YNBA - ECOLI - GREMLIN Contacts

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YNBA - Inner membrane protein YnbA

UniProt:	P76090	Sequences: MTLYQIKPLFQSLLRPTMFWLYKHHVTANHITLAALALSLLTGLLLMLAAQPILFLLLPIVLFIRMALNALDGMLARECNQQTRLGAILNETGDVISDIALYLPFLFLPESNASLVILMLFCTILTEFCGLLAQTINGVRSYAGPFGKSDRALIFGLWGLAVAIYPQWMQWNNLLWSIASILLLWTAINRCRSVLLMSAEI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13748
Length:	201 (182)
Sequences:	2153 (1504)
Seq/√Len:	111.5

ECOLI - YNBA YNJF
HALSA - Q9HQS2
SULSO - Q7LXU6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_T	30_H	4.403	1.00
22_Y	75_L	3.665	1.00
28_A	81_Q	3.513	1.00
26_V	34_A	3.161	1.00
36_L	93_G	2.892	1.00
96_I	184_L	2.815	1.00
20_W	24_H	2.693	1.00
18_M	78_E	2.633	1.00
85_L	195_L	2.460	1.00
39_S	97_S	2.449	1.00
45_L	61_V	2.402	1.00
31_I	75_L	2.226	1.00
158_W	175_L	2.161	1.00
21_L	26_V	2.155	1.00
122_C	184_L	2.024	1.00
74_M	78_E	2.007	1.00
46_L	159_G	1.996	1.00
106_L	116_V	1.970	1.00
43_G	104_P	1.897	1.00
95_V	98_D	1.891	1.00
119_M	180_S	1.880	1.00
19_F	78_E	1.777	1.00
40_L	100_A	1.773	1.00
69_N	90_N	1.771	1.00
95_V	148_K	1.718	1.00
144_G	186_T	1.690	1.00
18_M	75_L	1.659	1.00
21_L	71_L	1.654	1.00
35_A	68_L	1.650	1.00
22_Y	79_C	1.649	1.00
106_L	117_I	1.598	1.00
157_L	161_A	1.587	1.00
131_L	134_Q	1.586	1.00
46_L	104_P	1.567	1.00
43_G	100_A	1.551	1.00
146_F	182_L	1.542	1.00
49_A	55_F	1.540	1.00
87_A	132_L	1.512	1.00
88_I	129_C	1.497	1.00
96_I	122_C	1.482	1.00
45_L	57_L	1.482	1.00
98_D	151_R	1.478	1.00
91_E	132_L	1.466	1.00
29_N	85_L	1.460	1.00
41_L	61_V	1.454	1.00
99_I	121_F	1.454	1.00
20_W	23_K	1.448	1.00
192_R	195_L	1.398	1.00
95_V	128_F	1.396	1.00
144_G	190_R	1.371	1.00
188_I	192_R	1.366	1.00
126_T	186_T	1.353	1.00
11_Q	74_M	1.342	1.00
146_F	154_I	1.337	1.00
59_P	156_G	1.318	1.00
18_M	74_M	1.300	0.99
39_S	65_R	1.298	0.99
47_M	104_P	1.296	0.99
116_V	176_W	1.275	0.99
44_L	48_L	1.272	0.99
33_L	89_L	1.272	0.99
130_G	142_Y	1.270	0.99
186_T	190_R	1.268	0.99
38_L	61_V	1.251	0.99
88_I	194_V	1.246	0.99
147_G	150_D	1.236	0.99
98_D	148_K	1.221	0.99
71_L	74_M	1.211	0.99
19_F	23_K	1.197	0.99
95_V	151_R	1.194	0.99
91_E	130_G	1.161	0.99
181_I	185_W	1.147	0.99
16_P	20_W	1.145	0.99
192_R	196_L	1.134	0.99
91_E	151_R	1.131	0.98
164_I	167_Q	1.120	0.98
31_I	71_L	1.106	0.98
92_T	129_C	1.098	0.98
185_W	188_I	1.096	0.98
99_I	124_I	1.088	0.98
28_A	75_L	1.082	0.98
144_G	150_D	1.063	0.98
143_A	193_S	1.056	0.98
44_L	47_M	1.038	0.97
99_I	125_L	1.037	0.97
37_A	41_L	1.022	0.97
45_L	54_L	1.017	0.97
154_I	175_L	1.006	0.97
49_A	54_L	1.004	0.97
148_K	151_R	1.003	0.97
48_L	54_L	1.003	0.97
42_T	61_V	1.001	0.97
88_I	191_C	1.000	0.97
134_Q	140_R	0.996	0.97
180_S	184_L	0.992	0.97
28_A	82_Q	0.992	0.97
42_T	101_L	0.990	0.96
129_C	191_C	0.983	0.96
46_L	49_A	0.977	0.96
66_M	148_K	0.971	0.96
65_R	148_K	0.961	0.96
17_T	71_L	0.954	0.96
130_G	140_R	0.951	0.96
127_E	130_G	0.950	0.96
87_A	136_I	0.934	0.95
15_R	78_E	0.928	0.95
179_A	183_L	0.925	0.95
146_F	179_A	0.917	0.95
133_A	137_N	0.908	0.94
41_L	107_F	0.902	0.94
16_P	19_F	0.897	0.94
126_T	146_F	0.893	0.94
65_R	90_N	0.883	0.93
139_V	142_Y	0.877	0.93
128_F	134_Q	0.874	0.93
91_E	128_F	0.872	0.93
41_L	44_L	0.865	0.93
66_M	70_A	0.859	0.92
186_T	189_N	0.859	0.92
161_A	165_Y	0.856	0.92
27_T	75_L	0.855	0.92
40_L	48_L	0.855	0.92
122_C	187_A	0.853	0.92
90_N	148_K	0.850	0.92
128_F	132_L	0.850	0.92
38_L	60_I	0.842	0.92
37_A	166_P	0.838	0.92
9_L	12_S	0.838	0.92
88_I	136_I	0.832	0.91
56_L	164_I	0.831	0.91
96_I	187_A	0.829	0.91
32_T	62_L	0.824	0.91
83_T	158_W	0.822	0.91
14_L	74_M	0.821	0.91
172_N	175_L	0.817	0.91
63_F	66_M	0.816	0.90
12_S	16_P	0.815	0.90
28_A	46_L	0.814	0.90
130_G	134_Q	0.807	0.90
10_F	149_S	0.800	0.90
70_A	149_S	0.794	0.89
65_R	69_N	0.791	0.89
20_W	41_L	0.788	0.89
125_L	187_A	0.784	0.89
13_L	16_P	0.783	0.89
131_L	135_T	0.783	0.89
56_L	60_I	0.776	0.88
178_I	182_L	0.776	0.88
101_L	152_A	0.767	0.88
127_E	151_R	0.766	0.87
118_L	180_S	0.761	0.87
65_R	97_S	0.756	0.87
38_L	68_L	0.753	0.87
132_L	135_T	0.746	0.86
30_H	38_L	0.745	0.86
41_L	45_L	0.743	0.86
176_W	179_A	0.743	0.86
133_A	140_R	0.730	0.85
85_L	88_I	0.728	0.85
180_S	183_L	0.722	0.84
66_M	156_G	0.720	0.84
185_W	189_N	0.720	0.84
21_L	24_H	0.720	0.84
85_L	194_V	0.718	0.84
54_L	57_L	0.715	0.84
42_T	62_L	0.714	0.84
26_V	30_H	0.711	0.83
32_T	150_D	0.702	0.82
84_R	157_L	0.701	0.82
41_L	60_I	0.700	0.82
126_T	187_A	0.695	0.82
46_L	58_L	0.694	0.82
33_L	37_A	0.693	0.82
154_I	158_W	0.691	0.81
142_Y	147_G	0.689	0.81
33_L	192_R	0.689	0.81
158_W	172_N	0.688	0.81
32_T	93_G	0.687	0.81
11_Q	18_M	0.685	0.81
125_L	128_F	0.684	0.81
66_M	95_V	0.684	0.81
157_L	196_L	0.682	0.81
63_F	156_G	0.682	0.81
128_F	135_T	0.679	0.80
10_F	59_P	0.678	0.80
30_H	34_A	0.678	0.80
115_L	177_S	0.670	0.79
115_L	176_W	0.666	0.79
153_L	157_L	0.660	0.78
69_N	91_E	0.660	0.78
95_V	102_Y	0.658	0.78
29_N	192_R	0.658	0.78
69_N	148_K	0.657	0.78
29_N	81_Q	0.656	0.78
34_A	38_L	0.653	0.78
46_L	101_L	0.646	0.77
56_L	160_L	0.642	0.77
128_F	151_R	0.640	0.76
115_L	158_W	0.638	0.76
57_L	61_V	0.637	0.76
168_W	173_N	0.634	0.76
118_L	121_F	0.628	0.75
90_N	145_P	0.628	0.75
23_K	111_S	0.619	0.74
154_I	179_A	0.618	0.74
70_A	150_D	0.615	0.73
92_T	191_C	0.615	0.73
21_L	27_T	0.612	0.73
91_E	95_V	0.611	0.73
119_M	183_L	0.599	0.71
63_F	67_A	0.598	0.71
89_L	93_G	0.594	0.71
19_F	160_L	0.592	0.71
47_M	107_F	0.591	0.70
58_L	105_F	0.589	0.70
88_I	91_E	0.585	0.70
105_F	116_V	0.583	0.69
58_L	159_G	0.579	0.69
111_S	173_N	0.579	0.69
61_V	193_S	0.579	0.69
177_S	181_I	0.577	0.69
11_Q	15_R	0.576	0.69
122_C	180_S	0.572	0.68
106_L	178_I	0.572	0.68
193_S	196_L	0.571	0.68
82_Q	85_L	0.569	0.68
46_L	54_L	0.568	0.67
13_L	71_L	0.567	0.67
35_A	91_E	0.561	0.67
110_E	113_A	0.560	0.66
109_P	112_N	0.559	0.66
131_L	140_R	0.554	0.66
29_N	195_L	0.554	0.66
91_E	98_D	0.552	0.65
122_C	129_C	0.551	0.65
114_S	118_L	0.551	0.65
163_A	166_P	0.546	0.64
133_A	138_G	0.546	0.64
96_I	183_L	0.544	0.64
39_S	42_T	0.544	0.64
42_T	46_L	0.541	0.64
10_F	14_L	0.541	0.64
34_A	54_L	0.539	0.63
148_K	152_A	0.539	0.63
77_R	90_N	0.538	0.63
35_A	97_S	0.537	0.63
21_L	31_I	0.535	0.63
91_E	131_L	0.532	0.62
55_F	104_P	0.527	0.62
144_G	149_S	0.527	0.62
112_N	115_L	0.527	0.62
95_V	127_E	0.525	0.61
67_A	147_G	0.525	0.61
59_P	159_G	0.524	0.61
11_Q	14_L	0.520	0.61
162_V	165_Y	0.517	0.60
137_N	140_R	0.516	0.60
38_L	65_R	0.516	0.60
47_M	168_W	0.514	0.60
92_T	96_I	0.512	0.60
62_L	88_I	0.511	0.59
58_L	104_P	0.511	0.59
130_G	137_N	0.509	0.59
69_N	77_R	0.509	0.59
88_I	133_A	0.508	0.59
65_R	91_E	0.507	0.59
30_H	84_R	0.505	0.59
140_R	194_V	0.505	0.59
15_R	19_F	0.503	0.58
91_E	148_K	0.503	0.58
13_L	17_T	0.503	0.58
19_F	84_R	0.502	0.58
24_H	79_C	0.500	0.58

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
4o6mA	2	0.9353	100	0.337	Contact Map
4mndA	2	0.9303	100	0.43	Contact Map
4od4A	1	0.9254	1.9	0.961	Contact Map
2dlwA	1	0.3682	1.8	0.962	Contact Map
3tx3A	2	0.9254	1.7	0.962	Contact Map
2i15A	3	0.2239	1.6	0.963	Contact Map
4tq3A	1	0.9254	1.5	0.963	Contact Map
4uf1A	2	0.1891	1.3	0.965	Contact Map
2ww9A	1	0.4229	1.3	0.965	Contact Map
3j1rA	5	0.1294	1.3	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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