YRBG - BACSU - GREMLIN Contacts

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YRBG - UPF0702 transmembrane protein YrbG

UniProt:	O32050	Sequences: MEELLTIAFRTVVLYFVILVIFRFMGKREIGELSILDLVVFIMMAEIAVLAIENVDDHLFHTILPMLVLMIIQVTLAYFSLKNRKVRQLLDGKPTIIIKYGKIDEEAMKSQRYNFDDLMVQLRENSIDRVADVSFAILEPSGKLTIVKKENSGEHRQLEMPLIIDGFIQTENLSRISKDRKWLLESLQKHGYTNPSDISFCSFTDGEIYIDEKDGHRT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	218 (209)
Sequences:	1744 (1429)
Seq/√Len:	98.9

ECOLI - YCAP
BACSU - YRBG YETF YDFS YKJA YDFR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
186_S	189_K	7.192	1.00
170_T	180_R	7.057	1.00
132_D	152_S	4.157	1.00
95_T	107_A	3.727	1.00
127_I	148_K	3.459	1.00
192_Y	198_I	3.453	1.00
86_V	90_L	3.231	1.00
27_K	95_T	3.230	1.00
129_R	132_D	2.771	1.00
88_Q	93_K	2.724	1.00
192_Y	212_E	2.551	1.00
104_D	107_A	2.483	1.00
99_K	104_D	2.320	1.00
168_I	195_P	2.310	1.00
95_T	111_Q	2.307	1.00
122_L	133_V	2.245	1.00
178_K	182_W	2.205	1.00
124_E	143_K	2.163	1.00
168_I	183_L	2.121	1.00
127_I	133_V	2.006	1.00
100_Y	134_S	2.004	1.00
163_I	201_C	1.975	1.00
21_I	70_M	1.968	1.00
132_D	148_K	1.874	1.00
17_V	63_I	1.862	1.00
103_I	118_L	1.816	1.00
122_L	146_I	1.806	1.00
128_D	147_V	1.789	1.00
8_A	64_L	1.785	1.00
187_L	192_Y	1.768	1.00
180_R	184_L	1.745	1.00
98_I	118_L	1.744	1.00
113_Y	121_Q	1.710	1.00
168_I	182_W	1.705	1.00
38_L	41_F	1.705	1.00
198_I	201_C	1.704	1.00
173_L	182_W	1.658	1.00
98_I	130_V	1.622	1.00
162_L	203_F	1.602	1.00
197_D	212_E	1.586	1.00
201_C	210_I	1.573	1.00
181_K	185_E	1.568	1.00
190_H	210_I	1.519	1.00
29_E	41_F	1.502	1.00
97_I	138_L	1.497	1.00
133_V	146_I	1.435	1.00
38_L	43_M	1.407	1.00
133_V	136_A	1.390	0.99
87_R	116_D	1.375	0.99
134_S	149_K	1.338	0.99
168_I	184_L	1.327	0.99
168_I	173_L	1.311	0.99
8_A	68_V	1.304	0.99
14_L	52_I	1.267	0.99
103_I	130_V	1.255	0.99
187_L	191_G	1.253	0.99
84_R	88_Q	1.233	0.99
187_L	198_I	1.223	0.99
105_E	199_S	1.219	0.99
124_E	141_S	1.204	0.98
4_L	64_L	1.180	0.98
105_E	211_D	1.179	0.98
87_R	114_N	1.176	0.98
153_G	156_R	1.173	0.98
54_N	57_D	1.170	0.98
129_R	202_S	1.168	0.98
107_A	110_S	1.161	0.98
15_Y	72_I	1.145	0.98
79_F	86_V	1.135	0.98
188_Q	193_T	1.129	0.98
160_M	172_N	1.125	0.98
14_L	69_L	1.122	0.98
115_F	199_S	1.122	0.98
108_M	118_L	1.113	0.97
148_K	153_G	1.113	0.97
173_L	183_L	1.108	0.97
187_L	208_I	1.105	0.97
127_I	146_I	1.103	0.97
182_W	186_S	1.101	0.97
11_T	68_V	1.101	0.97
126_S	148_K	1.096	0.97
193_T	197_D	1.086	0.97
64_L	68_V	1.077	0.97
105_E	213_K	1.076	0.97
187_L	210_I	1.063	0.97
43_M	46_E	1.061	0.97
173_L	178_K	1.056	0.97
50_L	53_E	1.050	0.96
201_C	208_I	1.044	0.96
163_I	198_I	1.043	0.96
111_Q	138_L	1.038	0.96
19_L	36_L	1.027	0.96
98_I	122_L	1.027	0.96
162_L	208_I	1.026	0.96
22_F	43_M	1.021	0.96
7_I	61_H	1.014	0.96
102_K	211_D	1.014	0.96
97_I	113_Y	0.999	0.95
76_L	90_L	0.998	0.95
35_I	43_M	0.992	0.95
150_E	153_G	0.984	0.95
41_F	45_A	0.980	0.95
121_Q	144_L	0.979	0.95
163_I	195_P	0.975	0.95
98_I	136_A	0.956	0.94
13_V	17_V	0.950	0.94
29_E	38_L	0.943	0.94
186_S	190_H	0.941	0.94
169_Q	172_N	0.938	0.93
181_K	184_L	0.938	0.93
52_I	69_L	0.937	0.93
13_V	59_L	0.936	0.93
83_N	86_V	0.934	0.93
161_P	164_I	0.933	0.93
81_L	114_N	0.923	0.93
23_R	112_R	0.920	0.93
190_H	208_I	0.909	0.92
40_V	69_L	0.898	0.92
179_D	182_W	0.891	0.92
97_I	108_M	0.887	0.91
11_T	73_Q	0.886	0.91
113_Y	138_L	0.885	0.91
115_F	164_I	0.874	0.91
97_I	124_E	0.871	0.91
22_F	41_F	0.859	0.90
151_N	155_H	0.852	0.90
103_I	108_M	0.850	0.89
15_Y	76_L	0.844	0.89
114_N	117_D	0.843	0.89
161_P	200_F	0.840	0.89
12_V	72_I	0.836	0.89
171_E	174_S	0.823	0.88
113_Y	117_D	0.823	0.88
11_T	53_E	0.819	0.88
31_G	45_A	0.817	0.88
20_V	89_L	0.815	0.87
47_I	66_M	0.813	0.87
138_L	144_L	0.811	0.87
13_V	57_D	0.808	0.87
35_I	41_F	0.803	0.87
30_I	33_L	0.800	0.86
19_L	45_A	0.792	0.86
50_L	54_N	0.785	0.85
22_F	35_I	0.783	0.85
125_N	143_K	0.783	0.85
46_E	50_L	0.782	0.85
184_L	188_Q	0.772	0.84
27_K	111_Q	0.770	0.84
22_F	38_L	0.769	0.84
134_S	150_E	0.764	0.84
85_K	88_Q	0.760	0.84
173_L	180_R	0.760	0.84
187_L	195_P	0.757	0.83
75_T	79_F	0.755	0.83
94_P	135_F	0.752	0.83
29_E	33_L	0.746	0.82
63_I	67_L	0.745	0.82
5_L	9_F	0.744	0.82
94_P	137_I	0.743	0.82
162_L	183_L	0.742	0.82
51_A	62_T	0.742	0.82
181_K	193_T	0.742	0.82
17_V	64_L	0.735	0.81
78_Y	82_K	0.734	0.81
32_E	42_I	0.733	0.81
120_V	140_P	0.729	0.81
48_A	58_H	0.727	0.81
34_S	37_D	0.725	0.81
71_I	174_S	0.725	0.81
45_A	73_Q	0.719	0.80
96_I	137_I	0.716	0.80
97_I	136_A	0.712	0.79
25_M	74_V	0.712	0.79
28_R	73_Q	0.709	0.79
46_E	53_E	0.708	0.79
183_L	186_S	0.706	0.79
49_V	52_I	0.705	0.79
23_R	39_V	0.704	0.79
52_I	58_H	0.703	0.78
177_S	182_W	0.701	0.78
181_K	207_E	0.700	0.78
19_L	23_R	0.699	0.78
45_A	50_L	0.698	0.78
52_I	73_Q	0.696	0.78
19_L	72_I	0.696	0.78
42_I	45_A	0.695	0.78
203_F	207_E	0.694	0.78
25_M	77_A	0.692	0.77
162_L	176_I	0.690	0.77
45_A	53_E	0.688	0.77
70_M	74_V	0.687	0.77
4_L	7_I	0.686	0.77
32_E	38_L	0.682	0.76
40_V	73_Q	0.681	0.76
16_F	72_I	0.681	0.76
19_L	90_L	0.678	0.76
170_T	196_S	0.674	0.76
23_R	38_L	0.673	0.75
38_L	42_I	0.670	0.75
94_P	158_L	0.666	0.75
81_L	116_D	0.665	0.75
21_I	66_M	0.662	0.74
184_L	195_P	0.657	0.74
137_I	158_L	0.657	0.74
192_Y	195_P	0.653	0.73
37_D	111_Q	0.650	0.73
170_T	174_S	0.650	0.73
16_F	24_F	0.649	0.73
4_L	68_V	0.645	0.72
171_E	175_R	0.644	0.72
98_I	133_V	0.642	0.72
116_D	164_I	0.640	0.72
79_F	174_S	0.640	0.72
26_G	42_I	0.639	0.72
99_K	175_R	0.638	0.72
136_A	163_I	0.637	0.71
35_I	40_V	0.631	0.71
177_S	180_R	0.629	0.70
97_I	111_Q	0.628	0.70
33_L	121_Q	0.625	0.70
91_D	117_D	0.623	0.70
35_I	38_L	0.622	0.70
118_L	136_A	0.622	0.70
31_G	77_A	0.621	0.69
29_E	44_M	0.618	0.69
40_V	46_E	0.618	0.69
15_Y	23_R	0.618	0.69
174_S	188_Q	0.615	0.69
47_I	141_S	0.615	0.69
71_I	75_T	0.614	0.69
132_D	149_K	0.605	0.67
84_R	169_Q	0.598	0.67
97_I	118_L	0.596	0.66
31_G	73_Q	0.595	0.66
29_E	37_D	0.595	0.66
7_I	176_I	0.593	0.66
39_V	92_G	0.593	0.66
84_R	207_E	0.591	0.66
44_M	49_V	0.590	0.66
33_L	113_Y	0.590	0.66
74_V	112_R	0.586	0.65
33_L	91_D	0.585	0.65
53_E	73_Q	0.585	0.65
43_M	53_E	0.585	0.65
97_I	127_I	0.582	0.64
178_K	206_G	0.580	0.64
31_G	35_I	0.578	0.64
14_L	49_V	0.577	0.64
185_E	191_G	0.576	0.64
46_E	65_P	0.576	0.64
96_I	148_K	0.576	0.64
106_E	206_G	0.575	0.64
30_I	47_I	0.574	0.63
14_L	51_A	0.573	0.63
48_A	102_K	0.571	0.63
80_S	86_V	0.569	0.63
58_H	61_H	0.569	0.63
190_H	207_E	0.567	0.62
49_V	53_E	0.566	0.62
115_F	200_F	0.565	0.62
69_L	202_S	0.564	0.62
77_A	141_S	0.564	0.62
84_R	167_F	0.564	0.62
67_L	70_M	0.563	0.62
28_R	31_G	0.560	0.62
14_L	35_I	0.558	0.61
158_L	169_Q	0.557	0.61
17_V	67_L	0.554	0.61
24_F	74_V	0.554	0.61
167_F	199_S	0.553	0.61
18_I	35_I	0.550	0.60
32_E	41_F	0.550	0.60
125_N	206_G	0.549	0.60
41_F	50_L	0.543	0.59
69_L	114_N	0.543	0.59
82_K	110_S	0.541	0.59
186_S	208_I	0.540	0.59
29_E	117_D	0.539	0.59
18_I	36_L	0.538	0.58
99_K	102_K	0.537	0.58
40_V	50_L	0.536	0.58
130_V	200_F	0.535	0.58
44_M	118_L	0.532	0.58
40_V	77_A	0.532	0.58
54_N	77_A	0.532	0.58
103_I	183_L	0.530	0.57
27_K	34_S	0.529	0.57
70_M	121_Q	0.529	0.57
41_F	44_M	0.528	0.57
22_F	147_V	0.527	0.57
191_G	206_G	0.524	0.57
118_L	140_P	0.523	0.56
150_E	155_H	0.521	0.56
23_R	140_P	0.521	0.56
10_R	51_A	0.519	0.56
162_L	182_W	0.518	0.56
71_I	175_R	0.518	0.56
18_I	21_I	0.516	0.55
180_R	183_L	0.516	0.55
59_L	124_E	0.516	0.55
170_T	184_L	0.515	0.55
38_L	50_L	0.514	0.55
164_I	200_F	0.513	0.55
74_V	103_I	0.512	0.55
32_E	143_K	0.511	0.55
84_R	116_D	0.511	0.55
106_E	192_Y	0.511	0.55
6_T	130_V	0.510	0.55
130_V	152_S	0.508	0.54
46_E	49_V	0.507	0.54
16_F	20_V	0.505	0.54
171_E	196_S	0.504	0.54
23_R	62_T	0.503	0.54
25_M	137_I	0.500	0.53

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
3c6fA	4	0.5734	100	0.416	Contact Map
4b4aA	1	0.344	25.2	0.954	Contact Map
1tr8A	4	0.3303	8	0.963	Contact Map
3d6wA	3	0.1881	6.8	0.964	Contact Map
3iyzA	3	0.3578	5.7	0.965	Contact Map
1t44G	1	0.2156	5.3	0.966	Contact Map
4hvzA	5	0.3532	5.1	0.966	Contact Map
4i16A	1	0.3716	4.4	0.967	Contact Map
1whzA	1	0.3119	4.3	0.967	Contact Map
4pk1A	1	0.5872	4.3	0.967	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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