DKNYY - PFAM28P - GREMLIN Contacts

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DKNYY - DKNYY family

PFAM:	PF13644	Sequences: YAKDKNNVYYKGKKIEGADPKTFEVLNEGSNYAKDKNNVYYKGKKLPGADPETFEVLGNNYYKDGKNVYFYSGNSLDNDDESFEVLGNNGYFKDKNNVYYYDNDKKIKIKKIKGADPKTFEVLNDGYAKDKNNVYYKGKKLEGADPATFKVLGDNNGYAKDKNNVYYKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	169 (164)
Sequences:	1837 (1422)
Seq/√Len:	111.1
META:	0.846

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_E	34_K	4.311	1.00
133_N	140_K	3.652	1.00
19_D	36_K	3.580	1.00
50_D	53_T	3.375	1.00
64_D	69_Y	3.275	1.00
150_K	160_K	3.274	1.00
121_E	129_K	3.231	1.00
19_D	22_T	3.162	1.00
120_F	128_A	3.119	1.00
145_D	162_K	3.011	1.00
116_D	131_K	2.872	1.00
7_N	14_K	2.832	1.00
145_D	148_T	2.817	1.00
38_N	45_K	2.477	1.00
149_F	159_A	2.397	1.00
116_D	119_T	2.345	1.00
94_D	97_N	2.244	1.00
22_T	36_K	2.200	1.00
119_T	131_K	2.177	1.00
134_V	146_P	2.084	1.00
39_V	51_P	1.949	1.00
4_D	7_N	1.911	1.00
18_A	33_A	1.870	1.00
94_D	99_Y	1.860	1.00
134_V	144_A	1.829	1.00
83_F	87_G	1.806	1.00
83_F	86_L	1.775	1.00
23_F	33_A	1.769	1.00
22_T	35_D	1.755	1.00
148_T	161_D	1.689	1.00
98_V	117_P	1.646	1.00
64_D	68_V	1.641	1.00
141_L	144_A	1.565	1.00
158_Y	165_V	1.546	1.00
51_P	54_F	1.516	1.00
84_E	87_G	1.468	1.00
25_V	33_A	1.467	1.00
8_V	20_P	1.467	1.00
63_K	68_V	1.438	1.00
49_A	53_T	1.419	1.00
26_L	34_K	1.368	1.00
91_Y	128_A	1.361	1.00
119_T	130_D	1.350	1.00
158_Y	167_Y	1.346	1.00
148_T	162_K	1.338	1.00
49_A	54_F	1.307	0.99
19_D	35_D	1.307	0.99
15_I	33_A	1.282	0.99
8_V	18_A	1.278	0.99
127_Y	159_A	1.273	0.99
144_A	159_A	1.243	0.99
74_N	77_D	1.232	0.99
116_D	120_F	1.200	0.99
15_I	18_A	1.170	0.99
82_S	86_L	1.143	0.99
18_A	38_N	1.143	0.99
115_A	119_T	1.135	0.99
102_D	105_K	1.129	0.98
82_S	85_V	1.123	0.98
141_L	159_A	1.107	0.98
144_A	149_F	1.099	0.98
73_G	76_L	1.099	0.98
18_A	23_F	1.094	0.98
15_I	40_Y	1.083	0.98
129_K	132_N	1.083	0.98
1_Y	43_G	1.081	0.98
107_I	110_K	1.069	0.98
46_L	49_A	1.061	0.98
115_A	120_F	1.059	0.98
63_K	69_Y	1.048	0.97
91_Y	138_G	1.042	0.97
81_E	84_E	1.037	0.97
164_N	167_Y	1.026	0.97
86_L	89_N	1.025	0.97
18_A	22_T	1.016	0.97
151_V	159_A	1.004	0.97
20_P	23_F	1.004	0.97
65_G	68_V	1.001	0.97
98_V	128_A	0.998	0.97
94_D	98_V	0.976	0.96
75_S	78_N	0.969	0.96
116_D	132_N	0.954	0.96
144_A	148_T	0.946	0.95
20_P	33_A	0.935	0.95
98_V	115_A	0.925	0.95
61_Y	64_D	0.921	0.95
152_L	160_K	0.904	0.94
92_F	97_N	0.901	0.94
2_A	6_N	0.899	0.94
159_A	167_Y	0.897	0.94
124_N	151_V	0.881	0.93
72_S	75_S	0.862	0.93
64_D	67_N	0.859	0.92
160_K	165_V	0.858	0.92
2_A	12_G	0.836	0.91
85_V	89_N	0.833	0.91
48_G	51_P	0.830	0.91
115_A	128_A	0.829	0.91
75_S	79_D	0.827	0.91
120_F	130_D	0.827	0.91
32_Y	39_V	0.824	0.91
154_D	157_G	0.818	0.90
19_D	37_N	0.812	0.90
24_E	36_K	0.812	0.90
61_Y	68_V	0.808	0.90
55_E	63_K	0.804	0.90
65_G	70_F	0.793	0.89
35_D	38_N	0.791	0.89
17_G	20_P	0.786	0.89
84_E	93_K	0.772	0.88
91_Y	98_V	0.766	0.87
71_Y	75_S	0.759	0.87
142_E	146_P	0.756	0.87
54_F	57_L	0.753	0.86
134_V	141_L	0.751	0.86
62_Y	69_Y	0.750	0.86
15_I	25_V	0.749	0.86
127_Y	141_L	0.747	0.86
148_T	163_N	0.739	0.85
90_G	101_Y	0.736	0.85
144_A	164_N	0.734	0.85
82_S	87_G	0.731	0.85
82_S	89_N	0.730	0.85
3_K	20_P	0.729	0.85
4_D	9_Y	0.728	0.85
108_K	111_K	0.727	0.84
117_P	120_F	0.718	0.84
145_D	163_N	0.716	0.84
160_K	163_N	0.714	0.83
158_Y	164_N	0.710	0.83
63_K	70_F	0.707	0.83
129_K	149_F	0.704	0.83
133_N	164_N	0.700	0.82
74_N	78_N	0.690	0.81
130_D	133_N	0.689	0.81
26_L	32_Y	0.689	0.81
128_A	149_F	0.688	0.81
33_A	45_K	0.682	0.81
98_V	120_F	0.681	0.80
51_P	56_V	0.678	0.80
127_Y	144_A	0.677	0.80
107_I	111_K	0.675	0.80
128_A	138_G	0.675	0.80
100_Y	128_A	0.675	0.80
39_V	54_F	0.673	0.80
109_I	112_I	0.668	0.79
22_T	26_L	0.668	0.79
46_L	54_F	0.667	0.79
115_A	134_V	0.663	0.79
62_Y	66_K	0.659	0.78
153_G	157_G	0.658	0.78
123_L	126_G	0.658	0.78
127_Y	149_F	0.657	0.78
59_N	62_Y	0.654	0.78
74_N	79_D	0.643	0.77
81_E	86_L	0.642	0.76
93_K	130_D	0.642	0.76
39_V	46_L	0.640	0.76
53_T	65_G	0.637	0.76
138_G	141_L	0.632	0.75
105_K	109_I	0.632	0.75
103_N	139_K	0.631	0.75
118_K	131_K	0.631	0.75
140_K	144_A	0.628	0.75
91_Y	100_Y	0.624	0.74
53_T	64_D	0.617	0.74
4_D	8_V	0.615	0.73
116_D	129_K	0.612	0.73
98_V	102_D	0.612	0.73
57_L	60_N	0.608	0.72
83_F	88_N	0.607	0.72
118_K	147_A	0.606	0.72
2_A	7_N	0.606	0.72
129_K	146_P	0.602	0.72
8_V	25_V	0.601	0.72
5_K	10_Y	0.597	0.71
157_G	163_N	0.597	0.71
4_D	12_G	0.596	0.71
34_K	93_K	0.596	0.71
91_Y	120_F	0.596	0.71
160_K	166_Y	0.594	0.71
62_Y	67_N	0.594	0.71
50_D	54_F	0.592	0.70
160_K	164_N	0.590	0.70
50_D	55_E	0.588	0.70
102_D	109_I	0.588	0.70
39_V	45_K	0.586	0.70
53_T	57_L	0.582	0.69
18_A	35_D	0.582	0.69
162_K	166_Y	0.577	0.69
50_D	57_L	0.576	0.68
122_V	128_A	0.576	0.68
4_D	20_P	0.571	0.68
127_Y	153_G	0.571	0.68
125_D	154_D	0.568	0.67
1_Y	63_K	0.566	0.67
63_K	67_N	0.566	0.67
127_Y	130_D	0.565	0.67
16_E	29_G	0.563	0.67
71_Y	74_N	0.563	0.67
157_G	167_Y	0.559	0.66
76_L	79_D	0.556	0.66
92_F	102_D	0.552	0.65
93_K	98_V	0.548	0.65
103_N	108_K	0.544	0.64
20_P	36_K	0.542	0.64
143_G	157_G	0.542	0.64
159_A	164_N	0.541	0.64
73_G	77_D	0.541	0.64
116_D	130_D	0.540	0.63
14_K	48_G	0.539	0.63
100_Y	104_D	0.538	0.63
97_N	104_D	0.535	0.63
145_D	161_D	0.535	0.63
40_Y	75_S	0.534	0.63
103_N	109_I	0.534	0.63
119_T	129_K	0.534	0.63
68_V	75_S	0.532	0.62
3_K	6_N	0.531	0.62
146_P	149_F	0.530	0.62
50_D	65_G	0.528	0.62
134_V	149_F	0.526	0.61
10_Y	13_K	0.525	0.61
20_P	37_N	0.525	0.61
80_D	83_F	0.525	0.61
22_T	33_A	0.524	0.61
91_Y	127_Y	0.524	0.61
137_K	140_K	0.522	0.61
119_T	134_V	0.519	0.60
23_F	50_D	0.519	0.60
51_P	61_Y	0.517	0.60
9_Y	102_D	0.516	0.60
72_S	77_D	0.513	0.60
102_D	141_L	0.512	0.59
33_A	43_G	0.509	0.59
123_L	128_A	0.508	0.59
140_K	164_N	0.505	0.58
29_G	42_K	0.505	0.58
39_V	49_A	0.504	0.58
7_N	11_K	0.503	0.58
105_K	134_V	0.502	0.58
85_V	88_N	0.502	0.58
69_Y	76_L	0.502	0.58
152_L	157_G	0.500	0.58
51_P	58_G	0.500	0.58
102_D	106_K	0.500	0.58

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
3s25A	1	0.7515	3	0.934	Contact Map
4mzvA	2	0.3314	2.7	0.936	Contact Map
2plgA	4	0.2722	2.7	0.936	Contact Map
3bwsA	2	0.3846	2.2	0.938	Contact Map
4gojC	1	0.4734	1.6	0.943	Contact Map
2bklA	1	0.9231	1.5	0.944	Contact Map
1kqrA	1	0.3432	1.4	0.945	Contact Map
3dsmA	1	0.497	1.3	0.945	Contact Map
1mdaH	1	0.4438	1.3	0.945	Contact Map
1pbyB	1	0.4734	1.3	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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