56_E	63_E	1.556	0.96
17_G	35_D	1.530	0.95
9_R	16_V	1.453	0.94
86_S	89_S	1.446	0.94
33_L	40_Y	1.409	0.93
14_G	51_E	1.401	0.93
28_G	37_T	1.364	0.92
25_E	28_G	1.355	0.91
80_L	84_K	1.323	0.90
86_S	92_G	1.246	0.88
2_I	8_V	1.243	0.87
54_K	59_K	1.240	0.87
5_G	10_Y	1.217	0.86
11_P	14_G	1.216	0.86
54_K	58_K	1.198	0.85
25_E	29_E	1.191	0.85
2_I	19_V	1.188	0.85
10_Y	13_T	1.174	0.84
65_D	73_E	1.172	0.84
72_R	75_E	1.164	0.84
70_K	73_E	1.157	0.83
71_E	74_K	1.153	0.83
2_I	49_A	1.115	0.81
62_R	69_I	1.107	0.80
38_G	45_T	1.086	0.79
28_G	52_S	1.075	0.78
79_E	83_A	1.051	0.77
21_D	33_L	1.045	0.76
21_D	40_Y	1.029	0.75
4_V	26_E	1.017	0.74
66_L	75_E	1.005	0.74
18_K	48_P	0.993	0.73
57_K	61_D	0.989	0.72
3_K	6_S	0.987	0.72
63_E	69_I	0.956	0.70
88_Q	93_G	0.935	0.68
16_V	44_D	0.931	0.68
13_T	35_D	0.930	0.68
12_R	49_A	0.926	0.67
73_E	76_F	0.918	0.67
85_N	88_Q	0.917	0.67
62_R	65_D	0.911	0.66
60_E	66_L	0.892	0.64
39_L	46_L	0.889	0.64
33_L	38_G	0.859	0.61
64_E	70_K	0.857	0.61
65_D	68_E	0.852	0.61
20_L	38_G	0.852	0.61
30_V	60_E	0.851	0.61
88_Q	92_G	0.847	0.60
9_R	13_T	0.840	0.60
14_G	17_G	0.837	0.59
25_E	30_V	0.834	0.59
2_I	6_S	0.827	0.58
6_S	9_R	0.819	0.58
71_E	75_E	0.815	0.57
18_K	40_Y	0.811	0.57
19_V	32_A	0.810	0.57
10_Y	15_T	0.808	0.57
54_K	78_E	0.798	0.56
33_L	43_I	0.784	0.54
90_C	94_G	0.782	0.54
67_E	78_E	0.777	0.54
67_E	70_K	0.776	0.54
62_R	66_L	0.772	0.53
46_L	52_S	0.763	0.52
22_I	67_E	0.751	0.51
69_I	78_E	0.744	0.51
47_E	50_D	0.740	0.50
18_K	91_E	0.738	0.50
4_V	27_D	0.724	0.49
6_S	49_A	0.721	0.48
20_L	51_E	0.719	0.48
83_A	93_G	0.716	0.48
18_K	42_R	0.704	0.47
56_E	60_E	0.703	0.47
34_L	48_P	0.702	0.47
55_K	60_E	0.689	0.45
68_E	73_E	0.689	0.45
65_D	70_K	0.684	0.45
56_E	69_I	0.682	0.45
42_R	87_D	0.674	0.44
80_L	83_A	0.670	0.44
57_K	63_E	0.663	0.43
68_E	72_R	0.663	0.43
18_K	85_N	0.662	0.43
31_W	45_T	0.661	0.43
16_V	49_A	0.660	0.43
9_R	53_E	0.644	0.41
85_N	92_G	0.634	0.40
6_S	48_P	0.624	0.39
12_R	35_D	0.611	0.38
55_K	58_K	0.607	0.38
15_T	37_T	0.596	0.37
12_R	91_E	0.586	0.36
63_E	68_E	0.585	0.36
25_E	48_P	0.580	0.35
8_V	37_T	0.576	0.35
15_T	50_D	0.575	0.35
16_V	36_S	0.572	0.35
27_D	44_D	0.569	0.34
9_R	51_E	0.563	0.34
43_I	48_P	0.559	0.33
4_V	21_D	0.558	0.33
28_G	39_L	0.555	0.33
12_R	23_K	0.555	0.33
68_E	71_E	0.553	0.33
19_V	79_E	0.549	0.33
89_S	92_G	0.544	0.32
59_K	66_L	0.541	0.32
19_V	30_V	0.541	0.32
83_A	87_D	0.535	0.31
29_E	50_D	0.535	0.31
46_L	70_K	0.528	0.31
9_R	90_C	0.525	0.31
47_E	51_E	0.521	0.30
79_E	82_E	0.509	0.29
54_K	57_K	0.509	0.29
63_E	73_E	0.508	0.29
20_L	35_D	0.500	0.29

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
1qp2A	1	0.5957	49.5	0.87	Contact Map
2lt1A	1	0.6064	36.6	0.88	Contact Map
4l5gA	1	0.9255	33.9	0.882	Contact Map
2lt4A	1	0.617	25.5	0.889	Contact Map
4kbmB	1	0.8298	24.2	0.89	Contact Map
1ix5A	1	0.4574	22.9	0.892	Contact Map
3p8bB	2	0.5426	21.9	0.893	Contact Map
3mlqE	1	0.4468	19.5	0.895	Contact Map
4p5nA	2	0.5532	19.1	0.895	Contact Map
2lq8A	1	0.5213	16.9	0.898	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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