YSHE - BACSU - GREMLIN Contacts

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YSHE - UPF0719 transmembrane protein YshE

UniProt:	P94546	Sequences: MSDFWENELVEIAAYYSVAVLCLVLFLTVFELVTAYKNWEEIQKGNLAVAMATGGKILGIANVFQHSISQHNSLLQMIGWGVYGFVMLLISYFIFEFLTPRFKIDQEIENDNRAVGFISFVISVGLSFVVAAGI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	134 (124)
Sequences:	777 (547)
Seq/√Len:	49.1

ECOLI - YJFL
BACSU - YSHE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
107_E	112_N	4.673	1.00
54_G	121_V	4.119	1.00
120_F	124_V	3.064	1.00
51_M	120_F	2.983	1.00
49_V	108_I	2.904	1.00
37_K	40_E	2.890	1.00
103_K	106_Q	2.789	1.00
40_E	44_K	2.668	1.00
106_Q	110_N	2.615	1.00
59_G	127_S	2.585	1.00
62_N	127_S	2.581	1.00
55_G	116_G	2.401	1.00
63_V	84_G	2.326	1.00
51_M	116_G	2.118	1.00
68_I	133_G	2.027	1.00
66_H	70_Q	2.020	1.00
48_A	111_D	1.831	0.99
18_V	74_L	1.786	0.99
30_F	56_K	1.698	0.98
58_L	124_V	1.663	0.98
78_I	82_V	1.622	0.98
71_H	76_Q	1.613	0.98
51_M	113_R	1.609	0.98
111_D	114_A	1.564	0.97
22_C	81_G	1.549	0.97
68_I	77_M	1.501	0.96
63_V	127_S	1.455	0.96
15_Y	68_I	1.453	0.96
41_E	44_K	1.297	0.92
13_A	90_I	1.293	0.92
26_F	85_F	1.285	0.92
112_N	115_V	1.280	0.92
117_F	120_F	1.271	0.91
100_P	103_K	1.255	0.91
75_L	125_G	1.223	0.90
62_N	124_V	1.215	0.89
23_L	61_A	1.209	0.89
65_Q	128_F	1.205	0.89
76_Q	79_G	1.183	0.88
22_C	78_I	1.176	0.88
12_I	67_S	1.165	0.87
38_N	92_Y	1.155	0.87
14_A	74_L	1.150	0.87
26_F	60_I	1.129	0.85
104_I	115_V	1.112	0.85
90_I	93_F	1.110	0.84
56_K	130_V	1.082	0.83
117_F	121_V	1.075	0.83
18_V	21_L	1.071	0.82
62_N	65_Q	1.064	0.82
77_M	133_G	1.026	0.79
84_G	130_V	1.015	0.79
89_L	93_F	1.002	0.78
33_V	93_F	0.996	0.77
41_E	46_N	0.993	0.77
129_V	133_G	0.992	0.77
94_I	113_R	0.983	0.76
82_V	129_V	0.963	0.75
87_M	90_I	0.957	0.75
34_T	38_N	0.955	0.74
67_S	72_N	0.952	0.74
108_I	111_D	0.948	0.74
48_A	128_F	0.947	0.74
109_E	119_S	0.946	0.74
86_V	93_F	0.938	0.73
47_L	117_F	0.937	0.73
31_E	120_F	0.922	0.72
96_E	99_T	0.922	0.72
107_E	110_N	0.907	0.70
43_Q	132_A	0.907	0.70
36_Y	105_D	0.899	0.70
75_L	86_V	0.895	0.69
87_M	118_I	0.891	0.69
91_S	126_L	0.885	0.69
47_L	113_R	0.883	0.68
51_M	121_V	0.879	0.68
18_V	77_M	0.861	0.66
15_Y	71_H	0.861	0.66
18_V	78_I	0.852	0.66
34_T	80_W	0.852	0.66
27_L	57_I	0.838	0.64
17_S	98_L	0.837	0.64
21_L	86_V	0.827	0.63
126_L	130_V	0.822	0.63
36_Y	49_V	0.813	0.62
63_V	130_V	0.808	0.61
32_L	98_L	0.807	0.61
66_H	131_A	0.788	0.60
14_A	58_L	0.785	0.59
81_G	123_S	0.778	0.59
28_T	32_L	0.773	0.58
36_Y	107_E	0.769	0.58
63_V	88_L	0.767	0.57
105_D	128_F	0.767	0.57
70_Q	90_I	0.760	0.57
11_E	90_I	0.760	0.57
75_L	82_V	0.760	0.57
71_H	80_W	0.760	0.57
66_H	127_S	0.756	0.56
68_I	87_M	0.752	0.56
20_V	90_I	0.746	0.55
60_I	130_V	0.744	0.55
15_Y	91_S	0.734	0.54
30_F	84_G	0.733	0.54
78_I	81_G	0.727	0.53
16_Y	24_V	0.723	0.53
80_W	88_L	0.722	0.53
71_H	88_L	0.721	0.53
99_T	118_I	0.706	0.51
21_L	28_T	0.704	0.51
11_E	14_A	0.703	0.51
116_G	120_F	0.695	0.50
59_G	92_Y	0.695	0.50
67_S	83_Y	0.695	0.50
63_V	125_G	0.695	0.50
55_G	120_F	0.693	0.50
31_E	39_W	0.689	0.50
16_Y	26_F	0.689	0.50
26_F	56_K	0.680	0.49
38_N	125_G	0.678	0.48
105_D	108_I	0.664	0.47
48_A	118_I	0.663	0.47
10_V	82_V	0.660	0.47
13_A	75_L	0.658	0.46
40_E	94_I	0.655	0.46
44_K	58_L	0.652	0.46
59_G	88_L	0.647	0.45
50_A	70_Q	0.647	0.45
82_V	85_F	0.647	0.45
12_I	87_M	0.643	0.45
50_A	59_G	0.637	0.44
8_E	11_E	0.632	0.44
12_I	127_S	0.632	0.44
79_G	82_V	0.624	0.43
78_I	91_S	0.623	0.43
17_S	53_T	0.622	0.43
107_E	115_V	0.621	0.43
82_V	86_V	0.620	0.43
95_F	99_T	0.617	0.42
41_E	127_S	0.607	0.41
50_A	96_E	0.605	0.41
32_L	53_T	0.604	0.41
79_G	98_L	0.599	0.41
52_A	105_D	0.597	0.40
16_Y	121_V	0.588	0.39
49_V	115_V	0.585	0.39
76_Q	83_Y	0.584	0.39
106_Q	109_E	0.582	0.39
89_L	98_L	0.581	0.39
64_F	81_G	0.578	0.39
51_M	108_I	0.577	0.38
54_G	78_I	0.577	0.38
36_Y	126_L	0.575	0.38
72_N	76_Q	0.574	0.38
12_I	15_Y	0.571	0.38
60_I	85_F	0.567	0.37
12_I	133_G	0.564	0.37
74_L	78_I	0.559	0.37
41_E	130_V	0.556	0.36
9_L	37_K	0.555	0.36
11_E	58_L	0.555	0.36
58_L	128_F	0.549	0.36
86_V	113_R	0.548	0.36
57_I	104_I	0.548	0.36
39_W	98_L	0.546	0.35
124_V	129_V	0.546	0.35
41_E	88_L	0.545	0.35
57_I	116_G	0.541	0.35
57_I	94_I	0.539	0.35
60_I	77_M	0.539	0.35
18_V	25_L	0.535	0.34
59_G	123_S	0.532	0.34
20_V	23_L	0.529	0.34
117_F	128_F	0.529	0.34
95_F	119_S	0.522	0.33
37_K	42_I	0.516	0.33
67_S	89_L	0.509	0.32
15_Y	76_Q	0.509	0.32
21_L	47_L	0.508	0.32
29_V	36_Y	0.507	0.32
68_I	132_A	0.507	0.32
47_L	128_F	0.507	0.32
81_G	129_V	0.504	0.32
96_E	116_G	0.503	0.32
42_I	111_D	0.500	0.31
21_L	29_V	0.500	0.31

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
4he8H	1	0.8657	8.2	0.931	Contact Map
4n7wA	2	0.7388	6	0.935	Contact Map
3qnqA	2	0.3433	5.7	0.936	Contact Map
1rh1A	1	0.7537	3.5	0.942	Contact Map
2xq2A	2	0.3209	3.4	0.943	Contact Map
4z7fA	2	0.7239	3.1	0.944	Contact Map
4o93A	2	0.6716	2.5	0.946	Contact Map
3giaA	1	0.7015	2.2	0.948	Contact Map
3l1lA	2	0.6716	2.2	0.948	Contact Map
3zuxA	1	0.6866	2.1	0.948	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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