DUF4193 - PFAM28P - GREMLIN Contacts

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DUF4193 - Domain of unknown function (DUF4193)

PFAM:	PF13834	Sequences: MATDYDAPRKTDDELDEDSLEELKARRADKQSAVVDEDEAEAAESFELPGADLSGEELTVRVLPKQADEFTCSSCFLVKHRSQLADEKNGRMICRDCA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	98 (97)
Sequences:	2280 (1143)
Seq/√Len:	116.0
META:	0.82

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_L	66_Q	4.168	1.00
79_K	83_Q	3.553	1.00
65_K	71_T	2.815	1.00
24_K	27_R	2.295	1.00
88_K	91_R	2.271	1.00
84_L	92_M	2.232	1.00
93_I	98_A	2.032	1.00
21_E	24_K	2.004	1.00
51_A	54_S	1.966	1.00
86_D	91_R	1.950	1.00
61_R	71_T	1.909	1.00
19_S	24_K	1.895	1.00
86_D	98_A	1.884	1.00
74_S	93_I	1.774	1.00
83_Q	96_D	1.622	1.00
5_Y	9_R	1.590	1.00
86_D	93_I	1.551	1.00
86_D	89_N	1.512	1.00
57_E	68_D	1.442	1.00
24_K	28_A	1.413	1.00
68_D	80_H	1.404	1.00
22_E	27_R	1.388	1.00
23_L	29_D	1.332	1.00
27_R	31_Q	1.312	1.00
67_A	80_H	1.311	1.00
20_L	26_R	1.306	1.00
19_S	26_R	1.287	1.00
67_A	81_R	1.279	0.99
17_E	20_L	1.262	0.99
79_K	84_L	1.255	0.99
24_K	29_D	1.250	0.99
22_E	25_A	1.243	0.99
87_E	90_G	1.234	0.99
94_C	97_C	1.220	0.99
47_E	51_A	1.210	0.99
48_L	52_D	1.151	0.99
60_V	63_L	1.099	0.98
87_E	92_M	1.094	0.98
2_A	12_D	1.092	0.98
86_D	92_M	1.068	0.98
62_V	66_Q	1.065	0.98
25_A	28_A	1.062	0.98
29_D	32_S	1.061	0.98
39_E	43_A	1.041	0.98
56_E	60_V	1.028	0.98
15_L	18_D	1.016	0.97
79_K	82_S	0.998	0.97
48_L	54_S	0.998	0.97
48_L	51_A	0.992	0.97
73_S	93_I	0.985	0.97
50_G	54_S	0.981	0.97
26_R	29_D	0.981	0.97
7_A	11_T	0.971	0.97
47_E	50_G	0.970	0.96
86_D	95_R	0.966	0.96
2_A	10_K	0.966	0.96
81_R	87_E	0.952	0.96
85_A	88_K	0.951	0.96
19_S	27_R	0.951	0.96
73_S	91_R	0.941	0.96
85_A	95_R	0.935	0.96
76_F	88_K	0.925	0.95
92_M	98_A	0.924	0.95
58_L	82_S	0.921	0.95
71_T	92_M	0.920	0.95
72_C	75_C	0.915	0.95
27_R	30_K	0.909	0.95
10_K	13_D	0.899	0.95
78_V	81_R	0.896	0.95
88_K	92_M	0.894	0.94
73_S	92_M	0.893	0.94
7_A	10_K	0.890	0.94
89_N	92_M	0.875	0.94
56_E	62_V	0.864	0.93
49_P	52_D	0.859	0.93
69_E	75_C	0.859	0.93
33_A	36_D	0.836	0.92
25_A	29_D	0.830	0.92
50_G	55_G	0.802	0.91
49_P	56_E	0.800	0.90
5_Y	8_P	0.780	0.89
28_A	31_Q	0.774	0.89
3_T	8_P	0.771	0.89
58_L	66_Q	0.768	0.89
35_V	49_P	0.765	0.88
69_E	72_C	0.757	0.88
32_S	35_V	0.755	0.88
84_L	87_E	0.750	0.87
83_Q	95_R	0.744	0.87
11_T	14_E	0.734	0.86
33_A	37_E	0.730	0.86
81_R	92_M	0.730	0.86
87_E	91_R	0.727	0.86
63_L	80_H	0.721	0.85
56_E	59_T	0.712	0.85
23_L	28_A	0.709	0.84
12_D	37_E	0.703	0.84
42_A	45_S	0.693	0.83
51_A	55_G	0.692	0.83
52_D	55_G	0.690	0.83
71_T	80_H	0.685	0.82
21_E	27_R	0.685	0.82
34_V	37_E	0.679	0.82
44_E	50_G	0.677	0.82
79_K	93_I	0.675	0.81
60_V	68_D	0.653	0.79
65_K	83_Q	0.652	0.79
50_G	53_L	0.649	0.79
18_D	24_K	0.634	0.77
47_E	52_D	0.630	0.77
22_E	26_R	0.630	0.77
43_A	46_F	0.629	0.77
68_D	81_R	0.622	0.76
71_T	78_V	0.622	0.76
45_S	48_L	0.621	0.76
17_E	26_R	0.620	0.76
74_S	98_A	0.619	0.75
24_K	31_Q	0.610	0.74
6_D	9_R	0.606	0.74
59_T	65_K	0.602	0.73
38_D	41_E	0.600	0.73
23_L	31_Q	0.599	0.73
23_L	47_E	0.594	0.72
61_R	78_V	0.584	0.71
92_M	95_R	0.584	0.71
47_E	54_S	0.582	0.71
48_L	53_L	0.572	0.70
46_F	57_E	0.569	0.69
67_A	73_S	0.566	0.69
19_S	22_E	0.564	0.69
7_A	12_D	0.562	0.68
52_D	56_E	0.559	0.68
13_D	16_D	0.555	0.67
23_L	56_E	0.554	0.67
3_T	7_A	0.549	0.66
26_R	30_K	0.546	0.66
39_E	45_S	0.537	0.65
37_E	42_A	0.535	0.64
25_A	31_Q	0.533	0.64
2_A	13_D	0.518	0.62
38_D	64_P	0.516	0.62
46_F	52_D	0.513	0.61
74_S	78_V	0.506	0.60
57_E	63_L	0.504	0.60
70_F	84_L	0.500	0.59
91_R	95_R	0.500	0.59

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
3na7A	1	0.898	51.8	0.877	Contact Map
4iloA	3	0.898	30.7	0.892	Contact Map
3hctA	1	0.4184	27.1	0.895	Contact Map
3hcsA	2	0.4184	24.9	0.897	Contact Map
4tkpB	1	0.3571	24.7	0.897	Contact Map
2ecvA	1	0.4694	22.4	0.899	Contact Map
4cfgA	2	0	21.7	0.9	Contact Map
4txaA	1	0.3367	21.1	0.9	Contact Map
3h7hA	1	0.3776	20.7	0.9	Contact Map
2ecwA	1	0.4694	19.5	0.902	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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