Y2008 - HALSA - GREMLIN Contacts

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Y2008 - DNA-binding protein VNG_2008H

UniProt:	Q9HNP3	Sequences: MSGNPDDDRLEELRQRKKEQLKQQQQGGDAEREAQQQQAQQAEQQKQAMLKQNLTDGARKRLNTIRMSKPEFAEQAEQQVLALAQSGRVQGRIDEDQMKEILRELKPDSQSFNINRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	117 (107)
Sequences:	446 (310)
Seq/√Len:	29.9

HALSA - Y2008
SULSO - Y352

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_N	80_V	2.575	1.00
12_E	15_Q	2.572	1.00
36_Q	39_A	2.466	0.99
46_K	74_E	2.440	0.99
19_E	22_K	2.365	0.99
65_I	98_M	2.265	0.99
7_D	10_L	2.141	0.98
36_Q	40_Q	2.043	0.97
11_E	15_Q	2.012	0.97
55_T	94_D	2.000	0.97
12_E	16_R	1.976	0.97
65_I	73_A	1.971	0.97
60_K	64_T	1.891	0.96
66_R	83_L	1.788	0.94
111_S	114_I	1.774	0.94
56_D	60_K	1.771	0.94
80_V	98_M	1.770	0.94
64_T	68_S	1.744	0.94
76_A	94_D	1.737	0.93
93_I	98_M	1.682	0.92
66_R	77_E	1.680	0.92
53_N	81_L	1.633	0.91
94_D	97_Q	1.618	0.91
82_A	85_Q	1.616	0.91
43_E	66_R	1.605	0.90
89_V	93_I	1.588	0.90
42_A	46_K	1.578	0.90
46_K	81_L	1.549	0.89
35_Q	38_Q	1.546	0.89
42_A	85_Q	1.525	0.88
49_M	78_Q	1.462	0.86
65_I	72_F	1.417	0.84
18_K	89_V	1.384	0.82
34_A	37_Q	1.329	0.80
65_I	79_Q	1.328	0.80
64_T	73_A	1.308	0.78
14_R	18_K	1.299	0.78
60_K	69_K	1.257	0.76
38_Q	42_A	1.242	0.75
32_R	35_Q	1.231	0.74
65_I	95_E	1.189	0.71
42_A	45_Q	1.155	0.69
66_R	74_E	1.150	0.69
20_Q	23_Q	1.149	0.69
49_M	53_N	1.131	0.67
18_K	21_L	1.117	0.67
18_K	22_K	1.114	0.66
79_Q	88_R	1.097	0.65
66_R	99_K	1.079	0.64
80_V	104_E	1.072	0.63
50_L	84_A	1.056	0.62
14_R	21_L	1.048	0.61
80_V	97_Q	1.041	0.61
49_M	81_L	1.038	0.61
52_Q	92_R	1.033	0.60
33_E	36_Q	1.033	0.60
68_S	73_A	1.000	0.58
57_G	95_E	0.990	0.57
79_Q	83_L	0.954	0.54
65_I	84_A	0.953	0.54
25_Q	28_G	0.950	0.54
95_E	110_Q	0.948	0.54
13_L	64_T	0.926	0.52
9_R	12_E	0.922	0.52
95_E	99_K	0.920	0.52
10_L	14_R	0.910	0.51
103_R	108_D	0.907	0.50
84_A	98_M	0.907	0.50
32_R	105_L	0.900	0.50
9_R	34_A	0.888	0.49
14_R	17_K	0.884	0.49
55_T	75_Q	0.880	0.48
96_D	99_K	0.879	0.48
27_G	89_V	0.868	0.47
20_Q	24_Q	0.865	0.47
103_R	106_K	0.857	0.47
35_Q	39_A	0.832	0.45
47_Q	60_K	0.830	0.44
80_V	105_L	0.825	0.44
23_Q	27_G	0.817	0.43
68_S	93_I	0.811	0.43
33_E	37_Q	0.806	0.43
15_Q	22_K	0.802	0.42
27_G	71_E	0.791	0.41
78_Q	101_I	0.791	0.41
45_Q	83_L	0.761	0.39
66_R	73_A	0.759	0.39
41_Q	45_Q	0.750	0.38
92_R	106_K	0.746	0.38
59_R	104_E	0.743	0.38
76_A	90_Q	0.742	0.38
33_E	43_E	0.741	0.38
110_Q	114_I	0.734	0.37
89_V	97_Q	0.731	0.37
50_L	81_L	0.727	0.37
60_K	63_N	0.726	0.36
68_S	107_P	0.726	0.36
79_Q	101_I	0.721	0.36
47_Q	52_Q	0.718	0.36
37_Q	41_Q	0.710	0.35
34_A	38_Q	0.705	0.35
37_Q	40_Q	0.701	0.35
37_Q	105_L	0.693	0.34
65_I	76_A	0.693	0.34
72_F	106_K	0.687	0.34
25_Q	90_Q	0.679	0.33
86_S	90_Q	0.677	0.33
16_R	20_Q	0.676	0.33
50_L	54_L	0.674	0.33
82_A	86_S	0.669	0.32
67_M	97_Q	0.667	0.32
16_R	41_Q	0.666	0.32
8_D	12_E	0.662	0.32
18_K	57_G	0.661	0.32
73_A	110_Q	0.655	0.31
29_D	52_Q	0.646	0.31
39_A	80_V	0.644	0.31
39_A	43_E	0.643	0.31
70_P	87_G	0.627	0.30
95_E	109_S	0.625	0.29
41_Q	71_E	0.625	0.29
44_Q	49_M	0.622	0.29
59_R	70_P	0.614	0.29
78_Q	105_L	0.612	0.29
51_K	88_R	0.608	0.28
18_K	29_D	0.605	0.28
93_I	97_Q	0.603	0.28
29_D	39_A	0.601	0.28
42_A	49_M	0.598	0.28
13_L	21_L	0.597	0.28
11_E	74_E	0.595	0.27
91_G	105_L	0.592	0.27
98_M	108_D	0.589	0.27
16_R	69_K	0.586	0.27
58_A	84_A	0.584	0.27
15_Q	47_Q	0.572	0.26
8_D	11_E	0.563	0.25
19_E	69_K	0.558	0.25
48_A	51_K	0.556	0.25
45_Q	48_A	0.556	0.25
51_K	67_M	0.538	0.24
19_E	54_L	0.538	0.24
51_K	55_T	0.535	0.24
59_R	75_Q	0.534	0.24
82_A	99_K	0.532	0.24
20_Q	26_Q	0.532	0.24
71_E	75_Q	0.531	0.24
92_R	113_N	0.531	0.24
79_Q	94_D	0.531	0.24
19_E	23_Q	0.531	0.24
40_Q	57_G	0.530	0.24
86_S	93_I	0.529	0.23
83_L	99_K	0.525	0.23
67_M	82_A	0.525	0.23
37_Q	108_D	0.518	0.23
51_K	92_R	0.514	0.23
42_A	67_M	0.504	0.22
84_A	101_I	0.503	0.22
15_Q	38_Q	0.501	0.22
24_Q	27_G	0.500	0.22

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
2jxnA	1	0.9573	100	0.152	Contact Map
2cruA	1	0.9402	100	0.191	Contact Map
1eijA	1	0.6154	100	0.323	Contact Map
2fh0A	1	0.6667	99.9	0.369	Contact Map
1yybA	1	0.2222	96.4	0.83	Contact Map
4y66B	1	0.8718	10.3	0.934	Contact Map
4xhmA	1	0.641	7.5	0.938	Contact Map
2es4D	3	0.9829	6.8	0.94	Contact Map
3qryB	1	0.3675	4.5	0.945	Contact Map
2mvmA	1	0.265	4	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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