YPMS - BACSU - GREMLIN Contacts

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YPMS - Uncharacterized protein YpmS

UniProt:	P54179	Sequences: MNKWKRLFFILLAINFILAAGFVALVLLPGEQAQVKDASESEYGFQVTSTKESLAAFVNSYLNDKASNKLDYKVEIDDDVHVAGKIKAFSTSIDAFIAFEPTVKKNGDVELNVTKFSLGKLSIPISFVLNYMDSFYELPSFVHVHPGDKSIEVRLSEMPLTNGMYVKADKINLEKDEIEFSYYHPKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	187 (181)
Sequences:	300 (250)
Seq/√Len:	18.6

BACSU - YPMS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
172_N	175_K	4.630	1.00
109_V	171_I	4.034	1.00
12_L	15_N	3.715	1.00
170_K	177_E	2.899	0.99
169_D	181_S	2.862	0.99
173_L	178_I	2.815	0.98
108_D	156_S	2.809	0.98
55_A	59_N	2.687	0.98
118_L	121_L	2.613	0.97
43_Y	181_S	2.459	0.96
8_F	11_L	2.342	0.95
145_H	148_D	2.333	0.95
26_V	149_K	2.286	0.94
55_A	72_Y	2.246	0.94
61_Y	136_Y	2.187	0.93
76_I	178_I	2.166	0.93
62_L	167_K	2.131	0.92
72_Y	142_V	2.130	0.92
125_I	149_K	2.095	0.91
9_F	13_A	1.995	0.89
70_L	114_T	1.960	0.88
128_V	168_A	1.922	0.87
107_G	111_L	1.909	0.87
145_H	150_S	1.856	0.85
138_L	151_I	1.847	0.85
8_F	12_L	1.805	0.83
113_V	171_I	1.759	0.82
70_L	177_E	1.678	0.79
7_L	133_D	1.667	0.78
49_S	170_K	1.663	0.78
108_D	154_R	1.657	0.78
3_K	7_L	1.636	0.77
23_V	145_H	1.636	0.77
10_I	18_L	1.634	0.77
84_G	136_Y	1.586	0.74
40_E	109_V	1.586	0.74
36_K	148_D	1.548	0.73
107_G	124_P	1.538	0.72
61_Y	131_Y	1.524	0.71
30_G	96_F	1.523	0.71
113_V	152_E	1.505	0.70
113_V	129_L	1.464	0.68
62_L	165_Y	1.459	0.68
16_F	26_V	1.457	0.68
51_K	176_D	1.415	0.65
123_I	127_F	1.405	0.65
7_L	15_N	1.387	0.64
53_S	89_F	1.371	0.63
45_F	123_I	1.351	0.62
85_K	92_S	1.347	0.62
47_V	86_I	1.333	0.61
20_A	37_D	1.327	0.60
19_A	33_A	1.303	0.59
23_V	77_D	1.303	0.59
143_H	157_E	1.296	0.58
104_K	108_D	1.287	0.58
84_G	151_I	1.273	0.57
58_V	182_Y	1.261	0.56
38_A	75_E	1.258	0.56
54_L	74_V	1.236	0.55
72_Y	136_Y	1.236	0.55
77_D	81_H	1.226	0.54
131_Y	142_V	1.221	0.54
153_V	156_S	1.214	0.53
59_N	109_V	1.211	0.53
57_F	116_F	1.198	0.52
111_L	119_G	1.149	0.49
102_T	114_T	1.141	0.49
71_D	153_V	1.133	0.48
102_T	110_E	1.122	0.48
49_S	153_V	1.119	0.47
123_I	139_P	1.117	0.47
99_F	139_P	1.108	0.47
99_F	111_L	1.107	0.47
36_K	63_N	1.103	0.46
78_D	110_E	1.076	0.45
110_E	152_E	1.072	0.45
18_L	24_A	1.064	0.44
13_A	154_R	1.063	0.44
50_T	53_S	1.039	0.43
125_I	182_Y	1.036	0.42
76_I	153_V	1.031	0.42
55_A	123_I	1.023	0.42
49_S	89_F	1.020	0.41
126_S	144_V	1.006	0.41
84_G	95_A	1.002	0.40
169_D	182_Y	1.000	0.40
26_V	130_N	0.998	0.40
50_T	144_V	0.997	0.40
47_V	161_T	0.996	0.40
58_V	72_Y	0.995	0.40
74_V	113_V	0.987	0.39
23_V	27_L	0.985	0.39
4_W	8_F	0.982	0.39
125_I	129_L	0.977	0.39
22_F	63_N	0.975	0.39
12_L	34_Q	0.962	0.38
50_T	81_H	0.960	0.38
34_Q	62_L	0.959	0.38
49_S	53_S	0.958	0.38
116_F	125_I	0.940	0.37
111_L	173_L	0.940	0.37
107_G	178_I	0.935	0.36
134_S	162_N	0.933	0.36
47_V	182_Y	0.924	0.36
39_S	73_K	0.900	0.34
113_V	141_F	0.900	0.34
105_K	157_E	0.899	0.34
114_T	182_Y	0.890	0.34
53_S	113_V	0.887	0.34
70_L	153_V	0.885	0.33
104_K	164_M	0.883	0.33
33_A	37_D	0.882	0.33
53_S	171_I	0.880	0.33
49_S	95_A	0.880	0.33
36_K	40_E	0.876	0.33
44_G	49_S	0.870	0.33
60_S	106_N	0.865	0.32
54_L	117_S	0.854	0.32
112_N	146_P	0.851	0.32
80_V	146_P	0.845	0.31
58_V	76_I	0.843	0.31
12_L	177_E	0.829	0.30
158_M	163_G	0.827	0.30
46_Q	50_T	0.819	0.30
22_F	144_V	0.818	0.30
11_L	77_D	0.799	0.29
123_I	179_E	0.799	0.29
49_S	181_S	0.794	0.29
140_S	177_E	0.790	0.28
13_A	22_F	0.787	0.28
45_F	152_E	0.785	0.28
94_D	116_F	0.783	0.28
30_G	78_D	0.783	0.28
97_I	153_V	0.776	0.28
16_F	88_A	0.775	0.28
132_M	136_Y	0.771	0.27
92_S	105_K	0.766	0.27
83_A	94_D	0.765	0.27
107_G	173_L	0.760	0.27
20_A	23_V	0.758	0.27
41_S	149_K	0.747	0.26
89_F	153_V	0.746	0.26
27_L	164_M	0.746	0.26
83_A	128_V	0.743	0.26
34_Q	93_I	0.740	0.26
58_V	151_I	0.738	0.26
22_F	170_K	0.738	0.26
40_E	140_S	0.734	0.26
167_K	183_Y	0.733	0.26
138_L	175_K	0.730	0.25
10_I	46_Q	0.728	0.25
79_D	106_N	0.723	0.25
58_V	74_V	0.720	0.25
53_S	109_V	0.719	0.25
50_T	60_S	0.717	0.25
51_K	61_Y	0.705	0.24
99_F	183_Y	0.701	0.24
40_E	58_V	0.701	0.24
139_P	168_A	0.699	0.24
62_L	71_D	0.696	0.24
77_D	163_G	0.695	0.24
53_S	152_E	0.693	0.24
7_L	108_D	0.691	0.24
26_V	54_L	0.689	0.24
16_F	33_A	0.684	0.23
49_S	86_I	0.678	0.23
5_K	95_A	0.677	0.23
99_F	146_P	0.674	0.23
54_L	158_M	0.674	0.23
143_H	154_R	0.673	0.23
51_K	177_E	0.671	0.23
5_K	111_L	0.670	0.23
32_Q	79_D	0.660	0.22
3_K	6_R	0.658	0.22
70_L	85_K	0.658	0.22
109_V	131_Y	0.657	0.22
12_L	115_K	0.656	0.22
57_F	98_A	0.655	0.22
87_K	148_D	0.654	0.22
41_S	63_N	0.653	0.22
131_Y	136_Y	0.651	0.22
97_I	177_E	0.650	0.22
5_K	9_F	0.650	0.22
55_A	182_Y	0.647	0.22
126_S	160_L	0.646	0.22
79_D	93_I	0.643	0.22
96_F	117_S	0.643	0.22
54_L	180_F	0.642	0.22
100_E	104_K	0.641	0.21
110_E	150_S	0.641	0.21
76_I	168_A	0.639	0.21
17_I	140_S	0.639	0.21
82_V	88_A	0.638	0.21
7_L	77_D	0.636	0.21
140_S	157_E	0.635	0.21
50_T	178_I	0.632	0.21
97_I	113_V	0.627	0.21
6_R	13_A	0.626	0.21
88_A	142_V	0.623	0.21
55_A	95_A	0.622	0.21
97_I	118_L	0.621	0.21
3_K	9_F	0.621	0.21
94_D	139_P	0.618	0.21
112_N	140_S	0.617	0.20
17_I	175_K	0.614	0.20
7_L	47_V	0.614	0.20
84_G	117_S	0.613	0.20
19_A	151_I	0.611	0.20
62_L	157_E	0.610	0.20
42_E	172_N	0.609	0.20
62_L	105_K	0.607	0.20
36_K	62_L	0.604	0.20
65_K	97_I	0.598	0.20
3_K	12_L	0.598	0.20
108_D	155_L	0.598	0.20
14_I	172_N	0.597	0.20
10_I	14_I	0.596	0.20
84_G	142_V	0.595	0.20
75_E	144_V	0.595	0.20
4_W	11_L	0.595	0.20
64_D	135_F	0.594	0.20
111_L	124_P	0.594	0.20
159_P	165_Y	0.583	0.19
11_L	48_T	0.583	0.19
18_L	176_D	0.579	0.19
82_V	86_I	0.576	0.19
20_A	48_T	0.575	0.19
42_E	135_F	0.574	0.19
11_L	178_I	0.572	0.19
87_K	97_I	0.571	0.19
78_D	97_I	0.566	0.18
58_V	153_V	0.566	0.18
54_L	147_G	0.565	0.18
27_L	76_I	0.562	0.18
146_P	166_V	0.562	0.18
168_A	180_F	0.560	0.18
95_A	158_M	0.559	0.18
114_T	157_E	0.555	0.18
94_D	125_I	0.554	0.18
27_L	45_F	0.553	0.18
139_P	142_V	0.550	0.18
78_D	182_Y	0.546	0.18
71_D	134_S	0.545	0.18
99_F	155_L	0.543	0.18
96_F	171_I	0.542	0.18
53_S	66_A	0.539	0.17
130_N	134_S	0.536	0.17
44_G	151_I	0.536	0.17
31_E	130_N	0.533	0.17
113_V	125_I	0.532	0.17
13_A	102_T	0.532	0.17
59_N	116_F	0.531	0.17
102_T	112_N	0.529	0.17
71_D	84_G	0.526	0.17
47_V	57_F	0.523	0.17
80_V	154_R	0.521	0.17
21_G	133_D	0.521	0.17
27_L	182_Y	0.521	0.17
16_F	69_K	0.516	0.17
110_E	123_I	0.516	0.17
70_L	80_V	0.516	0.17
74_V	80_V	0.515	0.17
51_K	107_G	0.514	0.17
15_N	28_L	0.514	0.17
15_N	19_A	0.513	0.17
58_V	166_V	0.510	0.16
44_G	181_S	0.507	0.16
10_I	69_K	0.506	0.16
154_R	164_M	0.506	0.16
59_N	82_V	0.506	0.16
6_R	90_S	0.500	0.16

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
1q8kA	1	0.4064	8.6	0.958	Contact Map
4uu4A	1	0.6631	8.6	0.958	Contact Map
2g8sA	2	0.2941	8.2	0.958	Contact Map
1pfoA	2	0.5401	8.1	0.958	Contact Map
4tphA	2	0.1765	7.6	0.959	Contact Map
1twyA	5	0.7059	7.2	0.959	Contact Map
3aevA	1	0.3636	7.1	0.959	Contact Map
4nngA	1	0.4171	7	0.959	Contact Map
1wi5A	1	0.4439	6.4	0.96	Contact Map
3cw2C	1	0.3957	6.2	0.96	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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