YMFM - BACSU - GREMLIN Contacts

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YMFM - Uncharacterized membrane protein YmfM

UniProt:	O31771	Sequences: MSLDDLQAATKIQKRYLTALEEGNYDIIPGKFYVRAFIKQYAEAVGLDADQLFEEHKKDIPNTYHDDVSEKISGMNLQKEMPKPASKALELLPTILVILGVIVVIAIVYAIIQFANHKNSDDHNAASEKAITQSESKYEIPKDSTLKENQNNSSEKETDTKKETKENEDKKKENDSEKLEIKAAGTEGSLTTYEVSGADKIELELKASDSSWIRVRDENSSSLKEGTLKKDETYKKDITDQKQVDIRTGYAPNLKIKINGKVLSYELDPKKVMAQTIKIVNKKEEKSS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	288 (248)
Sequences:	2153 (1928)
Seq/√Len:	122.4

ECOLI - RODZ
BACSU - YMFM

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
207_A	228_L	4.322	1.00
3_L	17_L	4.290	1.00
209_D	253_N	4.077	1.00
212_W	249_G	3.968	1.00
24_N	27_I	3.666	1.00
6_L	44_A	3.492	1.00
214_R	225_E	3.481	1.00
210_S	229_K	3.268	1.00
208_S	255_K	3.250	1.00
48_D	51_Q	2.911	1.00
6_L	41_Y	2.897	1.00
18_T	22_E	2.858	1.00
206_K	233_T	2.726	1.00
250_Y	253_N	2.689	1.00
255_K	262_V	2.496	1.00
229_K	232_E	2.476	1.00
3_L	14_K	2.362	1.00
20_L	45_V	2.346	1.00
20_L	38_I	2.241	1.00
16_Y	37_F	2.200	1.00
210_S	227_T	2.156	1.00
12_I	16_Y	2.154	1.00
35_R	57_K	2.137	1.00
224_K	234_Y	2.108	1.00
13_Q	16_Y	2.098	1.00
10_T	44_A	2.067	1.00
216_R	222_S	2.061	1.00
32_F	36_A	2.026	1.00
201_I	259_N	2.017	1.00
211_S	248_T	2.003	1.00
204_E	257_K	1.974	1.00
36_A	40_Q	1.962	1.00
204_E	235_K	1.904	1.00
202_E	235_K	1.900	1.00
247_R	276_T	1.859	1.00
9_A	44_A	1.855	1.00
11_K	40_Q	1.826	1.00
108_V	112_I	1.818	1.00
211_S	254_L	1.799	1.00
207_A	254_L	1.794	1.00
214_R	247_R	1.787	1.00
43_E	49_A	1.740	1.00
14_K	18_T	1.729	1.00
206_K	255_K	1.709	1.00
203_L	258_I	1.685	1.00
15_R	37_F	1.662	1.00
10_T	243_Q	1.660	1.00
217_D	223_L	1.601	1.00
105_I	109_Y	1.598	1.00
53_F	56_H	1.584	1.00
12_I	37_F	1.567	1.00
251_A	270_K	1.541	1.00
160_T	165_K	1.491	1.00
252_P	270_K	1.480	1.00
240_D	244_V	1.479	1.00
209_D	250_Y	1.475	1.00
19_A	28_I	1.469	1.00
35_R	53_F	1.467	1.00
99_L	103_V	1.440	1.00
42_A	52_L	1.430	1.00
51_Q	54_E	1.401	1.00
49_A	52_L	1.399	1.00
69_S	73_S	1.397	1.00
38_I	52_L	1.397	1.00
4_D	14_K	1.382	1.00
169_D	175_D	1.369	1.00
30_G	40_Q	1.352	1.00
36_A	39_K	1.345	1.00
226_G	232_E	1.316	1.00
248_T	254_L	1.299	1.00
106_A	110_A	1.289	1.00
3_L	18_T	1.287	1.00
172_K	176_S	1.261	1.00
205_L	215_V	1.234	0.99
13_Q	40_Q	1.232	0.99
107_I	111_I	1.226	0.99
159_D	165_K	1.222	0.99
216_R	220_S	1.209	0.99
19_A	24_N	1.196	0.99
218_E	243_Q	1.193	0.99
164_T	171_K	1.189	0.99
11_K	15_R	1.179	0.99
228_L	232_E	1.178	0.99
29_P	37_F	1.175	0.99
72_I	76_N	1.174	0.99
70_E	73_S	1.168	0.99
226_G	234_Y	1.165	0.99
202_E	237_D	1.151	0.99
204_E	233_T	1.151	0.99
206_K	257_K	1.150	0.99
207_A	214_R	1.149	0.99
164_T	169_D	1.141	0.99
257_K	262_V	1.132	0.99
41_Y	44_A	1.131	0.99
136_S	166_E	1.117	0.99
6_L	17_L	1.117	0.99
218_E	223_L	1.113	0.99
188_G	191_T	1.107	0.99
98_I	101_V	1.102	0.99
207_A	211_S	1.100	0.99
4_D	17_L	1.091	0.99
161_K	165_K	1.087	0.99
267_L	270_K	1.065	0.98
217_D	240_D	1.059	0.98
34_V	56_H	1.058	0.98
93_P	96_L	1.049	0.98
17_L	44_A	1.047	0.98
16_Y	19_A	1.039	0.98
52_L	55_E	1.030	0.98
130_A	133_Q	1.018	0.98
11_K	228_L	1.000	0.98
7_Q	14_K	0.997	0.97
28_I	34_V	0.997	0.97
202_E	259_N	0.993	0.97
69_S	75_M	0.989	0.97
134_S	138_Y	0.988	0.97
4_D	8_A	0.984	0.97
72_I	75_M	0.984	0.97
49_A	53_F	0.981	0.97
214_R	222_S	0.977	0.97
246_I	277_I	0.973	0.97
30_G	37_F	0.972	0.97
273_M	277_I	0.971	0.97
252_P	267_L	0.962	0.97
13_Q	28_I	0.950	0.97
162_K	169_D	0.947	0.97
250_Y	274_A	0.942	0.96
160_T	163_E	0.942	0.96
161_K	164_T	0.942	0.96
50_D	54_E	0.938	0.96
11_K	37_F	0.938	0.96
164_T	170_K	0.934	0.96
170_K	174_N	0.933	0.96
93_P	97_V	0.933	0.96
222_S	225_E	0.927	0.96
13_Q	37_F	0.924	0.96
205_L	254_L	0.924	0.96
204_E	260_G	0.916	0.96
133_Q	138_Y	0.913	0.96
174_N	194_E	0.900	0.95
19_A	29_P	0.900	0.95
163_E	174_N	0.899	0.95
181_I	184_A	0.897	0.95
270_K	273_M	0.889	0.95
168_E	173_E	0.885	0.95
167_N	181_I	0.885	0.95
39_K	43_E	0.874	0.95
19_A	33_Y	0.869	0.94
89_L	92_L	0.868	0.94
218_E	240_D	0.863	0.94
131_I	136_S	0.857	0.94
91_L	95_I	0.854	0.94
160_T	172_K	0.853	0.94
228_L	234_Y	0.851	0.94
98_I	102_I	0.837	0.93
97_V	101_V	0.836	0.93
209_D	230_K	0.834	0.93
2_S	5_D	0.833	0.93
7_Q	20_L	0.830	0.93
173_E	177_E	0.829	0.93
251_A	273_M	0.828	0.93
37_F	41_Y	0.827	0.93
168_E	174_N	0.826	0.93
200_K	237_D	0.825	0.93
248_T	265_Y	0.824	0.93
20_L	32_F	0.823	0.93
90_E	93_P	0.819	0.93
71_K	75_M	0.814	0.92
165_K	170_K	0.812	0.92
236_K	240_D	0.810	0.92
245_D	278_K	0.799	0.92
189_S	193_Y	0.797	0.91
118_K	127_S	0.795	0.91
173_E	181_I	0.795	0.91
264_S	267_L	0.791	0.91
181_I	189_S	0.784	0.91
131_I	135_E	0.782	0.91
215_V	246_I	0.778	0.90
132_T	135_E	0.775	0.90
203_L	246_I	0.774	0.90
30_G	52_L	0.764	0.90
123_H	128_E	0.762	0.90
275_Q	279_I	0.761	0.89
39_K	53_F	0.761	0.89
253_N	270_K	0.761	0.89
165_K	171_K	0.760	0.89
218_E	242_K	0.758	0.89
160_T	164_T	0.755	0.89
73_S	76_N	0.754	0.89
32_F	35_R	0.753	0.89
248_T	275_Q	0.747	0.89
137_K	165_K	0.744	0.88
28_I	37_F	0.744	0.88
216_R	221_S	0.742	0.88
38_I	93_P	0.734	0.88
165_K	173_E	0.733	0.88
182_K	186_T	0.730	0.87
251_A	267_L	0.729	0.87
159_D	162_K	0.723	0.87
37_F	207_A	0.722	0.87
169_D	173_E	0.718	0.87
132_T	137_K	0.718	0.87
31_K	34_V	0.716	0.86
35_R	259_N	0.715	0.86
179_L	197_G	0.708	0.86
187_E	193_Y	0.707	0.86
70_E	74_G	0.706	0.86
161_K	169_D	0.704	0.86
36_A	231_D	0.704	0.86
212_W	247_R	0.704	0.86
60_I	66_D	0.699	0.85
215_V	220_S	0.699	0.85
96_L	111_I	0.697	0.85
247_R	274_A	0.694	0.85
25_Y	56_H	0.693	0.85
6_L	45_V	0.693	0.85
163_E	169_D	0.693	0.85
7_Q	10_T	0.692	0.85
7_Q	16_Y	0.692	0.85
16_Y	33_Y	0.692	0.85
92_L	97_V	0.692	0.85
7_Q	11_K	0.690	0.84
164_T	180_E	0.683	0.84
111_I	115_A	0.682	0.84
5_D	9_A	0.681	0.84
124_N	128_E	0.676	0.83
15_R	30_G	0.675	0.83
100_G	111_I	0.675	0.83
57_K	60_I	0.674	0.83
43_E	258_I	0.673	0.83
167_N	173_E	0.672	0.83
240_D	243_Q	0.670	0.83
23_G	29_P	0.665	0.82
171_K	177_E	0.665	0.82
170_K	181_I	0.664	0.82
207_A	213_I	0.662	0.82
205_L	256_I	0.661	0.82
213_I	248_T	0.661	0.82
133_Q	137_K	0.660	0.82
203_L	248_T	0.659	0.82
130_A	137_K	0.659	0.82
167_N	178_K	0.657	0.81
243_Q	278_K	0.656	0.81
45_V	56_H	0.655	0.81
166_E	172_K	0.653	0.81
135_E	164_T	0.653	0.81
172_K	185_G	0.649	0.81
38_I	56_H	0.647	0.80
203_L	279_I	0.645	0.80
173_E	176_S	0.643	0.80
168_E	172_K	0.639	0.80
66_D	72_I	0.637	0.79
6_L	37_F	0.636	0.79
99_L	277_I	0.633	0.79
35_R	234_Y	0.630	0.79
92_L	96_L	0.629	0.78
121_D	164_T	0.627	0.78
70_E	75_M	0.627	0.78
31_K	56_H	0.625	0.78
7_Q	12_I	0.625	0.78
216_R	271_K	0.624	0.78
2_S	249_G	0.622	0.78
5_D	8_A	0.621	0.78
201_I	237_D	0.619	0.77
35_R	61_P	0.615	0.77
190_L	193_Y	0.613	0.77
161_K	170_K	0.609	0.76
16_Y	29_P	0.609	0.76
163_E	189_S	0.608	0.76
180_E	184_A	0.608	0.76
47_L	52_L	0.606	0.76
212_W	215_V	0.601	0.75
223_L	227_T	0.600	0.75
17_L	29_P	0.599	0.75
137_K	159_D	0.598	0.75
13_Q	39_K	0.595	0.75
86_S	91_L	0.595	0.75
159_D	164_T	0.595	0.75
36_A	41_Y	0.594	0.74
103_V	108_V	0.593	0.74
175_D	178_K	0.591	0.74
12_I	207_A	0.587	0.74
184_A	187_E	0.587	0.74
252_P	273_M	0.586	0.73
125_A	128_E	0.586	0.73
172_K	178_K	0.583	0.73
264_S	268_D	0.583	0.73
173_E	186_T	0.583	0.73
271_K	275_Q	0.582	0.73
253_N	273_M	0.581	0.73
10_T	40_Q	0.581	0.73
217_D	236_K	0.578	0.72
132_T	136_S	0.577	0.72
107_I	114_F	0.576	0.72
252_P	269_P	0.576	0.72
16_Y	41_Y	0.575	0.72
102_I	105_I	0.575	0.72
169_D	196_S	0.573	0.72
92_L	95_I	0.571	0.72
188_G	193_Y	0.571	0.72
131_I	134_S	0.570	0.71
30_G	53_F	0.569	0.71
6_L	36_A	0.569	0.71
160_T	178_K	0.567	0.71
128_E	137_K	0.564	0.71
256_I	263_L	0.563	0.71
71_K	74_G	0.563	0.71
265_Y	274_A	0.561	0.70
216_R	229_K	0.560	0.70
73_S	90_E	0.560	0.70
10_T	14_K	0.559	0.70
5_D	249_G	0.557	0.70
13_Q	36_A	0.556	0.70
216_R	245_D	0.555	0.69
163_E	175_D	0.555	0.69
175_D	180_E	0.554	0.69
236_K	279_I	0.554	0.69
256_I	265_Y	0.552	0.69
159_D	175_D	0.551	0.69
163_E	167_N	0.551	0.69
87_K	99_L	0.551	0.69
225_E	248_T	0.551	0.69
204_E	227_T	0.551	0.69
187_E	192_T	0.551	0.69
130_A	167_N	0.549	0.69
251_A	265_Y	0.548	0.68
167_N	192_T	0.547	0.68
12_I	17_L	0.547	0.68
217_D	242_K	0.546	0.68
224_K	228_L	0.545	0.68
64_Y	68_V	0.544	0.68
39_K	279_I	0.544	0.68
162_K	168_E	0.537	0.67
169_D	177_E	0.537	0.67
40_Q	43_E	0.535	0.67
65_H	75_M	0.534	0.66
71_K	205_L	0.534	0.66
167_N	171_K	0.533	0.66
89_L	97_V	0.532	0.66
266_E	275_Q	0.531	0.66
160_T	176_S	0.531	0.66
35_R	223_L	0.530	0.66
163_E	172_K	0.526	0.65
88_A	96_L	0.525	0.65
96_L	110_A	0.524	0.65
181_I	186_T	0.523	0.65
226_G	278_K	0.523	0.65
29_P	34_V	0.522	0.65
159_D	163_E	0.522	0.65
90_E	94_T	0.517	0.64
166_E	184_A	0.517	0.64
134_S	137_K	0.516	0.64
181_I	185_G	0.513	0.63
7_Q	13_Q	0.513	0.63
2_S	65_H	0.513	0.63
211_S	249_G	0.513	0.63
201_I	258_I	0.512	0.63
172_K	183_A	0.510	0.63
97_V	108_V	0.509	0.63
3_L	7_Q	0.509	0.63
2_S	91_L	0.509	0.63
220_S	226_G	0.508	0.63
47_L	109_Y	0.508	0.63
39_K	102_I	0.507	0.63
66_D	69_S	0.507	0.63
168_E	175_D	0.505	0.62
15_R	19_A	0.505	0.62
265_Y	275_Q	0.504	0.62
175_D	185_G	0.503	0.62
17_L	36_A	0.502	0.62
205_L	212_W	0.502	0.62
137_K	173_E	0.500	0.61

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
3fymA	1	0.2326	99.3	0.753	Contact Map
2wusR	1	0.2361	98.5	0.823	Contact Map
4gqmA	2	0.2743	98.3	0.831	Contact Map
3kz3A	2	0.191	95.7	0.887	Contact Map
2ef8A	2	0.2118	95.5	0.889	Contact Map
2ofyA	2	0.1979	95.4	0.889	Contact Map
3f6wA	2	0.1944	95.4	0.889	Contact Map
1lmb3	2	0.2153	94.8	0.893	Contact Map
1y7yA	2	0.1632	94.7	0.894	Contact Map
3kxaA	4	0.2014	94.6	0.894	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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