YJKA - BACSU - GREMLIN Contacts

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YJKA - UPF0014 membrane protein YjkA

UniProt:	O34684	Sequences: MDYLSLSLTMIFVLIALFLSKSFKAGVEKDMIIATIRAAVQLLIIGYVLSLIFRGDHPVFILLMVLLMLAVAAQNVIKRKKNTIGSFWRVFAALAIVEIVTQGILLSLHIIPLTARYVIPISGMVIGNSMVLSSLFLNRLNSEVGVRKEEIQLILSLGGTPKQSIQRILTSAMKMSMIPTLESQKTLGLVQLPGMMTGQILAGADPIQAVRFQLLIVFTTMASAALTCVILSVLTYPSLFTVHQQLKQNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	250 (241)
Sequences:	1252 (909)
Seq/√Len:	58.6

ECOLI - FETB
BACSU - YJKA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
147_R	150_E	6.234	1.00
241_T	245_Q	5.297	1.00
45_I	192_L	5.157	1.00
13_V	35_T	3.406	1.00
93_A	230_I	3.363	1.00
124_M	195_M	3.340	1.00
20_S	25_A	3.309	1.00
65_V	122_S	3.138	1.00
160_T	163_Q	3.029	1.00
63_L	67_L	2.909	1.00
139_R	175_M	2.899	1.00
154_I	159_G	2.884	1.00
73_A	91_F	2.865	1.00
38_A	217_V	2.767	1.00
136_F	232_S	2.687	1.00
133_S	227_T	2.523	1.00
124_M	191_Q	2.464	1.00
138_N	175_M	2.328	1.00
187_L	217_V	2.183	1.00
29_K	33_I	2.167	1.00
71_V	189_L	2.124	1.00
18_F	22_S	2.107	1.00
50_S	205_D	2.077	1.00
20_S	28_E	2.002	1.00
117_Y	199_Q	1.987	1.00
188_G	194_G	1.900	1.00
128_N	220_T	1.851	1.00
199_Q	212_F	1.841	1.00
129_S	227_T	1.812	0.99
191_Q	195_M	1.793	0.99
148_K	152_Q	1.788	0.99
199_Q	204_A	1.714	0.99
144_V	165_I	1.698	0.99
34_A	221_M	1.678	0.99
53_F	197_T	1.666	0.99
61_I	115_A	1.635	0.99
80_K	83_T	1.623	0.99
139_R	143_E	1.592	0.99
46_G	210_V	1.583	0.99
161_P	244_Q	1.568	0.98
66_L	91_F	1.564	0.98
111_I	199_Q	1.554	0.98
6_L	215_L	1.507	0.98
124_M	220_T	1.477	0.98
87_F	91_F	1.477	0.98
34_A	185_K	1.476	0.98
91_F	95_A	1.454	0.97
192_L	197_T	1.451	0.97
68_M	126_I	1.449	0.97
7_S	67_L	1.422	0.97
192_L	210_V	1.419	0.97
182_E	185_K	1.412	0.97
166_Q	170_T	1.411	0.97
186_T	191_Q	1.406	0.97
34_A	184_Q	1.396	0.97
45_I	189_L	1.392	0.97
189_L	216_I	1.384	0.97
124_M	197_T	1.375	0.96
76_V	94_L	1.355	0.96
39_A	214_L	1.349	0.96
197_T	200_I	1.338	0.96
43_L	210_V	1.335	0.96
216_I	219_T	1.334	0.96
41_Q	198_G	1.333	0.96
142_S	147_R	1.332	0.96
190_V	195_M	1.331	0.96
20_S	31_M	1.316	0.95
180_T	224_A	1.311	0.95
13_V	221_M	1.298	0.95
186_T	192_L	1.277	0.95
35_T	218_F	1.262	0.94
85_G	88_W	1.255	0.94
70_A	74_Q	1.232	0.93
162_K	236_Y	1.228	0.93
18_F	26_G	1.210	0.93
151_I	178_I	1.201	0.93
123_G	194_G	1.200	0.93
71_V	186_T	1.184	0.92
10_M	14_L	1.177	0.92
44_I	48_V	1.170	0.92
197_T	201_L	1.159	0.91
184_Q	221_M	1.151	0.91
196_M	217_V	1.149	0.91
40_V	44_I	1.144	0.91
93_A	234_L	1.143	0.91
128_N	190_V	1.139	0.90
59_V	62_L	1.131	0.90
80_K	137_L	1.128	0.90
81_K	229_V	1.121	0.90
41_Q	188_G	1.117	0.90
38_A	214_L	1.107	0.89
76_V	134_S	1.103	0.89
12_F	222_A	1.096	0.89
153_L	156_S	1.088	0.88
51_L	130_M	1.081	0.88
190_V	194_G	1.080	0.88
200_I	210_V	1.069	0.87
161_P	241_T	1.054	0.87
38_A	187_L	1.047	0.86
33_I	237_P	1.047	0.86
194_G	198_G	1.044	0.86
17_L	32_I	1.044	0.86
162_K	233_V	1.033	0.86
105_L	136_F	1.033	0.86
126_I	191_Q	1.031	0.85
149_E	153_L	1.030	0.85
130_M	134_S	1.029	0.85
120_P	201_L	1.029	0.85
91_F	94_L	1.024	0.85
76_V	172_A	1.024	0.85
196_M	200_I	1.020	0.85
195_M	200_I	1.020	0.85
68_M	206_P	1.019	0.85
226_L	229_V	1.015	0.85
30_D	181_L	1.014	0.85
136_F	231_L	1.012	0.84
136_F	228_C	0.999	0.84
200_I	211_R	0.992	0.83
55_G	60_F	0.991	0.83
30_D	33_I	0.991	0.83
135_L	175_M	0.989	0.83
117_Y	121_I	0.989	0.83
96_I	230_I	0.978	0.82
41_Q	194_G	0.976	0.82
131_V	182_E	0.976	0.82
188_G	198_G	0.975	0.82
44_I	52_I	0.971	0.82
196_M	210_V	0.971	0.82
71_V	190_V	0.970	0.82
90_V	137_L	0.969	0.82
125_V	223_S	0.966	0.82
7_S	11_I	0.963	0.81
19_L	52_I	0.960	0.81
134_S	182_E	0.958	0.81
48_V	114_T	0.957	0.81
53_F	115_A	0.949	0.80
144_V	239_L	0.946	0.80
147_R	176_S	0.944	0.80
47_Y	51_L	0.935	0.79
132_L	224_A	0.928	0.79
48_V	130_M	0.924	0.79
49_L	197_T	0.917	0.78
124_M	216_I	0.912	0.78
154_I	157_L	0.911	0.78
123_G	127_G	0.909	0.77
103_G	118_V	0.907	0.77
147_R	168_I	0.905	0.77
60_F	63_L	0.897	0.76
69_L	140_L	0.887	0.76
44_I	47_Y	0.886	0.76
10_M	36_I	0.880	0.75
98_E	223_S	0.873	0.74
66_L	145_G	0.863	0.74
215_L	218_F	0.862	0.74
77_I	87_F	0.861	0.73
182_E	199_Q	0.859	0.73
136_F	176_S	0.858	0.73
12_F	218_F	0.854	0.73
52_I	64_M	0.853	0.73
197_T	220_T	0.848	0.72
140_L	144_V	0.844	0.72
129_S	223_S	0.844	0.72
101_T	223_S	0.838	0.71
81_K	93_A	0.836	0.71
76_V	137_L	0.830	0.71
69_L	210_V	0.826	0.70
117_Y	184_Q	0.824	0.70
194_G	197_T	0.822	0.70
68_M	72_A	0.821	0.70
132_L	216_I	0.819	0.70
121_I	187_L	0.818	0.70
139_R	171_S	0.817	0.69
143_E	146_V	0.813	0.69
42_L	123_G	0.809	0.69
92_A	234_L	0.808	0.69
68_M	197_T	0.806	0.68
95_A	230_I	0.805	0.68
150_E	190_V	0.801	0.68
17_L	24_K	0.801	0.68
121_I	230_I	0.795	0.67
143_E	171_S	0.787	0.67
65_V	118_V	0.783	0.66
23_F	233_V	0.783	0.66
122_S	126_I	0.780	0.66
74_Q	88_W	0.774	0.65
77_I	90_V	0.774	0.65
48_V	71_V	0.772	0.65
26_G	227_T	0.772	0.65
50_S	54_R	0.770	0.65
46_G	121_I	0.769	0.65
33_I	224_A	0.757	0.64
11_I	47_Y	0.744	0.62
10_M	215_L	0.740	0.62
20_S	27_V	0.736	0.61
184_Q	197_T	0.734	0.61
173_M	233_V	0.732	0.61
100_V	103_G	0.729	0.61
74_Q	110_I	0.725	0.60
62_L	66_L	0.723	0.60
33_I	36_I	0.723	0.60
50_S	207_I	0.723	0.60
239_L	245_Q	0.721	0.60
7_S	99_I	0.721	0.60
181_L	229_V	0.720	0.60
36_I	63_L	0.720	0.60
72_A	186_T	0.720	0.60
94_L	131_V	0.718	0.59
124_M	196_M	0.715	0.59
75_N	186_T	0.711	0.59
68_M	194_G	0.711	0.59
195_M	216_I	0.706	0.58
165_I	240_F	0.704	0.58
97_V	137_L	0.704	0.58
200_I	224_A	0.703	0.58
102_Q	105_L	0.695	0.57
144_V	151_I	0.691	0.57
140_L	172_A	0.690	0.56
94_L	129_S	0.682	0.56
180_T	221_M	0.679	0.55
141_N	152_Q	0.678	0.55
100_V	151_I	0.678	0.55
29_K	148_K	0.677	0.55
182_E	186_T	0.676	0.55
7_S	216_I	0.674	0.55
136_F	218_F	0.669	0.54
119_I	135_L	0.669	0.54
142_S	175_M	0.668	0.54
24_K	172_A	0.662	0.53
212_F	216_I	0.657	0.53
53_F	201_L	0.656	0.53
43_L	109_H	0.656	0.53
30_D	217_V	0.655	0.53
162_K	166_Q	0.653	0.52
138_N	142_S	0.646	0.52
40_V	102_Q	0.644	0.51
99_I	227_T	0.643	0.51
82_N	145_G	0.643	0.51
158_G	164_S	0.641	0.51
15_I	85_G	0.639	0.51
97_V	129_S	0.638	0.51
86_S	89_R	0.637	0.51
97_V	154_I	0.637	0.51
12_F	98_E	0.636	0.51
97_V	112_P	0.635	0.50
216_I	222_A	0.631	0.50
102_Q	122_S	0.631	0.50
72_A	240_F	0.629	0.50
85_G	238_S	0.627	0.50
97_V	152_Q	0.626	0.49
13_V	47_Y	0.625	0.49
53_F	119_I	0.622	0.49
194_G	213_Q	0.621	0.49
76_V	166_Q	0.618	0.49
36_I	169_L	0.616	0.48
37_R	41_Q	0.614	0.48
55_G	107_S	0.613	0.48
67_L	113_L	0.613	0.48
66_L	81_K	0.611	0.48
63_L	242_V	0.609	0.48
61_I	130_M	0.607	0.47
30_D	183_S	0.607	0.47
75_N	130_M	0.606	0.47
177_M	235_T	0.604	0.47
112_P	199_Q	0.601	0.47
26_G	178_I	0.597	0.46
25_A	164_S	0.597	0.46
71_V	219_T	0.597	0.46
61_I	221_M	0.595	0.46
126_I	130_M	0.595	0.46
120_P	212_F	0.594	0.46
75_N	192_L	0.593	0.46
88_W	215_L	0.593	0.46
37_R	188_G	0.593	0.46
53_F	206_P	0.593	0.46
89_R	93_A	0.593	0.46
75_N	80_K	0.591	0.46
73_A	205_D	0.589	0.45
156_S	235_T	0.585	0.45
175_M	227_T	0.583	0.45
233_V	237_P	0.583	0.45
150_E	226_L	0.582	0.45
220_T	223_S	0.580	0.44
45_I	211_R	0.578	0.44
79_R	151_I	0.578	0.44
128_N	183_S	0.577	0.44
195_M	199_Q	0.577	0.44
106_L	142_S	0.577	0.44
5_S	108_L	0.575	0.44
135_L	178_I	0.574	0.44
13_V	77_I	0.573	0.44
85_G	229_V	0.572	0.43
177_M	225_A	0.572	0.43
91_F	114_T	0.571	0.43
87_F	125_V	0.571	0.43
125_V	171_S	0.571	0.43
40_V	113_L	0.570	0.43
44_I	88_W	0.569	0.43
21_K	65_V	0.569	0.43
161_P	245_Q	0.568	0.43
135_L	194_G	0.567	0.43
46_G	192_L	0.566	0.43
203_G	206_P	0.564	0.43
37_R	212_F	0.563	0.42
14_L	18_F	0.563	0.42
12_F	170_T	0.562	0.42
73_A	87_F	0.561	0.42
111_I	182_E	0.558	0.42
74_Q	78_K	0.557	0.42
68_M	71_V	0.556	0.42
127_G	191_Q	0.556	0.42
139_R	142_S	0.555	0.42
108_L	117_Y	0.555	0.42
47_Y	174_K	0.554	0.41
206_P	212_F	0.553	0.41
64_M	214_L	0.550	0.41
17_L	36_I	0.547	0.41
140_L	168_I	0.546	0.41
12_F	191_Q	0.544	0.40
154_I	245_Q	0.544	0.40
110_I	126_I	0.538	0.40
196_M	211_R	0.538	0.40
114_T	184_Q	0.538	0.40
188_G	192_L	0.537	0.40
27_V	30_D	0.537	0.40
36_I	146_V	0.536	0.40
35_T	48_V	0.536	0.40
18_F	44_I	0.535	0.39
165_I	190_V	0.533	0.39
45_I	184_Q	0.531	0.39
93_A	231_L	0.530	0.39
42_L	188_G	0.530	0.39
72_A	135_L	0.530	0.39
178_I	205_D	0.529	0.39
16_A	23_F	0.528	0.39
30_D	52_I	0.527	0.39
55_G	91_F	0.527	0.39
22_S	103_G	0.525	0.38
93_A	214_L	0.523	0.38
80_K	141_N	0.521	0.38
146_V	234_L	0.521	0.38
24_K	95_A	0.519	0.38
138_N	182_E	0.519	0.38
53_F	116_R	0.519	0.38
93_A	232_S	0.518	0.38
135_L	224_A	0.518	0.38
140_L	157_L	0.517	0.38
167_R	171_S	0.516	0.37
18_F	21_K	0.516	0.37
123_G	190_V	0.512	0.37
230_I	233_V	0.510	0.37
190_V	212_F	0.509	0.37
89_R	151_I	0.508	0.37
99_I	102_Q	0.508	0.37
27_V	174_K	0.508	0.37
133_S	231_L	0.506	0.36
64_M	119_I	0.505	0.36
132_L	227_T	0.505	0.36
54_R	73_A	0.504	0.36
5_S	182_E	0.504	0.36
187_L	216_I	0.500	0.36
11_I	62_L	0.500	0.36
128_N	224_A	0.500	0.36

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
4ymuD	2	0.82	92.1	0.93	Contact Map
3aqpA	1	0.784	76.8	0.944	Contact Map
2onkC	2	0.88	72.7	0.946	Contact Map
3tuiA	2	0.828	66.4	0.948	Contact Map
3d31C	2	0.896	63.1	0.949	Contact Map
3ne5A	3	0.804	59.4	0.95	Contact Map
4k0jA	3	0.728	57.7	0.951	Contact Map
4tquN	1	0.916	53.2	0.952	Contact Map
3w9iA	3	0.768	36.3	0.957	Contact Map
4dx5A	3	0.796	32.4	0.958	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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