YLME - BACSU - GREMLIN Contacts

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YLME - UPF0001 protein YlmE

UniProt:	O31727	Sequences: MRVVDNLRHINERINEACNRSGRSSDEVTVIAVTKYVSPERAQEAVDAGITCLGENRDAELLRKQELMKGNPEWHFIGSLQSRKAKSVVNSVSYIHSLDRLSLAKEIEKRAEGTVRCFVQVNTSLEPSKHGMKKEEVIPFIQELSGFEHILVAGLMTMAPLTDDQDQIRSCFRSLRELRDQVQKLNQPNAPCTELSMGMSNDFEIAIEEGATYIRIGSSLVGNETGGVQQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	230 (218)
Sequences:	4678 (3309)
Seq/√Len:	224.1

ECOLI - YGGS
BACSU - YLME

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_C	73_E	3.495	1.00
116_R	151_L	3.316	1.00
108_E	149_H	2.800	1.00
169_R	209_E	2.789	1.00
13_R	204_E	2.778	1.00
37_V	41_R	2.585	1.00
79_S	130_H	2.550	1.00
82_S	102_S	2.512	1.00
176_R	180_D	2.472	1.00
132_M	140_F	2.361	1.00
18_C	28_V	2.322	1.00
116_R	153_A	2.237	1.00
43_Q	47_D	2.157	1.00
105_K	143_E	2.094	1.00
61_L	92_V	2.076	1.00
173_R	209_E	2.072	1.00
101_L	143_E	2.029	1.00
14_I	30_V	1.941	1.00
20_R	208_E	1.927	1.00
194_E	212_T	1.899	1.00
33_V	77_I	1.872	1.00
31_I	213_Y	1.851	1.00
106_E	110_R	1.844	1.00
106_E	109_K	1.830	1.00
169_R	208_E	1.827	1.00
13_R	203_F	1.807	1.00
51_T	71_N	1.697	1.00
98_L	107_I	1.690	1.00
46_V	51_T	1.665	1.00
46_V	72_P	1.664	1.00
14_I	207_I	1.656	1.00
11_N	25_S	1.654	1.00
155_L	195_L	1.628	1.00
43_Q	70_G	1.628	1.00
18_C	26_D	1.626	1.00
101_L	105_K	1.622	1.00
29_T	194_E	1.609	1.00
29_T	52_C	1.601	1.00
34_T	53_L	1.598	1.00
179_R	183_Q	1.597	1.00
38_S	41_R	1.596	1.00
108_E	148_E	1.589	1.00
94_Y	118_F	1.586	1.00
216_I	219_S	1.579	1.00
12_E	16_E	1.564	1.00
200_S	219_S	1.549	1.00
153_A	193_T	1.549	1.00
108_E	147_F	1.529	1.00
112_E	149_H	1.513	1.00
96_H	213_Y	1.512	1.00
114_T	151_L	1.507	1.00
111_A	115_V	1.493	1.00
138_I	181_Q	1.445	1.00
110_R	113_G	1.445	1.00
123_T	175_L	1.423	1.00
118_F	194_E	1.398	1.00
80_L	88_V	1.392	1.00
24_S	27_E	1.390	1.00
157_T	175_L	1.389	1.00
32_A	50_I	1.376	1.00
98_L	117_C	1.336	1.00
164_D	167_Q	1.336	1.00
143_E	146_G	1.335	1.00
104_A	147_F	1.325	1.00
134_K	178_L	1.323	1.00
119_V	140_F	1.322	1.00
176_R	209_E	1.310	1.00
104_A	144_L	1.293	1.00
58_D	76_F	1.273	1.00
121_V	137_V	1.272	1.00
125_L	133_K	1.271	1.00
136_E	139_P	1.269	1.00
119_V	141_I	1.265	1.00
73_E	93_S	1.239	1.00
194_E	213_Y	1.236	1.00
123_T	171_C	1.232	1.00
139_P	142_Q	1.229	1.00
7_L	11_N	1.216	1.00
46_V	53_L	1.214	1.00
85_A	103_L	1.202	1.00
63_R	67_L	1.198	1.00
176_R	179_R	1.185	1.00
16_E	19_N	1.182	1.00
89_V	115_V	1.180	1.00
15_N	19_N	1.178	1.00
31_I	52_C	1.173	1.00
41_R	44_E	1.169	1.00
10_I	216_I	1.169	1.00
141_I	152_V	1.163	1.00
125_L	135_E	1.158	1.00
46_V	71_N	1.144	1.00
174_S	177_E	1.139	1.00
82_S	100_R	1.138	1.00
134_K	174_S	1.136	1.00
65_Q	91_S	1.130	1.00
39_P	67_L	1.118	1.00
160_P	171_C	1.108	1.00
108_E	112_E	1.107	1.00
8_R	12_E	1.100	1.00
45_A	48_A	1.098	1.00
43_Q	68_M	1.097	1.00
59_A	83_R	1.094	1.00
76_F	88_V	1.080	1.00
20_R	204_E	1.069	1.00
58_D	80_L	1.059	1.00
65_Q	92_V	1.041	1.00
32_A	220_L	1.040	1.00
28_V	207_I	1.029	1.00
155_L	182_V	1.029	1.00
100_R	103_L	1.026	1.00
201_N	218_S	1.025	1.00
18_C	25_S	1.019	1.00
141_I	182_V	1.019	1.00
132_M	137_V	1.016	1.00
18_C	24_S	1.011	1.00
31_I	96_H	1.009	1.00
62_L	87_S	1.008	1.00
105_K	147_F	1.006	1.00
58_D	62_L	1.003	1.00
173_R	177_E	1.001	1.00
189_N	192_C	0.997	1.00
118_F	153_A	0.995	1.00
61_L	65_Q	0.987	1.00
45_A	220_L	0.981	1.00
118_F	213_Y	0.979	1.00
7_L	50_I	0.968	1.00
119_V	132_M	0.962	1.00
175_L	179_R	0.960	1.00
42_A	53_L	0.954	1.00
133_K	136_E	0.947	1.00
138_I	142_Q	0.947	1.00
155_L	178_L	0.946	1.00
105_K	109_K	0.946	1.00
177_E	181_Q	0.944	1.00
17_A	21_S	0.942	1.00
93_S	116_R	0.940	1.00
18_C	27_E	0.936	1.00
95_I	107_I	0.936	1.00
88_V	92_V	0.934	1.00
162_T	167_Q	0.932	1.00
29_T	213_Y	0.932	1.00
82_S	106_E	0.932	1.00
165_Q	205_I	0.928	1.00
169_R	205_I	0.925	1.00
121_V	178_L	0.923	1.00
82_S	103_L	0.923	1.00
168_I	205_I	0.918	0.99
39_P	68_M	0.906	0.99
95_I	98_L	0.903	0.99
12_E	15_N	0.898	0.99
28_V	214_I	0.893	0.99
79_S	99_D	0.892	0.99
7_L	45_A	0.889	0.99
11_N	15_N	0.887	0.99
62_L	91_S	0.885	0.99
9_H	13_R	0.882	0.99
104_A	150_I	0.879	0.99
170_S	174_S	0.874	0.99
36_Y	57_R	0.857	0.99
144_L	152_V	0.846	0.99
16_E	20_R	0.844	0.99
36_Y	56_N	0.844	0.99
94_Y	213_Y	0.840	0.99
162_T	168_I	0.836	0.99
85_A	106_E	0.832	0.99
66_E	91_S	0.828	0.99
122_N	125_L	0.824	0.99
94_Y	116_R	0.824	0.99
37_V	223_N	0.823	0.99
18_C	23_R	0.817	0.99
165_Q	168_I	0.816	0.99
99_D	103_L	0.812	0.99
123_T	157_T	0.808	0.99
98_L	140_F	0.807	0.99
15_N	18_C	0.805	0.99
137_V	178_L	0.805	0.99
68_M	72_P	0.800	0.99
138_I	182_V	0.797	0.99
137_V	155_L	0.797	0.99
94_Y	153_A	0.794	0.99
85_A	107_I	0.792	0.99
58_D	88_V	0.787	0.98
205_I	209_E	0.782	0.98
31_I	211_A	0.782	0.98
30_V	216_I	0.781	0.98
124_S	171_C	0.780	0.98
182_V	192_C	0.777	0.98
205_I	208_E	0.777	0.98
23_R	27_E	0.769	0.98
105_K	146_G	0.766	0.98
57_R	97_S	0.766	0.98
39_P	42_A	0.763	0.98
29_T	73_E	0.762	0.98
98_L	103_L	0.762	0.98
180_D	183_Q	0.760	0.98
151_L	191_P	0.758	0.98
34_T	221_V	0.755	0.98
88_V	91_S	0.753	0.98
117_C	150_I	0.753	0.98
75_H	94_Y	0.752	0.98
126_E	129_K	0.752	0.98
19_N	25_S	0.752	0.98
86_K	110_R	0.749	0.98
120_Q	158_M	0.741	0.98
181_Q	184_K	0.738	0.98
80_L	103_L	0.735	0.98
124_S	160_P	0.735	0.98
58_D	87_S	0.732	0.98
85_A	89_V	0.729	0.97
137_V	182_V	0.724	0.97
76_F	80_L	0.723	0.97
207_I	214_I	0.720	0.97
79_S	100_R	0.717	0.97
172_F	197_M	0.712	0.97
111_A	114_T	0.712	0.97
15_N	25_S	0.706	0.97
45_A	221_V	0.704	0.97
43_Q	67_L	0.699	0.97
183_Q	193_T	0.694	0.97
101_L	147_F	0.690	0.96
34_T	50_I	0.686	0.96
42_A	68_M	0.684	0.96
203_F	207_I	0.682	0.96
139_P	143_E	0.682	0.96
5_D	8_R	0.680	0.96
165_Q	170_S	0.679	0.96
153_A	194_E	0.668	0.96
157_T	197_M	0.660	0.95
95_I	115_V	0.659	0.95
52_C	96_H	0.653	0.95
109_K	113_G	0.650	0.95
23_R	26_D	0.650	0.95
123_T	174_S	0.649	0.95
36_Y	225_T	0.648	0.95
46_V	68_M	0.645	0.95
90_N	115_V	0.644	0.95
58_D	61_L	0.643	0.95
44_E	47_D	0.643	0.95
54_G	77_I	0.643	0.95
143_E	147_F	0.640	0.95
50_I	53_L	0.638	0.95
130_H	158_M	0.638	0.95
36_Y	60_E	0.637	0.94
9_H	12_E	0.631	0.94
43_Q	69_K	0.631	0.94
183_Q	192_C	0.628	0.94
53_L	72_P	0.627	0.94
61_L	88_V	0.625	0.94
94_Y	194_E	0.624	0.94
6_N	9_H	0.624	0.94
141_I	192_C	0.622	0.94
60_E	224_E	0.620	0.94
85_A	110_R	0.620	0.94
142_Q	145_S	0.619	0.94
14_I	28_V	0.619	0.94
45_A	50_I	0.617	0.93
124_S	159_A	0.616	0.93
179_R	192_C	0.607	0.93
124_S	157_T	0.606	0.93
39_P	64_K	0.605	0.93
13_R	219_S	0.601	0.93
98_L	104_A	0.600	0.93
87_S	90_N	0.595	0.92
169_R	173_R	0.594	0.92
55_E	64_K	0.589	0.92
25_S	28_V	0.588	0.92
34_T	64_K	0.586	0.92
75_H	96_H	0.586	0.92
142_Q	188_P	0.584	0.92
7_L	220_L	0.582	0.91
39_P	43_Q	0.577	0.91
161_L	201_N	0.575	0.91
17_A	204_E	0.575	0.91
112_E	148_E	0.575	0.91
80_L	95_I	0.572	0.91
40_E	67_L	0.567	0.90
65_Q	69_K	0.567	0.90
60_E	64_K	0.566	0.90
8_R	11_N	0.566	0.90
158_M	199_M	0.562	0.90
40_E	43_Q	0.561	0.90
125_L	134_K	0.561	0.90
23_R	28_V	0.560	0.90
145_S	189_N	0.559	0.90
180_D	184_K	0.559	0.90
138_I	178_L	0.559	0.90
119_V	137_V	0.557	0.90
121_V	175_L	0.557	0.90
83_R	87_S	0.556	0.89
65_Q	74_W	0.555	0.89
10_I	17_A	0.553	0.89
102_S	105_K	0.550	0.89
57_R	158_M	0.550	0.89
36_Y	42_A	0.549	0.89
132_M	136_E	0.549	0.89
21_S	24_S	0.549	0.89
134_K	138_I	0.547	0.89
58_D	92_V	0.546	0.89
159_A	171_C	0.544	0.88
121_V	132_M	0.543	0.88
107_I	150_I	0.543	0.88
177_E	180_D	0.538	0.88
37_V	218_S	0.536	0.88
32_A	221_V	0.534	0.87
101_L	140_F	0.533	0.87
123_T	134_K	0.533	0.87
98_L	119_V	0.532	0.87
53_L	74_W	0.529	0.87
17_A	207_I	0.528	0.87
179_R	212_T	0.528	0.87
138_I	141_I	0.528	0.87
10_I	219_S	0.526	0.87
13_R	17_A	0.523	0.86
10_I	203_F	0.518	0.86
5_D	9_H	0.518	0.86
101_L	139_P	0.517	0.86
166_D	170_S	0.516	0.86
168_I	171_C	0.513	0.85
203_F	219_S	0.511	0.85
218_S	222_G	0.506	0.85
183_Q	188_P	0.504	0.84
34_T	57_R	0.503	0.84
17_A	20_R	0.503	0.84
16_E	204_E	0.502	0.84
117_C	153_A	0.501	0.84
34_T	74_W	0.501	0.84
164_D	169_R	0.500	0.84

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
3cpgA	1	0.9609	100	0.52	Contact Map
1ct5A	1	0.8826	100	0.522	Contact Map
3sy1A	1	0.9565	100	0.525	Contact Map
3r79A	2	0.9478	100	0.537	Contact Map
1bd0A	2	0.9391	100	0.639	Contact Map
3e5pA	2	0.9435	100	0.64	Contact Map
4bhyA	2	0.8522	100	0.641	Contact Map
4beuA	2	0.9609	100	0.641	Contact Map
4a3qA	2	0.9	100	0.642	Contact Map
3kw3A	2	0.9261	100	0.644	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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