YSHB - BACSU - GREMLIN Contacts

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YSHB - Uncharacterized transmembrane protein YshB

UniProt:	P94543	Sequences: MLDIIILILLLMGTLLGLKRGFILQFIRLTSFILSIAFAALFYKNVAPHLHWIPAPDFSAGQPALSFFTGNLEAAYYNAIAFIVLFIIAKILLRIIGSFLSIVAGIPVIKQINQMLGAVLGFLEVYLFTFVLLYVASVLPVDALQQMMGQSSLANVIINHTPYLSGLLQELWTQYGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	177 (166)
Sequences:	652 (571)
Seq/√Len:	44.3

ECOLI - CVPA
BACSU - YSHB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_F	116_L	5.065	1.00
14_T	118_A	3.943	1.00
13_G	125_V	3.565	1.00
38_F	89_A	3.249	1.00
126_Y	130_F	2.522	1.00
107_P	113_N	2.495	1.00
126_Y	157_I	2.412	1.00
126_Y	161_T	2.379	1.00
148_M	158_I	2.369	1.00
46_V	85_L	2.299	1.00
35_S	89_A	2.257	1.00
27_I	97_G	2.257	1.00
151_S	154_A	2.237	1.00
104_A	113_N	1.988	0.99
157_I	161_T	1.986	0.99
13_G	121_G	1.974	0.99
54_P	77_Y	1.917	0.99
9_L	13_G	1.872	0.99
30_T	34_L	1.859	0.99
101_S	113_N	1.832	0.99
14_T	122_F	1.832	0.99
111_Q	114_Q	1.826	0.99
85_L	89_A	1.771	0.98
67_F	137_S	1.743	0.98
85_L	88_I	1.644	0.97
9_L	125_V	1.615	0.97
90_K	93_L	1.581	0.96
31_S	93_L	1.511	0.95
46_V	84_V	1.488	0.95
48_P	79_A	1.483	0.95
6_I	153_L	1.476	0.95
76_Y	80_I	1.429	0.94
130_F	164_L	1.428	0.94
7_L	156_V	1.411	0.93
27_I	100_L	1.398	0.93
3_D	153_L	1.395	0.93
44_K	67_F	1.394	0.93
29_L	128_F	1.386	0.93
104_A	110_K	1.379	0.92
11_L	110_K	1.372	0.92
31_S	89_A	1.369	0.92
7_L	83_I	1.368	0.92
33_I	83_I	1.367	0.92
49_H	132_L	1.361	0.92
106_I	109_I	1.330	0.91
67_F	72_L	1.312	0.90
47_A	81_A	1.311	0.90
100_L	123_L	1.294	0.90
46_V	95_I	1.290	0.90
129_T	153_L	1.288	0.90
3_D	154_A	1.281	0.89
29_L	132_L	1.276	0.89
85_L	100_L	1.261	0.89
130_F	161_T	1.254	0.88
37_A	41_L	1.250	0.88
17_G	21_G	1.235	0.87
28_R	101_S	1.233	0.87
127_L	159_N	1.213	0.86
13_G	79_A	1.207	0.86
133_L	157_I	1.204	0.86
130_F	157_I	1.201	0.86
44_K	166_G	1.183	0.85
23_I	104_A	1.178	0.85
140_P	145_Q	1.170	0.84
113_N	117_G	1.164	0.84
107_P	117_G	1.152	0.83
3_D	152_S	1.149	0.83
132_L	155_N	1.145	0.83
136_A	144_L	1.143	0.83
10_L	13_G	1.137	0.83
68_F	135_V	1.134	0.83
86_F	89_A	1.125	0.82
20_R	25_Q	1.119	0.82
84_V	123_L	1.115	0.81
10_L	129_T	1.114	0.81
33_I	37_A	1.114	0.81
39_A	162_P	1.102	0.81
4_I	8_I	1.086	0.80
29_L	32_F	1.086	0.80
22_F	117_G	1.081	0.79
66_S	69_T	1.080	0.79
25_Q	31_S	1.059	0.78
26_F	158_I	1.051	0.77
93_L	115_M	1.051	0.77
94_R	101_S	1.048	0.77
21_G	117_G	1.046	0.77
30_T	96_I	1.039	0.77
83_I	87_I	1.037	0.76
137_S	148_M	1.029	0.76
42_F	45_N	1.028	0.76
39_A	82_F	1.013	0.75
78_N	121_G	1.003	0.74
27_I	93_L	0.999	0.74
56_P	76_Y	0.989	0.73
16_L	119_V	0.980	0.72
35_S	42_F	0.972	0.72
38_F	90_K	0.970	0.71
112_I	116_L	0.966	0.71
112_I	117_G	0.956	0.70
82_F	162_P	0.954	0.70
25_Q	97_G	0.953	0.70
133_L	161_T	0.949	0.70
27_I	31_S	0.948	0.70
110_K	131_V	0.938	0.69
25_Q	120_L	0.934	0.69
7_L	135_V	0.932	0.68
46_V	49_H	0.926	0.68
162_P	165_S	0.916	0.67
3_D	48_P	0.910	0.67
9_L	118_A	0.904	0.66
111_Q	115_M	0.900	0.66
16_L	19_K	0.894	0.65
95_I	99_F	0.886	0.64
55_A	59_S	0.883	0.64
104_A	107_P	0.883	0.64
9_L	76_Y	0.862	0.62
9_L	132_L	0.858	0.62
45_N	48_P	0.839	0.60
29_L	73_E	0.834	0.60
67_F	71_N	0.824	0.59
4_I	31_S	0.823	0.59
8_I	70_G	0.816	0.58
50_L	81_A	0.816	0.58
156_V	160_H	0.812	0.58
35_S	86_F	0.796	0.56
34_L	123_L	0.791	0.56
5_I	30_T	0.788	0.55
109_I	121_G	0.788	0.55
43_Y	78_N	0.784	0.55
85_L	120_L	0.776	0.54
8_I	84_V	0.776	0.54
90_K	94_R	0.773	0.54
37_A	156_V	0.773	0.54
24_L	28_R	0.771	0.54
22_F	107_P	0.760	0.53
56_P	73_E	0.756	0.52
93_L	124_E	0.750	0.52
32_F	93_L	0.749	0.52
30_T	93_L	0.746	0.51
70_G	127_L	0.745	0.51
54_P	81_A	0.743	0.51
48_P	131_V	0.736	0.50
10_L	122_F	0.735	0.50
61_G	157_I	0.734	0.50
73_E	77_Y	0.731	0.50
130_F	133_L	0.731	0.50
11_L	84_V	0.727	0.49
70_G	84_V	0.726	0.49
132_L	136_A	0.722	0.49
58_F	97_G	0.720	0.49
34_L	81_A	0.720	0.49
3_D	14_T	0.719	0.49
127_L	156_V	0.717	0.49
34_L	44_K	0.711	0.48
136_A	148_M	0.710	0.48
152_S	156_V	0.707	0.48
135_V	157_I	0.696	0.47
28_R	90_K	0.694	0.46
88_I	155_N	0.690	0.46
11_L	27_I	0.689	0.46
22_F	136_A	0.682	0.45
77_Y	140_P	0.681	0.45
107_P	111_Q	0.678	0.45
76_Y	165_S	0.676	0.45
110_K	113_N	0.672	0.44
136_A	149_G	0.671	0.44
123_L	163_Y	0.665	0.44
126_Y	164_L	0.664	0.43
3_D	79_A	0.662	0.43
129_T	146_Q	0.658	0.43
32_F	124_E	0.650	0.42
96_I	152_S	0.650	0.42
103_V	139_L	0.635	0.41
20_R	24_L	0.632	0.40
122_F	147_M	0.631	0.40
38_F	135_V	0.624	0.40
81_A	96_I	0.623	0.40
41_L	148_M	0.620	0.39
46_V	134_Y	0.620	0.39
117_G	130_F	0.617	0.39
13_G	124_E	0.616	0.39
163_Y	167_L	0.615	0.39
59_S	63_P	0.614	0.39
38_F	85_L	0.613	0.39
119_V	122_F	0.608	0.38
72_L	155_N	0.608	0.38
113_N	156_V	0.606	0.38
3_D	72_L	0.606	0.38
86_F	90_K	0.600	0.38
50_L	84_V	0.600	0.38
72_L	79_A	0.599	0.37
12_M	16_L	0.597	0.37
42_F	85_L	0.596	0.37
4_I	119_V	0.595	0.37
92_L	164_L	0.595	0.37
23_I	138_V	0.595	0.37
80_I	119_V	0.592	0.37
151_S	165_S	0.591	0.37
135_V	152_S	0.587	0.36
89_A	104_A	0.587	0.36
67_F	164_L	0.585	0.36
78_N	116_L	0.585	0.36
12_M	42_F	0.583	0.36
6_I	29_L	0.581	0.36
42_F	53_I	0.578	0.36
23_I	32_F	0.577	0.35
87_I	132_L	0.574	0.35
136_A	147_M	0.574	0.35
73_E	95_I	0.574	0.35
26_F	150_Q	0.571	0.35
74_A	78_N	0.568	0.35
14_T	18_L	0.566	0.34
20_R	28_R	0.562	0.34
72_L	83_I	0.559	0.34
37_A	159_N	0.557	0.34
3_D	151_S	0.554	0.33
18_L	32_F	0.554	0.33
41_L	92_L	0.553	0.33
3_D	35_S	0.553	0.33
40_A	82_F	0.545	0.33
24_L	130_F	0.544	0.33
115_M	132_L	0.542	0.32
4_I	88_I	0.540	0.32
12_M	127_L	0.531	0.32
18_L	103_V	0.528	0.31
11_L	91_I	0.527	0.31
35_S	127_L	0.524	0.31
45_N	96_I	0.522	0.31
54_P	58_F	0.522	0.31
135_V	148_M	0.521	0.31
91_I	121_G	0.519	0.31
82_F	100_L	0.517	0.30
5_I	129_T	0.515	0.30
7_L	142_D	0.514	0.30
10_L	126_Y	0.514	0.30
33_I	132_L	0.513	0.30
122_F	126_Y	0.513	0.30
60_A	64_A	0.511	0.30
34_L	89_A	0.510	0.30
43_Y	154_A	0.510	0.30
125_V	167_L	0.509	0.30
84_V	163_Y	0.506	0.29
25_Q	140_P	0.505	0.29
111_Q	163_Y	0.505	0.29
69_T	84_V	0.504	0.29
137_S	144_L	0.504	0.29
132_L	141_V	0.503	0.29
109_I	112_I	0.501	0.29
50_L	75_A	0.500	0.29

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
2zy9A	2	0.4802	6.9	0.945	Contact Map
2kluA	1	0.3729	4.7	0.949	Contact Map
3hzqA	3	0.4576	2.1	0.957	Contact Map
3j01B	1	0.548	1.8	0.959	Contact Map
2hi2A	1	0.3107	1.7	0.959	Contact Map
1ji6A	1	0.4237	1.6	0.96	Contact Map
2kwtA	1	0.0847	1.5	0.961	Contact Map
3sokA	1	0.2938	1.4	0.962	Contact Map
3j9pD	4	0.7684	1.2	0.963	Contact Map
4u9nA	2	0.4746	1.1	0.964	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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