YFJF - BACSU - GREMLIN Contacts

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YFJF - UPF0060 membrane protein YfjF

UniProt:	O31553	Sequences: MMLITILLFLAAGLAEIGGGYLVWLWLREAKPAGYGIAGALILIVYGILPTFQSFPSFGRVYAAYGGVFIVLAVLWGWLVDRKTPDLYDWIGAFICLIGVCVILFAPRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	109 (105)
Sequences:	1114 (524)
Seq/√Len:	51.1

ECOLI - YNFA
BACSU - YFJF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
95_I	102_V	6.897	1.00
78_W	85_P	3.676	1.00
27_L	51_T	3.275	1.00
70_I	96_C	3.202	1.00
40_A	44_I	2.865	1.00
97_L	101_C	2.332	1.00
58_F	81_D	2.159	1.00
13_G	72_L	2.032	1.00
100_V	104_L	1.922	0.99
88_Y	107_P	1.840	0.99
90_W	94_F	1.790	0.99
87_L	90_W	1.726	0.99
62_Y	77_G	1.725	0.99
31_K	70_I	1.671	0.98
23_V	47_G	1.667	0.98
34_G	37_I	1.648	0.98
71_V	93_A	1.639	0.98
21_Y	25_L	1.604	0.98
61_V	81_D	1.565	0.98
15_A	42_I	1.529	0.97
8_L	11_A	1.502	0.97
8_L	15_A	1.438	0.96
88_Y	106_A	1.390	0.95
10_L	71_V	1.387	0.95
46_Y	69_F	1.367	0.95
26_W	36_G	1.366	0.95
10_L	72_L	1.322	0.94
28_R	39_G	1.300	0.93
47_G	58_F	1.245	0.91
27_L	64_A	1.233	0.91
75_L	79_L	1.224	0.91
74_V	93_A	1.220	0.90
74_V	100_V	1.217	0.90
87_L	91_I	1.170	0.88
15_A	49_L	1.167	0.88
22_L	61_V	1.164	0.88
68_V	101_C	1.164	0.88
57_S	83_K	1.159	0.88
58_F	61_V	1.109	0.86
42_I	50_P	1.101	0.85
42_I	45_V	1.093	0.85
101_C	105_F	1.079	0.84
91_I	102_V	1.078	0.84
58_F	69_F	1.063	0.83
14_L	75_L	1.034	0.81
93_A	101_C	1.026	0.81
14_L	18_G	1.016	0.80
84_T	87_L	1.004	0.79
10_L	14_L	0.997	0.79
50_P	69_F	0.994	0.79
46_Y	58_F	0.983	0.78
78_W	84_T	0.974	0.77
86_D	108_R	0.973	0.77
91_I	98_I	0.965	0.77
9_F	25_L	0.964	0.77
31_K	35_Y	0.961	0.76
11_A	14_L	0.951	0.76
9_F	22_L	0.949	0.75
50_P	77_G	0.949	0.75
36_G	40_A	0.944	0.75
46_Y	50_P	0.936	0.74
85_P	107_P	0.929	0.74
37_I	102_V	0.918	0.73
20_G	50_P	0.915	0.73
26_W	32_P	0.912	0.72
23_V	31_K	0.906	0.72
52_F	57_S	0.892	0.71
96_C	99_G	0.882	0.70
13_G	20_G	0.876	0.69
18_G	39_G	0.874	0.69
64_A	68_V	0.858	0.68
96_C	100_V	0.850	0.67
94_F	98_I	0.841	0.66
53_Q	61_V	0.837	0.66
20_G	42_I	0.825	0.65
35_Y	42_I	0.809	0.63
12_A	17_I	0.808	0.63
46_Y	77_G	0.802	0.63
78_W	89_D	0.797	0.62
29_E	39_G	0.793	0.62
64_A	104_L	0.788	0.61
74_V	103_I	0.784	0.61
22_L	81_D	0.781	0.60
20_G	69_F	0.780	0.60
23_V	53_Q	0.778	0.60
73_A	100_V	0.765	0.59
58_F	72_L	0.750	0.57
9_F	49_L	0.750	0.57
41_L	45_V	0.744	0.57
69_F	77_G	0.741	0.56
20_G	62_Y	0.736	0.56
85_P	108_R	0.736	0.56
47_G	69_F	0.736	0.56
74_V	82_R	0.735	0.56
86_D	106_A	0.727	0.55
86_D	107_P	0.726	0.55
20_G	46_Y	0.723	0.55
13_G	40_A	0.700	0.52
25_L	73_A	0.686	0.51
27_L	45_V	0.684	0.51
17_I	73_A	0.683	0.50
25_L	31_K	0.682	0.50
90_W	103_I	0.679	0.50
23_V	40_A	0.675	0.50
27_L	48_I	0.672	0.49
67_G	93_A	0.671	0.49
24_W	28_R	0.658	0.48
5_T	15_A	0.658	0.48
33_A	37_I	0.657	0.48
59_G	104_L	0.656	0.48
24_W	61_V	0.652	0.47
85_P	105_F	0.641	0.46
22_L	108_R	0.632	0.45
22_L	25_L	0.631	0.45
4_I	41_L	0.631	0.45
40_A	73_A	0.630	0.45
29_E	71_V	0.621	0.44
31_K	47_G	0.616	0.44
34_G	38_A	0.612	0.43
95_I	98_I	0.604	0.42
79_L	103_I	0.604	0.42
4_I	15_A	0.602	0.42
35_Y	50_P	0.596	0.42
12_A	53_Q	0.590	0.41
12_A	72_L	0.589	0.41
98_I	101_C	0.584	0.40
23_V	44_I	0.583	0.40
12_A	24_W	0.579	0.40
39_G	86_D	0.578	0.40
51_T	61_V	0.578	0.40
94_F	102_V	0.574	0.39
68_V	97_L	0.573	0.39
40_A	54_S	0.569	0.39
6_I	91_I	0.568	0.39
49_L	71_V	0.559	0.38
90_W	93_A	0.558	0.38
11_A	49_L	0.557	0.38
4_I	7_L	0.556	0.38
11_A	73_A	0.556	0.38
7_L	49_L	0.552	0.37
56_P	83_K	0.550	0.37
70_I	100_V	0.544	0.36
84_T	98_I	0.541	0.36
8_L	54_S	0.540	0.36
92_G	99_G	0.536	0.36
55_F	104_L	0.535	0.36
7_L	90_W	0.528	0.35
25_L	102_V	0.527	0.35
53_Q	69_F	0.525	0.35
18_G	73_A	0.521	0.34
27_L	36_G	0.517	0.34
8_L	53_Q	0.516	0.34
8_L	52_F	0.515	0.34
45_V	101_C	0.507	0.33
85_P	96_C	0.506	0.33
25_L	29_E	0.505	0.33
7_L	68_V	0.505	0.33
24_W	39_G	0.500	0.32

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
2i68A	2	0.6972	95.9	0.86	Contact Map
3b5dA	2	0.9174	94.5	0.871	Contact Map
4q65A	1	0.7431	25.7	0.932	Contact Map
4tphA	2	0.7523	25.5	0.932	Contact Map
3o7qA	1	1	14.7	0.939	Contact Map
4pypA	1	0.7156	13.2	0.941	Contact Map
4uvmA	1	0.7982	13	0.941	Contact Map
4m64A	1	0.9725	12.6	0.941	Contact Map
2cfqA	1	0.7798	12.4	0.941	Contact Map
3wajA	1	0.9358	10.8	0.943	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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