YMCC - BACSU - GREMLIN Contacts

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YMCC - Uncharacterized membrane protein YmcC

UniProt:	O31780	Sequences: MNGIAWMIVFCEIAFWVVIVLGLAVRYVFKRHTLGLLFLALTPVIDLILLAATGVDLYRGASATAAHGIAAVYIGISIAYGKQMIQWADEKFQYYVTKKGTKPLKRFGMDHAKHGAKGWLRHVLAYLIGAGLLAGMIYFINDSSRTEALSGILKLWTVIIGIDFLITASYFIWPKKEKASANLRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	185 (174)
Sequences:	412 (310)
Seq/√Len:	23.5

BACSU - YMCC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_V	38_F	4.480	1.00
116_A	171_F	3.630	1.00
29_F	38_F	3.005	1.00
25_V	29_F	2.930	1.00
24_A	28_V	2.855	0.99
122_H	163_D	2.830	0.99
79_A	128_I	2.506	0.98
40_A	77_S	2.391	0.98
31_R	34_L	2.367	0.98
161_G	165_L	2.349	0.98
28_V	92_F	2.231	0.97
80_Y	122_H	2.209	0.97
134_A	138_Y	2.168	0.96
11_C	49_L	2.164	0.96
83_Q	121_R	2.108	0.95
122_H	156_W	2.093	0.95
132_L	136_M	2.050	0.95
142_D	145_R	2.000	0.94
126_Y	157_T	1.941	0.93
75_G	79_A	1.929	0.93
156_W	163_D	1.919	0.93
152_I	155_L	1.910	0.92
37_L	40_A	1.801	0.90
41_L	44_V	1.780	0.89
122_H	167_T	1.741	0.88
32_H	35_G	1.731	0.88
68_G	133_L	1.709	0.87
116_A	167_T	1.703	0.87
163_D	167_T	1.695	0.87
130_A	153_L	1.671	0.86
18_V	45_I	1.669	0.86
164_F	168_A	1.657	0.86
7_M	52_A	1.553	0.82
92_F	96_V	1.548	0.81
166_I	169_S	1.496	0.79
76_I	88_A	1.483	0.78
72_V	152_I	1.479	0.78
68_G	152_I	1.478	0.78
25_V	34_L	1.464	0.78
130_A	157_T	1.439	0.76
72_V	156_W	1.439	0.76
83_Q	117_K	1.425	0.76
163_D	169_S	1.421	0.75
94_Y	102_K	1.419	0.75
118_G	163_D	1.393	0.74
21_L	35_G	1.375	0.73
117_K	121_R	1.371	0.73
80_Y	163_D	1.353	0.72
111_H	115_G	1.344	0.71
111_H	116_A	1.334	0.71
167_T	170_Y	1.325	0.70
116_A	164_F	1.291	0.68
42_T	46_D	1.285	0.68
88_A	92_F	1.245	0.65
163_D	168_A	1.222	0.64
21_L	38_F	1.221	0.63
31_R	78_I	1.220	0.63
119_W	164_F	1.211	0.63
47_L	132_L	1.182	0.61
122_H	126_Y	1.177	0.61
140_I	146_T	1.174	0.60
134_A	153_L	1.163	0.60
95_Y	99_K	1.159	0.59
115_G	118_G	1.156	0.59
116_A	168_A	1.154	0.59
120_L	124_L	1.148	0.59
156_W	167_T	1.146	0.58
169_S	174_P	1.141	0.58
87_W	91_K	1.130	0.57
100_G	104_L	1.112	0.56
166_I	170_Y	1.108	0.56
171_F	174_P	1.101	0.55
111_H	168_A	1.093	0.55
76_I	84_M	1.093	0.55
25_V	51_A	1.090	0.55
113_K	117_K	1.082	0.54
5_A	9_V	1.077	0.54
93_Q	96_V	1.072	0.53
51_A	159_I	1.069	0.53
116_A	156_W	1.068	0.53
115_G	119_W	1.057	0.52
49_L	73_Y	1.052	0.52
111_H	175_K	1.043	0.51
84_M	88_A	1.037	0.51
20_V	51_A	1.030	0.50
80_Y	106_R	1.013	0.49
123_V	127_L	1.006	0.49
119_W	123_V	1.006	0.49
122_H	160_I	0.992	0.48
156_W	169_S	0.991	0.48
62_S	77_S	0.991	0.48
94_Y	103_P	0.988	0.47
51_A	112_A	0.987	0.47
116_A	120_L	0.981	0.47
30_K	36_L	0.975	0.47
100_G	103_P	0.971	0.46
22_G	42_T	0.968	0.46
48_I	52_A	0.960	0.46
72_V	155_L	0.960	0.46
80_Y	123_V	0.953	0.45
7_M	77_S	0.952	0.45
168_A	172_I	0.946	0.45
126_Y	160_I	0.933	0.44
63_A	146_T	0.932	0.44
91_K	100_G	0.924	0.43
133_L	137_I	0.923	0.43
158_V	163_D	0.920	0.43
79_A	125_A	0.907	0.42
119_W	163_D	0.903	0.42
44_V	144_S	0.901	0.41
126_Y	156_W	0.891	0.41
79_A	124_L	0.889	0.41
52_A	93_Q	0.887	0.40
6_W	143_S	0.869	0.39
68_G	71_A	0.862	0.39
82_K	96_V	0.857	0.38
169_S	173_W	0.854	0.38
86_Q	175_K	0.848	0.38
83_Q	118_G	0.848	0.38
5_A	106_R	0.846	0.38
4_I	165_L	0.845	0.38
79_A	121_R	0.840	0.37
164_F	167_T	0.836	0.37
118_G	122_H	0.828	0.37
9_V	13_I	0.828	0.37
4_I	85_I	0.826	0.36
80_Y	85_I	0.817	0.36
119_W	122_H	0.813	0.36
162_I	166_I	0.798	0.35
53_T	70_A	0.798	0.35
45_I	77_S	0.797	0.35
112_A	170_Y	0.795	0.34
5_A	66_A	0.794	0.34
63_A	148_A	0.790	0.34
73_Y	85_I	0.778	0.33
53_T	58_Y	0.777	0.33
126_Y	153_L	0.773	0.33
164_F	176_K	0.772	0.33
132_L	135_G	0.771	0.33
25_V	32_H	0.770	0.33
92_F	97_T	0.765	0.33
7_M	10_F	0.763	0.32
50_L	131_G	0.759	0.32
32_H	37_L	0.755	0.32
143_S	146_T	0.754	0.32
42_T	74_I	0.750	0.32
14_A	18_V	0.747	0.31
74_I	132_L	0.745	0.31
83_Q	105_K	0.742	0.31
112_A	116_A	0.737	0.31
104_L	147_E	0.736	0.31
29_F	176_K	0.732	0.31
157_T	160_I	0.731	0.30
21_L	36_L	0.730	0.30
168_A	174_P	0.727	0.30
30_K	85_I	0.725	0.30
24_A	44_V	0.722	0.30
72_V	122_H	0.722	0.30
20_V	92_F	0.718	0.30
44_V	47_L	0.715	0.30
112_A	175_K	0.707	0.29
170_Y	174_P	0.704	0.29
19_I	77_S	0.703	0.29
22_G	35_G	0.701	0.29
18_V	41_L	0.697	0.28
102_K	105_K	0.697	0.28
63_A	85_I	0.684	0.28
9_V	151_G	0.683	0.28
118_G	129_G	0.679	0.27
127_L	143_S	0.676	0.27
156_W	160_I	0.676	0.27
109_M	171_F	0.675	0.27
155_L	163_D	0.667	0.27
109_M	164_F	0.666	0.27
169_S	172_I	0.666	0.27
109_M	113_K	0.664	0.27
107_F	112_A	0.664	0.27
133_L	136_M	0.661	0.26
64_T	153_L	0.661	0.26
38_F	45_I	0.656	0.26
93_Q	97_T	0.654	0.26
40_A	45_I	0.652	0.26
10_F	18_V	0.650	0.26
51_A	143_S	0.648	0.26
63_A	68_G	0.647	0.26
57_L	63_A	0.645	0.26
43_P	75_G	0.644	0.26
91_K	102_K	0.644	0.26
163_D	170_Y	0.644	0.26
141_N	151_G	0.644	0.26
143_S	151_G	0.643	0.26
97_T	100_G	0.638	0.25
121_R	138_Y	0.638	0.25
76_I	163_D	0.638	0.25
126_Y	130_A	0.636	0.25
17_V	65_A	0.636	0.25
136_M	141_N	0.634	0.25
65_A	93_Q	0.634	0.25
34_L	37_L	0.632	0.25
163_D	174_P	0.632	0.25
78_I	154_K	0.624	0.24
58_Y	86_Q	0.620	0.24
85_I	105_K	0.618	0.24
118_G	156_W	0.617	0.24
11_C	142_D	0.616	0.24
24_A	147_E	0.614	0.24
91_K	94_Y	0.612	0.24
61_A	155_L	0.611	0.24
32_H	66_A	0.607	0.24
16_W	23_L	0.607	0.24
94_Y	101_T	0.606	0.24
102_K	177_E	0.600	0.23
123_V	159_I	0.592	0.23
8_I	73_Y	0.591	0.23
6_W	10_F	0.588	0.23
91_K	103_P	0.588	0.23
54_G	58_Y	0.586	0.23
39_L	43_P	0.585	0.23
116_A	163_D	0.585	0.23
8_I	96_V	0.582	0.22
20_V	69_I	0.578	0.22
100_G	105_K	0.577	0.22
16_W	46_D	0.576	0.22
71_A	133_L	0.575	0.22
124_L	144_S	0.570	0.22
116_A	122_H	0.565	0.22
65_A	178_K	0.564	0.22
20_V	61_A	0.561	0.21
87_W	92_F	0.560	0.21
54_G	115_G	0.559	0.21
90_E	104_L	0.554	0.21
45_I	173_W	0.553	0.21
129_G	163_D	0.552	0.21
8_I	87_W	0.551	0.21
55_V	123_V	0.550	0.21
69_I	99_K	0.547	0.21
168_A	173_W	0.546	0.21
75_G	121_R	0.543	0.21
156_W	170_Y	0.543	0.21
53_T	68_G	0.540	0.20
7_M	14_A	0.540	0.20
79_A	146_T	0.539	0.20
20_V	140_I	0.538	0.20
66_A	74_I	0.531	0.20
60_G	87_W	0.530	0.20
104_L	124_L	0.529	0.20
46_D	92_F	0.528	0.20
126_Y	167_T	0.527	0.20
158_V	176_K	0.526	0.20
45_I	136_M	0.526	0.20
39_L	101_T	0.523	0.20
80_Y	118_G	0.523	0.20
76_I	156_W	0.522	0.20
134_A	139_F	0.520	0.19
96_V	99_K	0.512	0.19
40_A	44_V	0.510	0.19
22_G	77_S	0.508	0.19
84_M	92_F	0.505	0.19
93_Q	99_K	0.503	0.19
44_V	166_I	0.503	0.19
123_V	162_I	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
3aqpA	1	0.8216	72.5	0.938	Contact Map
3ne5A	3	0.9081	55.6	0.944	Contact Map
4k0jA	3	0.8162	35.8	0.951	Contact Map
4dx5A	3	0.8973	26.2	0.954	Contact Map
3w9iA	3	0.8595	25.7	0.954	Contact Map
4mt1A	3	0.8541	23.7	0.955	Contact Map
3h90A	3	0.7622	14.3	0.959	Contact Map
4mndA	2	0.7784	9.3	0.962	Contact Map
2a65A	2	0.9027	9.2	0.962	Contact Map
2mgyA	1	0.373	6.8	0.965	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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