YPMB - BACSU - GREMLIN Contacts

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YPMB - Uncharacterized protein YpmB

UniProt:	P54396	Sequences: MRKKALIFTVIFGIIFLAVLLVSASIYKSAMAQKEEGHEAAAAEAKKETDLAHVDQVETFVGKEKYYVVKGTDKKGTALYVWVPADKKAKILSKEAKEGISEDKAAKIIKDEGLVSKQKEVHLAREGNVLLWEVTYLDKEGQYSLSYVDFTTGKILKNITP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	161 (150)
Sequences:	406 (347)
Seq/√Len:	28.3

BACSU - YPMB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
99_G	150_F	6.558	1.00
109_I	134_V	4.389	1.00
149_D	152_T	3.853	1.00
105_A	121_V	3.308	1.00
102_E	106_A	3.287	1.00
105_A	148_V	2.945	1.00
100_I	105_A	2.924	1.00
68_V	82_W	2.804	1.00
73_D	77_T	2.326	0.99
124_A	145_L	2.293	0.99
80_Y	96_A	2.253	0.98
51_L	81_V	2.211	0.98
60_F	133_E	2.041	0.97
62_G	147_Y	2.038	0.97
37_G	57_V	1.955	0.96
62_G	133_E	1.939	0.96
129_V	149_D	1.908	0.95
126_E	147_Y	1.864	0.95
82_W	94_K	1.857	0.95
51_L	79_L	1.839	0.94
53_H	72_T	1.814	0.94
123_L	130_L	1.754	0.93
147_Y	156_L	1.681	0.91
125_R	130_L	1.672	0.91
81_V	150_F	1.545	0.87
60_F	126_E	1.518	0.86
44_E	91_I	1.506	0.86
83_V	91_I	1.454	0.84
58_E	70_K	1.388	0.81
30_A	123_L	1.376	0.80
64_E	98_E	1.315	0.77
19_V	134_V	1.313	0.77
41_A	57_V	1.313	0.77
42_A	69_V	1.310	0.76
73_D	79_L	1.305	0.76
124_A	133_E	1.302	0.76
76_G	100_I	1.294	0.76
62_G	82_W	1.286	0.75
62_G	126_E	1.272	0.74
106_A	110_K	1.257	0.73
52_A	74_K	1.250	0.73
62_G	131_L	1.242	0.73
9_T	14_I	1.222	0.71
57_V	83_V	1.212	0.71
48_E	141_G	1.195	0.70
137_L	145_L	1.185	0.69
82_W	147_Y	1.166	0.68
7_I	11_I	1.164	0.67
43_A	47_K	1.162	0.67
99_G	123_L	1.160	0.67
123_L	150_F	1.160	0.67
126_E	157_K	1.150	0.67
74_K	90_K	1.136	0.66
57_V	69_V	1.126	0.65
100_I	104_K	1.115	0.64
74_K	139_K	1.108	0.64
60_F	66_Y	1.097	0.63
124_A	131_L	1.089	0.62
135_T	144_S	1.077	0.61
59_T	82_W	1.065	0.60
60_F	124_A	1.054	0.60
146_S	158_N	1.051	0.59
138_D	144_S	1.050	0.59
109_I	150_F	1.049	0.59
113_G	116_S	1.014	0.57
37_G	65_K	1.006	0.56
102_E	121_V	1.000	0.56
136_Y	146_S	0.979	0.54
77_T	95_E	0.964	0.53
21_L	25_S	0.960	0.52
106_A	118_Q	0.952	0.52
46_K	61_V	0.949	0.52
54_V	78_A	0.949	0.52
37_G	67_Y	0.944	0.51
100_I	148_V	0.943	0.51
137_L	152_T	0.939	0.51
109_I	116_S	0.937	0.51
70_K	80_Y	0.935	0.51
103_D	114_L	0.934	0.50
66_Y	83_V	0.929	0.50
126_E	131_L	0.926	0.50
27_Y	46_K	0.920	0.49
18_A	60_F	0.915	0.49
68_V	124_A	0.908	0.48
138_D	142_Q	0.905	0.48
49_T	71_G	0.899	0.48
10_V	47_K	0.893	0.47
15_I	148_V	0.891	0.47
80_Y	123_L	0.887	0.47
110_K	118_Q	0.883	0.47
18_A	74_K	0.877	0.46
106_A	152_T	0.874	0.46
109_I	113_G	0.871	0.46
11_I	63_K	0.866	0.45
41_A	83_V	0.860	0.45
136_Y	143_Y	0.860	0.45
107_K	110_K	0.855	0.44
120_E	135_T	0.855	0.44
129_V	156_L	0.850	0.44
82_W	123_L	0.850	0.44
135_T	143_Y	0.844	0.44
119_K	143_Y	0.839	0.43
50_D	73_D	0.837	0.43
39_E	43_A	0.836	0.43
97_K	134_V	0.834	0.43
8_F	15_I	0.833	0.43
16_F	95_E	0.829	0.42
52_A	107_K	0.827	0.42
61_V	142_Q	0.821	0.42
86_D	139_K	0.816	0.41
103_D	141_G	0.815	0.41
97_K	101_S	0.814	0.41
51_L	71_G	0.811	0.41
33_Q	93_S	0.791	0.40
30_A	150_F	0.788	0.39
79_L	93_S	0.785	0.39
94_K	123_L	0.770	0.38
20_L	124_A	0.769	0.38
7_I	148_V	0.768	0.38
92_L	125_R	0.758	0.37
105_A	134_V	0.753	0.37
104_K	117_K	0.750	0.37
10_V	16_F	0.748	0.36
138_D	147_Y	0.742	0.36
66_Y	119_K	0.742	0.36
62_G	68_V	0.741	0.36
80_Y	131_L	0.740	0.36
95_E	98_E	0.739	0.36
58_E	143_Y	0.738	0.36
122_H	146_S	0.736	0.36
119_K	137_L	0.733	0.35
42_A	46_K	0.731	0.35
46_K	49_T	0.731	0.35
61_V	158_N	0.730	0.35
131_L	156_L	0.729	0.35
62_G	122_H	0.729	0.35
31_M	35_E	0.726	0.35
22_V	27_Y	0.725	0.35
51_L	70_K	0.722	0.35
92_L	103_D	0.722	0.35
73_D	157_K	0.716	0.34
73_D	116_S	0.706	0.34
155_I	158_N	0.704	0.33
71_G	81_V	0.697	0.33
45_A	99_G	0.695	0.33
56_Q	118_Q	0.690	0.32
56_Q	151_T	0.689	0.32
137_L	143_Y	0.686	0.32
9_T	16_F	0.683	0.32
113_G	136_Y	0.680	0.32
41_A	45_A	0.678	0.32
104_K	108_I	0.674	0.31
31_M	80_Y	0.671	0.31
110_K	117_K	0.668	0.31
131_L	147_Y	0.667	0.31
27_Y	104_K	0.661	0.30
9_T	17_L	0.649	0.30
94_K	137_L	0.647	0.30
16_F	39_E	0.644	0.29
31_M	125_R	0.641	0.29
57_V	82_W	0.640	0.29
81_V	93_S	0.636	0.29
7_I	10_V	0.632	0.29
113_G	158_N	0.632	0.29
46_K	156_L	0.628	0.28
44_E	48_E	0.626	0.28
30_A	99_G	0.620	0.28
147_Y	155_I	0.619	0.28
56_Q	102_E	0.618	0.28
101_S	121_V	0.618	0.28
21_L	58_E	0.616	0.28
114_L	137_L	0.611	0.27
10_V	20_L	0.610	0.27
19_V	95_E	0.610	0.27
33_Q	99_G	0.607	0.27
116_S	139_K	0.606	0.27
69_V	128_N	0.605	0.27
55_D	154_K	0.603	0.27
36_E	72_T	0.603	0.27
44_E	83_V	0.602	0.27
107_K	141_G	0.599	0.27
52_A	76_G	0.598	0.27
100_I	108_I	0.597	0.26
90_K	100_I	0.595	0.26
22_V	26_I	0.587	0.26
52_A	72_T	0.586	0.26
94_K	151_T	0.585	0.26
78_A	137_L	0.585	0.26
21_L	120_E	0.583	0.26
67_Y	122_H	0.577	0.25
10_V	23_S	0.576	0.25
100_I	134_V	0.576	0.25
94_K	125_R	0.575	0.25
115_V	137_L	0.573	0.25
66_Y	91_I	0.571	0.25
133_E	147_Y	0.568	0.25
43_A	148_V	0.567	0.25
40_A	55_D	0.559	0.24
27_Y	136_Y	0.557	0.24
41_A	157_K	0.553	0.24
92_L	96_A	0.553	0.24
16_F	75_K	0.549	0.24
32_A	36_E	0.544	0.23
37_G	158_N	0.542	0.23
38_H	109_I	0.541	0.23
115_V	136_Y	0.540	0.23
84_P	87_K	0.540	0.23
143_Y	157_K	0.539	0.23
122_H	133_E	0.535	0.23
70_K	78_A	0.535	0.23
16_F	68_V	0.530	0.23
80_Y	144_S	0.529	0.23
132_W	153_G	0.528	0.23
81_V	84_P	0.523	0.22
68_V	94_K	0.523	0.22
38_H	59_T	0.518	0.22
59_T	67_Y	0.517	0.22
39_E	72_T	0.512	0.22
61_V	132_W	0.508	0.21
27_Y	83_V	0.506	0.21
91_I	107_K	0.504	0.21
124_A	150_F	0.503	0.21
6_L	10_V	0.502	0.21
112_E	148_V	0.501	0.21
57_V	67_Y	0.500	0.21

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
2gu3A	1	0.795	100	0.246	Contact Map
4exrA	2	0.8199	99	0.745	Contact Map
2kgyA	1	0.5404	72.3	0.912	Contact Map
2o3oA	2	0.9503	56.7	0.921	Contact Map
4k90B	1	0.882	41	0.928	Contact Map
4ml1A	4	0.2795	34.3	0.931	Contact Map
3nqzA	1	0.8323	30.4	0.933	Contact Map
1rz2A	1	0.7578	19.8	0.939	Contact Map
1yr2A	1	0.6025	18.1	0.939	Contact Map
1t3bA	2	0.3416	15.8	0.941	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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