YNJF - ECOLI - GREMLIN Contacts

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YNJF - Inner membrane protein YnjF

UniProt:	P76226	Sequences: MLDRHLHPRIKPLLHQCVRVLDKPGITPDGLTLVGFAIGVLALPFLALGWYLAALVVILLNRLLDGLDGALARRRELTDAGGFLDISLDFLFYALVPFGFILAAPEQNALAGGWLLFAFIGTGSSFLAFAALAAKHQIDNPGYAHKSFYYLGGLTEGTETILLFVLGCLFPAWFAWFAWIFGALCWMTTFTRVWSGYLTLKSLQRQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14008
Length:	206 (183)
Sequences:	2399 (1716)
Seq/√Len:	126.8

ECOLI - YNJF YNBA
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_G	5.159	1.00
22_D	71_L	4.180	1.00
26_I	34_V	3.300	1.00
20_V	24_P	3.205	1.00
28_P	77_L	3.173	1.00
36_F	88_L	2.948	1.00
91_L	186_W	2.883	1.00
39_G	92_F	2.671	1.00
18_V	74_R	2.500	1.00
80_A	197_Y	2.477	1.00
21_L	26_I	2.376	1.00
45_F	57_V	2.287	1.00
70_A	74_R	2.221	1.00
31_L	71_L	2.177	1.00
46_L	168_C	2.114	1.00
43_L	99_G	2.072	1.00
33_L	84_L	1.971	1.00
167_G	177_F	1.963	1.00
22_D	75_R	1.906	1.00
29_D	80_A	1.833	1.00
125_S	186_W	1.783	1.00
18_V	71_L	1.782	1.00
65_D	85_D	1.777	1.00
19_R	74_R	1.763	1.00
40_V	95_L	1.727	1.00
188_T	192_R	1.713	1.00
129_F	133_A	1.682	1.00
91_L	125_S	1.663	1.00
166_L	170_F	1.622	1.00
130_A	133_A	1.619	1.00
90_F	93_Y	1.617	1.00
163_L	177_F	1.579	1.00
194_W	197_Y	1.573	1.00
82_G	135_K	1.572	1.00
21_L	67_L	1.548	1.00
28_P	71_L	1.446	1.00
130_A	136_H	1.442	1.00
45_F	53_A	1.424	1.00
43_L	95_L	1.399	1.00
46_L	99_G	1.388	1.00
11_K	70_A	1.384	1.00
183_A	187_M	1.370	1.00
131_A	134_A	1.344	1.00
52_L	56_V	1.331	1.00
47_A	99_G	1.308	1.00
18_V	70_A	1.293	1.00
181_F	185_C	1.288	1.00
31_L	67_L	1.287	1.00
155_T	184_L	1.282	1.00
37_A	41_L	1.280	1.00
35_G	64_L	1.272	1.00
16_Q	20_V	1.271	1.00
20_V	23_K	1.238	1.00
115_L	118_A	1.232	1.00
83_F	193_V	1.228	0.99
19_R	23_K	1.226	0.99
27_T	71_L	1.214	0.99
114_W	182_G	1.205	0.99
93_Y	160_T	1.200	0.99
194_W	198_L	1.193	0.99
99_G	103_A	1.193	0.99
86_I	160_T	1.189	0.99
39_G	61_N	1.185	0.99
38_I	57_V	1.182	0.99
155_T	163_L	1.178	0.99
46_L	54_A	1.170	0.99
42_A	57_V	1.166	0.99
41_L	57_V	1.148	0.99
153_G	188_T	1.146	0.99
174_F	178_A	1.144	0.99
14_L	70_A	1.141	0.99
55_L	165_V	1.138	0.99
45_F	50_W	1.137	0.99
44_P	47_A	1.129	0.99
21_L	24_P	1.114	0.99
173_W	176_W	1.104	0.99
33_L	37_A	1.099	0.99
90_F	160_T	1.098	0.99
90_F	157_G	1.096	0.99
42_A	96_V	1.096	0.99
59_L	62_R	1.092	0.99
119_F	178_A	1.081	0.99
67_L	70_A	1.072	0.99
50_W	53_A	1.069	0.99
47_A	102_L	1.064	0.99
116_L	119_F	1.048	0.98
12_P	16_Q	1.043	0.98
101_I	112_G	1.042	0.98
87_S	132_L	1.040	0.98
86_I	133_A	1.039	0.98
163_L	167_G	1.028	0.98
62_R	157_G	1.022	0.98
149_Y	152_G	1.005	0.98
93_Y	157_G	0.993	0.98
180_I	184_L	0.986	0.98
48_L	51_Y	0.970	0.97
179_W	183_A	0.968	0.97
127_L	130_A	0.967	0.97
66_G	158_T	0.966	0.97
187_M	191_T	0.961	0.97
28_P	46_L	0.951	0.97
20_V	41_L	0.947	0.97
46_L	103_A	0.939	0.97
45_F	48_L	0.934	0.97
17_C	67_L	0.933	0.97
38_I	64_L	0.923	0.96
121_G	125_S	0.922	0.96
59_L	63_L	0.920	0.96
176_W	179_W	0.920	0.96
85_D	157_G	0.920	0.96
90_F	131_A	0.917	0.96
41_L	45_F	0.916	0.96
157_G	160_T	0.911	0.96
190_F	194_W	0.903	0.96
153_G	192_R	0.898	0.96
148_F	199_T	0.896	0.96
155_T	181_F	0.891	0.96
62_R	66_G	0.891	0.96
122_T	125_S	0.882	0.95
32_T	88_L	0.881	0.95
131_A	135_K	0.878	0.95
7_H	11_K	0.876	0.95
188_T	191_T	0.876	0.95
38_I	61_N	0.872	0.95
61_N	85_D	0.859	0.95
94_A	128_A	0.854	0.94
182_G	186_W	0.852	0.94
153_G	159_E	0.847	0.94
86_I	135_K	0.847	0.94
16_Q	19_R	0.839	0.94
78_T	167_G	0.838	0.94
91_L	128_A	0.824	0.93
186_W	189_T	0.822	0.93
144_A	147_S	0.819	0.93
192_R	196_G	0.818	0.93
83_F	132_L	0.807	0.93
133_A	151_L	0.807	0.93
7_H	18_V	0.806	0.93
154_L	159_E	0.802	0.92
13_L	16_Q	0.801	0.92
53_A	57_V	0.794	0.92
30_G	34_V	0.794	0.92
82_G	147_S	0.791	0.92
126_F	131_A	0.786	0.92
174_F	180_I	0.784	0.92
175_A	178_A	0.781	0.91
126_F	129_F	0.781	0.91
51_Y	103_A	0.763	0.90
100_F	174_F	0.762	0.90
82_G	86_I	0.761	0.90
101_I	114_W	0.757	0.90
125_S	130_A	0.756	0.90
15_H	74_R	0.755	0.90
10_I	158_T	0.753	0.90
42_A	46_L	0.753	0.90
172_A	180_I	0.749	0.90
112_G	115_L	0.747	0.89
61_N	92_F	0.744	0.89
158_T	162_L	0.743	0.89
100_F	103_A	0.741	0.89
26_I	30_G	0.740	0.89
177_F	181_F	0.740	0.89
175_A	179_W	0.739	0.89
129_F	188_T	0.737	0.89
94_A	127_L	0.732	0.89
61_N	65_D	0.730	0.88
65_D	157_G	0.725	0.88
29_D	197_Y	0.720	0.88
130_A	134_A	0.719	0.88
187_M	190_F	0.719	0.88
84_L	88_L	0.719	0.88
58_I	66_G	0.717	0.87
59_L	165_V	0.712	0.87
129_F	135_K	0.711	0.87
83_F	144_A	0.709	0.87
29_D	77_L	0.699	0.86
172_A	175_A	0.698	0.86
36_F	91_L	0.697	0.86
154_L	157_G	0.696	0.86
24_P	75_R	0.693	0.86
144_A	150_Y	0.692	0.86
91_L	189_T	0.690	0.85
11_K	18_V	0.687	0.85
11_K	15_H	0.686	0.85
54_A	168_C	0.679	0.85
83_F	196_G	0.677	0.84
14_L	66_G	0.675	0.84
61_N	157_G	0.667	0.83
51_Y	99_G	0.664	0.83
126_F	133_A	0.659	0.83
174_F	177_F	0.658	0.83
121_G	186_W	0.658	0.83
114_W	118_A	0.655	0.82
52_L	169_L	0.654	0.82
29_D	194_W	0.652	0.82
91_L	131_A	0.647	0.82
65_D	86_I	0.647	0.82
62_R	159_E	0.645	0.81
163_L	181_F	0.639	0.81
90_F	192_R	0.638	0.81
119_F	122_T	0.631	0.80
85_D	154_L	0.631	0.80
136_H	196_G	0.631	0.80
62_R	90_F	0.630	0.80
62_R	165_V	0.630	0.80
156_E	159_E	0.624	0.79
82_G	146_K	0.621	0.79
42_A	58_I	0.621	0.79
144_A	148_F	0.621	0.79
195_S	199_T	0.617	0.78
173_W	182_G	0.616	0.78
108_N	113_G	0.615	0.78
30_G	79_D	0.613	0.78
179_W	190_F	0.609	0.78
114_W	179_W	0.608	0.77
66_G	159_E	0.607	0.77
9_R	12_P	0.606	0.77
151_L	156_E	0.603	0.77
128_A	133_A	0.601	0.77
182_G	185_C	0.600	0.77
41_L	56_V	0.598	0.76
133_A	156_E	0.598	0.76
115_L	119_F	0.596	0.76
10_I	14_L	0.594	0.76
153_G	158_T	0.593	0.76
64_L	67_L	0.589	0.75
48_L	53_A	0.582	0.74
8_P	12_P	0.582	0.74
167_G	170_F	0.581	0.74
165_V	168_C	0.580	0.74
46_L	164_F	0.578	0.74
185_C	188_T	0.577	0.74
55_L	169_L	0.576	0.74
41_L	102_L	0.574	0.73
42_A	45_F	0.572	0.73
157_G	161_I	0.571	0.73
28_P	173_W	0.566	0.72
172_A	179_W	0.564	0.72
86_I	156_E	0.556	0.71
131_A	136_H	0.556	0.71
15_H	19_R	0.553	0.71
34_V	38_I	0.549	0.70
32_T	58_I	0.549	0.70
61_N	86_I	0.544	0.69
41_L	44_P	0.543	0.69
123_G	130_A	0.543	0.69
64_L	78_T	0.540	0.69
65_D	154_L	0.536	0.68
86_I	157_G	0.534	0.68
130_A	154_L	0.533	0.68
124_S	127_L	0.532	0.68
10_I	66_G	0.532	0.68
51_Y	54_A	0.531	0.67
19_R	169_L	0.530	0.67
80_A	83_F	0.529	0.67
175_A	183_A	0.529	0.67
36_F	40_V	0.528	0.67
56_V	60_L	0.527	0.67
78_T	159_E	0.525	0.67
118_A	121_G	0.520	0.66
10_I	70_A	0.518	0.66
86_I	90_F	0.518	0.66
27_T	77_L	0.517	0.65
54_A	100_F	0.515	0.65
193_V	196_G	0.513	0.65
11_K	14_L	0.512	0.65
146_K	150_Y	0.511	0.65
86_I	93_Y	0.510	0.64
87_S	193_V	0.506	0.64
12_P	23_K	0.504	0.63
177_F	180_I	0.504	0.63
58_I	61_N	0.503	0.63
122_T	130_A	0.501	0.63
7_H	35_G	0.500	0.63

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	0.932	100	0.362	Contact Map
4mndA	2	0.8981	99.9	0.453	Contact Map
4tq3A	1	0.8738	15.4	0.94	Contact Map
4od4A	1	0.9175	14.5	0.941	Contact Map
4leuA	1	0.335	10.4	0.944	Contact Map
4bw5A	2	0.5534	4.9	0.952	Contact Map
4twkA	2	0.5728	3.8	0.955	Contact Map
3j1rA	5	0.1262	3.7	0.955	Contact Map
4bwzA	2	0.8932	3.5	0.956	Contact Map
2gfpA	2	0.8058	3.4	0.956	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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