DICT - PFAM28P - GREMLIN Contacts

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DICT - Sensory domain in DIguanylate Cyclases and Two-component system

PFAM:	PF10069	Sequences: DSSLYQLLLRALPPLRPQVLSKRTLLALSRAIEDEALARAERPVLFAAFQRERFYRQEAERYRRLARTADQVVVFADGLPDTGFAEHPREPAPGVRGVPLDPDDPLAREWFVVVDGPHFAAALVAREP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	128 (106)
Sequences:	2431 (1641)
Seq/√Len:	159.4
META:	0.812

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_A	111_F	4.669	1.00
47_A	62_Y	3.601	1.00
22_K	54_F	2.848	1.00
46_F	75_F	2.343	1.00
30_R	58_E	2.129	1.00
56_R	59_A	2.042	1.00
50_Q	110_W	2.010	1.00
26_L	30_R	2.009	1.00
59_A	63_R	1.923	1.00
29_S	123_L	1.912	1.00
33_E	110_W	1.895	1.00
22_K	26_L	1.891	1.00
44_V	71_Q	1.851	1.00
64_R	67_R	1.807	1.00
34_D	61_R	1.718	1.00
101_D	104_D	1.662	1.00
51_R	107_A	1.594	1.00
49_F	110_W	1.594	1.00
45_L	114_V	1.583	1.00
113_V	122_A	1.583	1.00
41_E	116_G	1.576	1.00
55_Y	59_A	1.545	1.00
36_A	43_P	1.520	1.00
55_Y	95_V	1.506	1.00
91_P	94_G	1.475	1.00
29_S	112_V	1.463	1.00
43_P	114_V	1.407	1.00
46_F	73_V	1.399	1.00
51_R	54_F	1.312	1.00
100_L	107_A	1.297	1.00
25_L	125_A	1.263	1.00
52_E	56_R	1.248	1.00
91_P	96_R	1.242	1.00
29_S	110_W	1.207	1.00
26_L	29_S	1.206	1.00
111_F	124_V	1.191	1.00
21_S	24_T	1.182	1.00
36_A	114_V	1.143	1.00
51_R	77_D	1.133	1.00
42_R	70_D	1.131	1.00
32_I	121_A	1.129	1.00
63_R	92_A	1.128	1.00
112_V	123_L	1.127	1.00
35_E	38_A	1.125	1.00
52_E	76_A	1.119	1.00
35_E	39_R	1.116	1.00
36_A	112_V	1.108	1.00
58_E	62_Y	1.102	1.00
22_K	25_L	1.102	1.00
33_E	49_F	1.080	0.99
32_I	114_V	1.055	0.99
62_Y	124_V	1.043	0.99
31_A	34_D	1.041	0.99
60_E	63_R	1.039	0.99
33_E	65_L	1.021	0.99
33_E	50_Q	1.013	0.99
34_D	37_L	1.010	0.99
25_L	44_V	1.007	0.99
29_S	50_Q	0.989	0.99
62_Y	114_V	0.983	0.99
45_L	69_A	0.970	0.99
48_A	100_L	0.963	0.99
28_L	31_A	0.940	0.98
103_D	107_A	0.938	0.98
104_D	107_A	0.937	0.98
24_T	119_F	0.933	0.98
36_A	116_G	0.933	0.98
100_L	104_D	0.933	0.98
39_R	43_P	0.913	0.98
115_D	120_A	0.908	0.98
40_A	43_P	0.906	0.98
50_Q	127_E	0.896	0.98
66_A	95_V	0.895	0.98
39_R	42_R	0.878	0.98
100_L	109_E	0.878	0.98
44_V	122_A	0.878	0.98
21_S	48_A	0.874	0.98
29_S	33_E	0.864	0.97
18_Q	45_L	0.851	0.97
32_I	123_L	0.851	0.97
65_L	110_W	0.845	0.97
62_Y	72_V	0.845	0.97
22_K	50_Q	0.844	0.97
44_V	73_V	0.839	0.97
86_E	89_R	0.827	0.97
20_L	24_T	0.826	0.97
35_E	40_A	0.816	0.96
90_E	97_G	0.815	0.96
122_A	125_A	0.805	0.96
29_S	65_L	0.795	0.96
90_E	93_P	0.791	0.96
32_I	112_V	0.784	0.95
31_A	35_E	0.780	0.95
55_Y	74_V	0.779	0.95
27_A	48_A	0.773	0.95
25_L	49_F	0.759	0.94
24_T	31_A	0.742	0.94
31_A	38_A	0.739	0.94
45_L	72_V	0.738	0.94
37_L	120_A	0.737	0.94
86_E	92_A	0.713	0.92
36_A	41_E	0.712	0.92
45_L	65_L	0.707	0.92
26_L	51_R	0.692	0.91
43_P	69_A	0.690	0.91
36_A	117_P	0.684	0.91
38_A	47_A	0.679	0.90
106_L	119_F	0.663	0.89
102_P	107_A	0.662	0.89
39_R	116_G	0.661	0.89
29_S	49_F	0.653	0.89
44_V	115_D	0.653	0.89
31_A	121_A	0.653	0.89
33_E	76_A	0.650	0.88
84_F	89_R	0.645	0.88
32_I	115_D	0.644	0.88
107_A	111_F	0.631	0.87
28_L	38_A	0.619	0.86
85_A	93_P	0.613	0.85
89_R	97_G	0.612	0.85
36_A	119_F	0.605	0.85
28_L	32_I	0.602	0.84
53_R	89_R	0.601	0.84
50_Q	65_L	0.594	0.84
25_L	92_A	0.583	0.82
30_R	51_R	0.582	0.82
42_R	105_P	0.580	0.82
60_E	73_V	0.579	0.82
43_P	48_A	0.577	0.82
64_R	68_T	0.572	0.81
27_A	45_L	0.567	0.81
65_L	68_T	0.566	0.81
18_Q	115_D	0.566	0.81
34_D	58_E	0.564	0.80
23_R	37_L	0.555	0.79
90_E	96_R	0.554	0.79
23_R	107_A	0.553	0.79
91_P	97_G	0.548	0.78
75_F	111_F	0.545	0.78
34_D	38_A	0.543	0.78
88_P	91_P	0.542	0.78
69_A	75_F	0.541	0.78
18_Q	60_E	0.538	0.77
71_Q	96_R	0.537	0.77
46_F	109_E	0.537	0.77
114_V	119_F	0.535	0.77
37_L	62_Y	0.524	0.75
70_D	111_F	0.521	0.75
92_A	95_V	0.519	0.75
99_P	122_A	0.519	0.75
16_R	103_D	0.511	0.74
37_L	64_R	0.509	0.73
27_A	31_A	0.509	0.73
41_E	114_V	0.508	0.73
49_F	56_R	0.506	0.73
88_P	99_P	0.503	0.72
16_R	123_L	0.503	0.72
91_P	95_V	0.501	0.72
39_R	123_L	0.500	0.72

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
1ju2A	1	0.3516	14.8	0.911	Contact Map
1gpeA	2	0.3359	9.3	0.919	Contact Map
2i0zA	1	0.1641	3.9	0.932	Contact Map
2e1mA	2	0.4688	3.3	0.934	Contact Map
3pl8A	4	0.1562	2.9	0.936	Contact Map
2dkhA	2	0.3984	2.7	0.938	Contact Map
3hdqA	4	0.1875	2.6	0.938	Contact Map
2zxiA	2	0.2188	2.6	0.938	Contact Map
1kaeA	2	0.4297	2.2	0.94	Contact Map
4ci6B	1	0.7656	2.2	0.94	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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