YRKN - BACSU - GREMLIN Contacts

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YRKN - Uncharacterized protein YrkN

UniProt:	P54441	Sequences: MKTKNEPKVILELAKESDLPEFQKKLQEAFAIAVIETFGDCEDGPIPSDNDVQESFNAPGAVVYHILQDGKNVGGAVVRINSQTNHNSLDLFYVSPEYHSQGIGLSAWKAIEAQYPDTVLWETVTPYFEKRNINFYVNKCGFHIVEFYNEHHSNPHMHRNGREDDKPLLNDDDFFRFVKIMKKKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	185 (143)
Sequences:	487 (359)
Seq/√Len:	30.0

BACSU - YRKN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
87_N	118_T	5.135	1.00
112_E	142_F	3.911	1.00
64_Y	114_Q	2.859	1.00
75_G	93_Y	2.853	1.00
65_H	72_N	2.806	1.00
104_G	135_F	2.785	1.00
94_V	103_I	2.727	1.00
66_I	107_A	2.668	1.00
125_T	132_N	2.620	1.00
110_A	113_A	2.459	0.99
108_W	140_C	2.451	0.99
14_A	18_D	2.315	0.99
76_A	111_I	2.287	0.99
77_V	91_L	2.276	0.99
62_V	115_Y	2.192	0.98
12_E	65_H	2.185	0.98
105_L	139_K	2.144	0.98
45_P	49_D	2.134	0.98
18_D	65_H	1.991	0.97
64_Y	115_Y	1.951	0.97
80_I	87_N	1.922	0.96
89_L	123_T	1.916	0.96
20_P	24_K	1.758	0.94
108_W	142_F	1.735	0.93
85_N	119_V	1.715	0.93
35_I	39_G	1.704	0.93
14_A	63_V	1.600	0.90
13_L	62_V	1.584	0.90
22_F	75_G	1.570	0.89
50_N	59_P	1.521	0.88
33_A	129_E	1.514	0.88
73_V	103_I	1.492	0.87
14_A	22_F	1.415	0.84
23_Q	47_P	1.404	0.83
39_G	44_G	1.385	0.82
23_Q	49_D	1.352	0.81
35_I	40_D	1.347	0.81
69_D	94_V	1.331	0.80
12_E	67_L	1.284	0.77
22_F	95_S	1.266	0.76
34_V	40_D	1.193	0.72
22_F	33_A	1.186	0.71
26_L	123_T	1.167	0.70
78_V	121_W	1.145	0.69
34_V	45_P	1.126	0.67
131_R	134_N	1.111	0.66
69_D	97_E	1.105	0.66
138_N	144_I	1.090	0.65
10_I	119_V	1.083	0.64
26_L	47_P	1.068	0.63
19_L	56_F	1.062	0.63
82_S	105_L	1.059	0.62
33_A	126_P	1.056	0.62
144_I	147_F	1.035	0.61
86_H	120_L	1.024	0.60
44_G	47_P	1.015	0.59
33_A	91_L	1.009	0.59
14_A	19_L	1.005	0.58
88_S	91_L	1.002	0.58
29_A	95_S	0.989	0.57
115_Y	121_W	0.984	0.57
85_N	118_T	0.982	0.57
76_A	89_L	0.978	0.56
13_L	106_S	0.977	0.56
78_V	134_N	0.967	0.55
75_G	135_F	0.962	0.55
60_G	100_S	0.957	0.55
94_V	107_A	0.948	0.54
9_V	68_Q	0.945	0.54
48_S	129_E	0.928	0.52
22_F	52_V	0.926	0.52
67_L	72_N	0.926	0.52
9_V	71_K	0.926	0.52
56_F	93_Y	0.920	0.52
70_G	98_Y	0.917	0.51
68_Q	150_E	0.915	0.51
10_I	24_K	0.906	0.51
16_E	57_N	0.902	0.50
66_I	94_V	0.899	0.50
26_L	37_T	0.899	0.50
74_G	121_W	0.897	0.50
89_L	108_W	0.894	0.50
37_T	44_G	0.892	0.49
71_K	97_E	0.891	0.49
129_E	132_N	0.888	0.49
125_T	136_Y	0.882	0.49
31_A	48_S	0.879	0.48
21_E	67_L	0.876	0.48
28_E	95_S	0.872	0.48
31_A	35_I	0.871	0.48
129_E	133_I	0.870	0.48
107_A	129_E	0.866	0.47
9_V	16_E	0.861	0.47
13_L	115_Y	0.855	0.46
10_I	13_L	0.853	0.46
31_A	45_P	0.843	0.46
15_K	98_Y	0.843	0.46
10_I	15_K	0.832	0.45
47_P	75_G	0.832	0.45
126_P	129_E	0.823	0.44
84_T	111_I	0.820	0.44
53_Q	106_S	0.816	0.43
78_V	109_K	0.809	0.43
97_E	101_Q	0.802	0.42
84_T	87_N	0.799	0.42
64_Y	71_K	0.791	0.41
63_V	94_V	0.790	0.41
148_Y	152_H	0.787	0.41
8_K	64_Y	0.784	0.41
88_S	124_V	0.781	0.41
34_V	139_K	0.780	0.41
82_S	87_N	0.779	0.41
89_L	140_C	0.779	0.41
30_F	93_Y	0.776	0.40
124_V	151_H	0.773	0.40
116_P	121_W	0.764	0.39
82_S	118_T	0.763	0.39
112_E	121_W	0.762	0.39
15_K	70_G	0.751	0.38
33_A	44_G	0.749	0.38
26_L	39_G	0.748	0.38
14_A	26_L	0.736	0.37
105_L	117_D	0.733	0.37
30_F	136_Y	0.724	0.36
21_E	71_K	0.720	0.36
68_Q	103_I	0.712	0.36
20_P	113_A	0.712	0.36
146_E	152_H	0.707	0.35
74_G	140_C	0.706	0.35
91_L	128_F	0.705	0.35
111_I	144_I	0.703	0.35
91_L	129_E	0.700	0.35
58_A	94_V	0.699	0.35
11_L	33_A	0.698	0.35
20_P	109_K	0.698	0.35
19_L	23_Q	0.697	0.34
19_L	99_H	0.688	0.34
81_N	85_N	0.686	0.34
89_L	126_P	0.681	0.33
44_G	49_D	0.674	0.33
13_L	143_H	0.670	0.33
78_V	85_N	0.668	0.32
17_S	72_N	0.666	0.32
105_L	140_C	0.665	0.32
37_T	50_N	0.665	0.32
70_G	113_A	0.665	0.32
30_F	129_E	0.662	0.32
123_T	138_N	0.661	0.32
69_D	143_H	0.661	0.32
31_A	92_F	0.657	0.32
61_A	113_A	0.656	0.32
9_V	59_P	0.649	0.31
86_H	122_E	0.641	0.31
16_E	54_E	0.640	0.30
46_I	111_I	0.639	0.30
8_K	106_S	0.629	0.30
13_L	110_A	0.627	0.30
31_A	66_I	0.623	0.29
134_N	139_K	0.619	0.29
39_G	47_P	0.615	0.29
38_F	72_N	0.613	0.29
121_W	131_R	0.612	0.29
80_I	85_N	0.609	0.28
61_A	77_V	0.606	0.28
17_S	101_Q	0.603	0.28
34_V	37_T	0.603	0.28
104_G	128_F	0.602	0.28
142_F	151_H	0.598	0.28
12_E	64_Y	0.594	0.27
121_W	134_N	0.594	0.27
31_A	107_A	0.588	0.27
135_F	144_I	0.588	0.27
30_F	33_A	0.587	0.27
111_I	117_D	0.583	0.27
13_L	24_K	0.579	0.27
138_N	146_E	0.578	0.26
30_F	133_I	0.575	0.26
108_W	134_N	0.573	0.26
30_F	142_F	0.572	0.26
62_V	70_G	0.564	0.26
57_N	106_S	0.563	0.26
92_F	122_E	0.563	0.26
21_E	106_S	0.562	0.25
13_L	68_Q	0.561	0.25
61_A	89_L	0.561	0.25
17_S	50_N	0.559	0.25
140_C	148_Y	0.558	0.25
118_T	139_K	0.557	0.25
11_L	110_A	0.557	0.25
86_H	101_Q	0.554	0.25
20_P	119_V	0.551	0.25
21_E	72_N	0.547	0.25
73_V	94_V	0.547	0.25
138_N	149_N	0.545	0.24
71_K	113_A	0.542	0.24
89_L	144_I	0.541	0.24
20_P	97_E	0.541	0.24
67_L	76_A	0.535	0.24
58_A	79_R	0.532	0.24
29_A	101_Q	0.530	0.24
29_A	69_D	0.529	0.24
26_L	34_V	0.525	0.23
79_R	88_S	0.525	0.23
45_P	93_Y	0.525	0.23
11_L	121_W	0.523	0.23
15_K	71_K	0.521	0.23
61_A	118_T	0.519	0.23
138_N	143_H	0.518	0.23
113_A	116_P	0.515	0.23
100_S	151_H	0.511	0.23
13_L	71_K	0.511	0.23
68_Q	106_S	0.510	0.22
71_K	120_L	0.502	0.22
22_F	36_E	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
2fiaA	1	0.8486	99.8	0.667	Contact Map
2oh1A	1	0.8432	99.7	0.673	Contact Map
2pc1A	1	0.8432	99.7	0.675	Contact Map
3blnA	2	0.7676	99.7	0.686	Contact Map
3d8pA	1	0.8486	99.7	0.686	Contact Map
4m85A	1	0.8108	99.7	0.687	Contact Map
3fncA	2	0.8486	99.7	0.688	Contact Map
3pp9A	2	0.8811	99.7	0.689	Contact Map
2q7bA	2	0.8541	99.7	0.69	Contact Map
2ob0A	1	0.827	99.7	0.691	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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