DNase_NucA_NucB - PFAM28P - GREMLIN Contacts

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DNase_NucA_NucB - Deoxyribonuclease NucA/NucB

PFAM:	PF14040	Sequences: LTISRSKYPEIAQHIEDAQAAGKPSVLTIDRDSAGADANRKAALRSGIPTKGPPYPPPGKDRDEYPFASTKEGGAGASVRYIPPSDNRGAGGSLGNFYRKRRIPDGDKFRVVI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	113 (102)
Sequences:	1076 (941)
Seq/√Len:	93.2
META:	0.682

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_D	80_R	3.782	1.00
61_D	88_R	3.602	1.00
5_R	16_E	2.941	1.00
14_H	78_S	2.856	1.00
40_R	68_A	2.396	1.00
28_T	72_E	2.225	1.00
70_T	109_F	2.183	1.00
69_S	98_Y	2.141	1.00
11_I	82_I	2.094	1.00
11_I	86_D	2.089	1.00
10_E	86_D	1.947	1.00
62_R	81_Y	1.901	1.00
93_S	98_Y	1.786	1.00
92_G	96_N	1.785	1.00
74_G	77_A	1.704	1.00
62_R	79_V	1.695	1.00
39_N	43_A	1.630	1.00
104_P	107_D	1.620	1.00
61_D	87_N	1.582	1.00
8_Y	89_G	1.566	1.00
38_A	42_A	1.551	1.00
31_R	105_D	1.525	1.00
19_Q	65_Y	1.522	1.00
15_I	19_Q	1.513	1.00
28_T	108_K	1.502	1.00
27_L	65_Y	1.445	1.00
15_I	67_F	1.410	0.99
84_P	88_R	1.399	0.99
10_E	83_P	1.377	0.99
103_I	107_D	1.373	0.99
44_L	62_R	1.348	0.99
11_I	90_A	1.329	0.99
67_F	94_L	1.320	0.99
61_D	84_P	1.296	0.99
98_Y	103_I	1.285	0.99
60_K	81_Y	1.235	0.98
95_G	99_R	1.194	0.98
39_N	44_L	1.166	0.98
21_A	78_S	1.162	0.98
16_E	20_A	1.157	0.98
51_K	81_Y	1.151	0.98
13_Q	17_D	1.133	0.97
89_G	92_G	1.127	0.97
71_K	105_D	1.121	0.97
93_S	97_F	1.114	0.97
24_P	27_L	1.097	0.97
24_P	65_Y	1.086	0.96
29_I	69_S	1.068	0.96
92_G	95_G	1.057	0.96
30_D	35_G	1.048	0.96
13_Q	16_E	1.047	0.96
11_I	87_N	1.032	0.95
87_N	91_G	1.026	0.95
8_Y	93_S	1.017	0.95
45_R	62_R	1.009	0.95
35_G	39_N	1.005	0.95
82_I	90_A	1.000	0.94
87_N	90_A	0.987	0.94
44_L	48_I	0.985	0.94
86_D	90_A	0.981	0.94
88_R	92_G	0.979	0.94
30_D	39_N	0.967	0.93
67_F	70_T	0.942	0.92
25_S	110_R	0.933	0.92
19_Q	25_S	0.919	0.92
12_A	15_I	0.907	0.91
5_R	12_A	0.906	0.91
29_I	103_I	0.887	0.90
82_I	86_D	0.887	0.90
27_L	70_T	0.880	0.90
12_A	19_Q	0.875	0.89
28_T	31_R	0.872	0.89
97_F	101_R	0.837	0.87
14_H	17_D	0.829	0.87
60_K	83_P	0.822	0.86
94_L	97_F	0.818	0.86
12_A	16_E	0.813	0.86
94_L	98_Y	0.787	0.84
61_D	90_A	0.769	0.82
47_G	50_T	0.767	0.82
39_N	68_A	0.763	0.82
65_Y	70_T	0.761	0.82
61_D	92_G	0.761	0.82
89_G	93_S	0.759	0.82
42_A	75_A	0.723	0.78
45_R	48_I	0.719	0.78
17_D	78_S	0.718	0.78
44_L	47_G	0.715	0.78
84_P	87_N	0.713	0.77
95_G	101_R	0.712	0.77
10_E	13_Q	0.696	0.76
59_G	84_P	0.695	0.76
42_A	45_R	0.695	0.76
18_A	21_A	0.694	0.75
26_V	110_R	0.694	0.75
29_I	39_N	0.693	0.75
72_E	108_K	0.686	0.75
83_P	86_D	0.683	0.74
32_D	37_D	0.670	0.73
5_R	15_I	0.655	0.71
18_A	65_Y	0.653	0.71
102_R	107_D	0.629	0.68
29_I	105_D	0.627	0.68
8_Y	87_N	0.624	0.67
10_E	17_D	0.623	0.67
11_I	15_I	0.623	0.67
37_D	41_K	0.621	0.67
38_A	41_K	0.612	0.66
33_S	44_L	0.612	0.66
15_I	63_D	0.604	0.65
64_E	91_G	0.601	0.65
104_P	109_F	0.593	0.64
13_Q	20_A	0.589	0.63
86_D	89_G	0.589	0.63
9_P	12_A	0.588	0.63
97_F	102_R	0.586	0.63
45_R	79_V	0.580	0.62
44_L	50_T	0.578	0.62
28_T	106_G	0.578	0.62
69_S	94_L	0.578	0.62
36_A	44_L	0.572	0.61
63_D	90_A	0.566	0.60
9_P	86_D	0.562	0.59
30_D	71_K	0.562	0.59
30_D	105_D	0.562	0.59
67_F	111_V	0.560	0.59
101_R	104_P	0.556	0.59
11_I	67_F	0.554	0.58
25_S	58_P	0.554	0.58
14_H	18_A	0.553	0.58
48_I	81_Y	0.550	0.58
25_S	60_K	0.545	0.57
49_P	81_Y	0.542	0.57
50_T	62_R	0.539	0.56
23_K	76_G	0.537	0.56
7_K	10_E	0.536	0.56
5_R	8_Y	0.530	0.55
10_E	60_K	0.528	0.55
14_H	80_R	0.528	0.55
85_S	92_G	0.525	0.54
18_A	24_P	0.524	0.54
12_A	97_F	0.523	0.54
98_Y	109_F	0.519	0.54
15_I	90_A	0.517	0.53
12_A	17_D	0.509	0.52
57_P	60_K	0.508	0.52
31_R	36_A	0.507	0.52
35_G	70_T	0.507	0.52
33_S	39_N	0.503	0.51
70_T	98_Y	0.503	0.51
87_N	95_G	0.502	0.51
102_R	110_R	0.502	0.51
96_N	101_R	0.500	0.51

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
2xqyA	1	0.4779	8.1	0.927	Contact Map
2cmyB	1	0.1858	6.6	0.93	Contact Map
3b9tA	4	0.3628	5.6	0.932	Contact Map
3ml4A	2	0.2566	3.9	0.938	Contact Map
2mc5A	1	0.2301	2.9	0.941	Contact Map
2plxB	1	0.2301	2.6	0.943	Contact Map
2l66A	2	0.3186	2.6	0.943	Contact Map
4go6B	3	0.2655	2.2	0.945	Contact Map
1olgA	3	0.1239	2.2	0.945	Contact Map
2peqA	2	0.531	2	0.946	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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