YRKE - BACSU - GREMLIN Contacts

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YRKE - Uncharacterized protein YrkE

UniProt:	P54432	Sequences: MTEQTKRTTIVLFSGDYDKAMAAYIIANGAAAYDHEVTIFHTFWGFNALRKEELIPVKKGFLEKMFGKMMPRGADKMGLSKMNFAGMGPKMIKNVMKKHNVLTLPQLIEMAQEQGVKLVACTMTMDLLGLQEKELLDDIDYAGVAAYLADAEEGSVNLFI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	160 (155)
Sequences:	597 (313)
Seq/√Len:	25.1

BACSU - YRKE
HALSA - O54564
SULSO - Q97Z17 Q97VJ2 Q97Z18

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
117_K	140_D	4.824	1.00
147_Y	157_N	4.795	1.00
122_T	141_Y	4.144	1.00
20_A	48_A	4.121	1.00
29_G	144_V	3.778	1.00
12_L	39_I	3.305	1.00
94_N	98_K	3.134	1.00
28_N	114_Q	2.966	1.00
31_A	116_V	2.639	0.99
21_M	92_I	2.472	0.99
151_A	156_V	2.374	0.98
102_L	106_Q	2.330	0.98
78_G	89_P	2.155	0.97
36_E	117_K	2.126	0.96
47_N	70_M	2.074	0.96
109_E	113_E	2.057	0.96
24_Y	39_I	1.982	0.95
24_Y	108_I	1.916	0.94
35_H	152_E	1.915	0.94
24_Y	41_H	1.908	0.94
38_T	119_V	1.902	0.93
7_R	36_E	1.892	0.93
39_I	118_L	1.850	0.92
92_I	127_L	1.737	0.90
70_M	73_G	1.729	0.90
90_K	93_K	1.697	0.89
125_M	135_L	1.666	0.88
62_L	94_N	1.656	0.87
147_Y	156_V	1.653	0.87
60_G	63_E	1.642	0.87
28_N	111_A	1.634	0.87
75_D	93_K	1.629	0.87
89_P	92_I	1.611	0.86
12_L	23_A	1.606	0.86
111_A	116_V	1.604	0.86
147_Y	151_A	1.579	0.85
10_I	160_I	1.556	0.84
74_A	93_K	1.551	0.84
119_V	142_A	1.451	0.79
11_V	26_I	1.368	0.75
9_T	147_Y	1.364	0.75
112_Q	138_D	1.363	0.75
99_H	127_L	1.356	0.74
77_M	80_S	1.345	0.74
89_P	93_K	1.324	0.73
10_I	26_I	1.299	0.71
14_S	19_K	1.299	0.71
11_V	61_F	1.291	0.71
106_Q	110_M	1.237	0.67
50_R	73_G	1.201	0.65
55_I	72_R	1.186	0.64
25_I	107_L	1.175	0.63
8_T	35_H	1.172	0.63
75_D	105_P	1.157	0.62
49_L	136_L	1.125	0.60
35_H	155_S	1.119	0.59
6_K	35_H	1.116	0.59
84_F	89_P	1.095	0.58
26_I	144_V	1.082	0.57
25_I	92_I	1.074	0.56
63_E	95_V	1.061	0.55
12_L	41_H	1.038	0.54
59_K	134_E	1.015	0.52
87_M	98_K	1.007	0.51
124_T	127_L	0.991	0.50
143_G	146_A	0.986	0.50
67_G	71_P	0.974	0.49
15_G	25_I	0.973	0.49
7_R	153_E	0.972	0.49
117_K	150_D	0.965	0.48
101_V	123_M	0.942	0.47
23_A	26_I	0.937	0.46
78_G	81_K	0.935	0.46
8_T	156_V	0.925	0.45
24_Y	141_Y	0.923	0.45
17_Y	93_K	0.920	0.45
31_A	145_A	0.917	0.45
51_K	137_D	0.915	0.45
12_L	26_I	0.909	0.44
21_M	48_A	0.903	0.44
78_G	139_I	0.898	0.43
33_Y	148_L	0.872	0.42
50_R	67_G	0.872	0.42
125_M	142_A	0.868	0.41
67_G	160_I	0.866	0.41
74_A	103_T	0.865	0.41
52_E	113_E	0.863	0.41
13_F	19_K	0.856	0.40
7_R	150_D	0.847	0.40
33_Y	150_D	0.843	0.40
130_L	135_L	0.833	0.39
8_T	26_I	0.833	0.39
127_L	141_Y	0.832	0.39
92_I	99_H	0.830	0.39
9_T	157_N	0.814	0.38
44_W	128_L	0.810	0.37
61_F	66_F	0.799	0.37
11_V	63_E	0.799	0.37
103_T	106_Q	0.791	0.36
59_K	66_F	0.785	0.36
63_E	67_G	0.780	0.35
32_A	143_G	0.779	0.35
38_T	147_Y	0.777	0.35
93_K	117_K	0.776	0.35
23_A	85_A	0.772	0.35
17_Y	89_P	0.766	0.34
26_I	35_H	0.765	0.34
19_K	44_W	0.765	0.34
17_Y	21_M	0.761	0.34
82_M	88_G	0.760	0.34
119_V	151_A	0.758	0.34
6_K	155_S	0.756	0.34
15_G	33_Y	0.756	0.34
113_E	137_D	0.754	0.34
92_I	119_V	0.751	0.33
83_N	89_P	0.751	0.33
29_G	44_W	0.749	0.33
21_M	107_L	0.748	0.33
23_A	39_I	0.747	0.33
101_V	127_L	0.736	0.32
100_N	123_M	0.735	0.32
25_I	126_D	0.733	0.32
31_A	156_V	0.721	0.31
145_A	149_A	0.721	0.31
21_M	25_I	0.718	0.31
106_Q	155_S	0.716	0.31
90_K	153_E	0.701	0.30
95_V	98_K	0.697	0.30
100_N	122_T	0.693	0.30
109_E	132_E	0.693	0.30
28_N	31_A	0.691	0.30
61_F	68_K	0.691	0.30
49_L	130_L	0.679	0.29
17_Y	103_T	0.676	0.29
119_V	148_L	0.676	0.29
13_F	88_G	0.671	0.28
24_Y	157_N	0.665	0.28
7_R	102_L	0.665	0.28
122_T	126_D	0.663	0.28
11_V	51_K	0.661	0.28
13_F	22_A	0.658	0.28
17_Y	34_D	0.657	0.28
66_F	69_M	0.656	0.28
54_L	160_I	0.656	0.28
106_Q	151_A	0.647	0.27
8_T	11_V	0.647	0.27
89_P	108_I	0.645	0.27
131_Q	139_I	0.639	0.27
93_K	105_P	0.638	0.27
49_L	140_D	0.636	0.26
9_T	119_V	0.635	0.26
66_F	71_P	0.635	0.26
102_L	110_M	0.631	0.26
94_N	116_V	0.628	0.26
17_Y	101_V	0.628	0.26
108_I	130_L	0.628	0.26
63_E	116_V	0.625	0.26
16_D	78_G	0.625	0.26
123_M	143_G	0.623	0.26
103_T	155_S	0.619	0.25
50_R	130_L	0.612	0.25
46_F	126_D	0.610	0.25
103_T	107_L	0.607	0.25
50_R	72_R	0.606	0.25
41_H	77_M	0.604	0.25
97_K	140_D	0.598	0.24
13_F	18_D	0.597	0.24
15_G	78_G	0.596	0.24
108_I	122_T	0.593	0.24
104_L	159_F	0.591	0.24
74_A	115_G	0.590	0.24
16_D	85_A	0.589	0.24
81_K	87_M	0.587	0.24
26_I	96_M	0.587	0.24
48_A	118_L	0.586	0.24
87_M	91_M	0.584	0.24
8_T	106_Q	0.583	0.24
109_E	112_Q	0.583	0.24
109_E	114_Q	0.583	0.24
118_L	160_I	0.582	0.23
118_L	139_I	0.578	0.23
95_V	131_Q	0.578	0.23
52_E	72_R	0.577	0.23
11_V	16_D	0.576	0.23
73_G	130_L	0.574	0.23
122_T	143_G	0.573	0.23
62_L	91_M	0.571	0.23
26_I	148_L	0.568	0.23
100_N	130_L	0.563	0.22
46_F	128_L	0.560	0.22
6_K	98_K	0.556	0.22
38_T	152_E	0.556	0.22
83_N	127_L	0.555	0.22
64_K	117_K	0.552	0.22
60_G	68_K	0.551	0.22
31_A	114_Q	0.550	0.22
112_Q	140_D	0.550	0.22
22_A	96_M	0.550	0.22
119_V	146_A	0.547	0.22
152_E	155_S	0.546	0.22
8_T	152_E	0.545	0.22
84_F	87_M	0.545	0.22
32_A	145_A	0.544	0.22
50_R	134_E	0.539	0.21
16_D	19_K	0.539	0.21
56_P	98_K	0.536	0.21
28_N	107_L	0.535	0.21
8_T	115_G	0.533	0.21
107_L	124_T	0.533	0.21
49_L	142_A	0.528	0.21
142_A	146_A	0.525	0.21
74_A	105_P	0.523	0.21
26_I	160_I	0.523	0.21
63_E	66_F	0.522	0.20
118_L	126_D	0.521	0.20
22_A	144_V	0.519	0.20
6_K	118_L	0.517	0.20
110_M	113_E	0.517	0.20
7_R	35_H	0.516	0.20
41_H	136_L	0.516	0.20
37_V	44_W	0.516	0.20
130_L	159_F	0.515	0.20
31_A	111_A	0.512	0.20
63_E	131_Q	0.510	0.20
97_K	141_Y	0.510	0.20
39_I	108_I	0.509	0.20
112_Q	118_L	0.508	0.20
14_S	21_M	0.508	0.20
82_M	134_E	0.508	0.20
38_T	117_K	0.501	0.20
46_F	120_A	0.500	0.19
59_K	80_S	0.500	0.19

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
3pnxA	4	0.9938	100	0.318	Contact Map
2qs7A	3	0.85	100	0.469	Contact Map
3mc3A	3	0.6625	99.8	0.7	Contact Map
2hy5B	1	0.7125	99.5	0.76	Contact Map
1jx7A	5	0.7063	99.5	0.76	Contact Map
1l1sA	3	0.6562	99.5	0.771	Contact Map
2d1pB	1	0.7188	99.1	0.812	Contact Map
2pd2A	3	0.6375	98.9	0.824	Contact Map
2hy5A	2	0.7125	98.9	0.825	Contact Map
2d1pA	2	0.7188	98.5	0.844	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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