YNGC - BACSU - GREMLIN Contacts

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YNGC - Uncharacterized membrane protein YngC

UniProt:	O31823	Sequences: MGSLISEILTWLTNMGYAGIAIGLMIEIIPSEIVLAYGGYMVSEGTIGFIGAIIAGVIGGTIAQIFIYWIGRYGGRPFLDKYGKYLLIKKHHIDMSENWFQKYGAGVVFSARFIPVVRHAISIPAGIARMPFLKFVVLTVLAIIPWSILFVYLGIQLGSQWDDVENIAGTYTTPIMILAVVVIALYFVIKKRTAIFKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	198 (184)
Sequences:	6856 (4886)
Seq/√Len:	360.2

ECOLI - YABI YGHB YQJA DEDA YOHD YDJZ YDJX
BACSU - YNGC YKOX YBFM YHJE YQED YTXB
SULSO - Q97V45

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_I	132_F	3.383	1.00
48_G	51_G	3.195	1.00
57_V	144_I	2.811	1.00
185_L	189_I	2.690	1.00
187_F	191_K	2.662	1.00
61_T	140_V	2.530	1.00
103_Y	106_G	2.462	1.00
42_V	155_I	2.440	1.00
65_I	136_V	2.421	1.00
109_F	141_L	2.387	1.00
105_A	134_K	2.373	1.00
25_M	66_F	2.359	1.00
53_I	148_I	2.326	1.00
188_V	192_R	2.144	1.00
89_K	92_H	2.129	1.00
131_P	134_K	2.120	1.00
55_A	59_G	2.029	1.00
97_E	101_Q	2.016	1.00
56_G	147_S	2.009	1.00
105_A	138_L	1.941	1.00
173_T	177_I	1.931	1.00
49_F	152_Y	1.831	1.00
12_L	16_G	1.824	1.00
182_V	186_Y	1.799	1.00
53_I	151_V	1.797	1.00
24_L	59_G	1.755	1.00
72_R	129_R	1.748	1.00
25_M	62_I	1.711	1.00
152_Y	156_Q	1.688	1.00
21_A	59_G	1.660	1.00
170_T	174_P	1.646	1.00
17_Y	48_G	1.633	1.00
49_F	53_I	1.626	1.00
21_A	55_A	1.603	1.00
76_R	97_E	1.575	1.00
90_K	94_D	1.566	1.00
35_L	151_V	1.528	1.00
27_E	31_S	1.527	1.00
132_F	136_V	1.523	1.00
38_G	52_A	1.511	1.00
69_W	73_Y	1.498	1.00
17_Y	51_G	1.490	1.00
49_F	151_V	1.486	1.00
64_Q	112_R	1.430	1.00
20_I	56_G	1.413	1.00
52_A	151_V	1.395	1.00
94_D	98_N	1.394	1.00
69_W	132_F	1.383	1.00
21_A	58_I	1.379	1.00
17_Y	55_A	1.377	1.00
71_G	127_I	1.353	1.00
113_F	145_P	1.347	1.00
186_Y	190_K	1.344	1.00
15_M	19_G	1.319	1.00
174_P	178_L	1.291	1.00
106_G	110_S	1.290	1.00
80_D	90_K	1.278	1.00
168_A	171_Y	1.278	1.00
133_L	137_V	1.276	1.00
42_V	49_F	1.255	1.00
51_G	55_A	1.247	1.00
91_H	95_M	1.245	1.00
61_T	143_I	1.240	1.00
111_A	121_I	1.215	1.00
10_T	13_T	1.206	1.00
167_I	170_T	1.202	1.00
165_E	169_G	1.186	1.00
184_A	188_V	1.185	1.00
50_I	152_Y	1.177	1.00
39_G	154_G	1.151	1.00
35_L	56_G	1.146	1.00
83_G	88_I	1.145	1.00
54_I	58_I	1.140	1.00
97_E	128_A	1.138	1.00
76_R	80_D	1.132	1.00
83_G	86_L	1.125	1.00
67_I	123_I	1.125	1.00
98_N	102_K	1.114	1.00
183_I	186_Y	1.114	1.00
50_I	54_I	1.113	1.00
61_T	136_V	1.108	1.00
188_V	191_K	1.092	1.00
10_T	14_N	1.088	1.00
73_Y	77_P	1.066	1.00
57_V	61_T	1.064	1.00
43_S	155_I	1.055	1.00
15_M	18_A	1.049	1.00
100_F	125_A	1.046	1.00
169_G	173_T	1.041	1.00
109_F	145_P	1.041	1.00
53_I	57_V	1.037	1.00
171_Y	174_P	1.036	1.00
35_L	39_G	1.033	1.00
47_I	52_A	1.031	1.00
176_M	180_V	1.031	1.00
108_V	130_M	1.022	1.00
57_V	147_S	1.006	1.00
190_K	193_T	0.998	1.00
65_I	69_W	0.996	1.00
179_A	182_V	0.993	1.00
94_D	97_E	0.988	1.00
39_G	151_V	0.972	1.00
162_D	166_N	0.972	1.00
139_T	143_I	0.967	1.00
56_G	151_V	0.961	1.00
77_P	81_K	0.960	1.00
69_W	72_R	0.959	1.00
145_P	148_I	0.958	1.00
53_I	152_Y	0.957	1.00
118_R	146_W	0.944	1.00
137_V	141_L	0.943	1.00
21_A	62_I	0.943	1.00
20_I	52_A	0.942	1.00
79_L	88_I	0.941	1.00
32_E	118_R	0.941	1.00
17_Y	47_I	0.941	1.00
133_L	136_V	0.932	1.00
122_S	139_T	0.927	1.00
54_I	57_V	0.925	1.00
183_I	187_F	0.919	1.00
50_I	53_I	0.919	1.00
186_Y	189_I	0.918	1.00
40_Y	43_S	0.908	1.00
79_L	93_I	0.905	1.00
70_I	74_G	0.895	1.00
92_H	95_M	0.886	1.00
43_S	159_S	0.886	1.00
60_G	143_I	0.880	1.00
99_W	107_V	0.870	1.00
74_G	77_P	0.859	1.00
24_L	147_S	0.854	1.00
178_L	182_V	0.849	1.00
96_S	128_A	0.848	1.00
51_G	54_I	0.846	1.00
189_I	193_T	0.845	1.00
58_I	62_I	0.845	1.00
68_Y	132_F	0.840	1.00
176_M	179_A	0.840	1.00
64_Q	139_T	0.838	1.00
16_G	19_G	0.836	1.00
172_T	176_M	0.836	1.00
160_Q	163_D	0.836	1.00
177_I	180_V	0.835	1.00
148_I	152_Y	0.832	1.00
82_Y	86_L	0.832	1.00
189_I	192_R	0.827	1.00
77_P	80_D	0.813	1.00
162_D	165_E	0.803	1.00
104_G	130_M	0.799	1.00
175_I	179_A	0.798	1.00
61_T	139_T	0.793	1.00
37_Y	41_M	0.791	1.00
114_I	117_V	0.784	1.00
8_I	12_L	0.781	1.00
76_R	79_L	0.774	1.00
181_V	185_L	0.773	1.00
164_V	167_I	0.769	1.00
136_V	140_V	0.768	1.00
180_V	184_A	0.764	1.00
40_Y	161_W	0.763	1.00
60_G	112_R	0.761	1.00
75_G	79_L	0.760	1.00
149_L	152_Y	0.758	1.00
14_N	18_A	0.754	1.00
106_G	138_L	0.745	1.00
137_V	140_V	0.742	1.00
185_L	188_V	0.741	1.00
12_L	15_M	0.736	1.00
107_V	110_S	0.727	1.00
157_L	160_Q	0.726	1.00
65_I	139_T	0.716	0.99
20_I	38_G	0.711	0.99
186_Y	191_K	0.710	0.99
144_I	148_I	0.710	0.99
112_R	118_R	0.706	0.99
39_G	52_A	0.704	0.99
28_I	112_R	0.703	0.99
98_N	101_Q	0.702	0.99
67_I	119_H	0.689	0.99
153_L	156_Q	0.687	0.99
163_D	167_I	0.686	0.99
42_V	52_A	0.685	0.99
74_G	78_F	0.682	0.99
166_N	170_T	0.682	0.99
107_V	121_I	0.678	0.99
182_V	185_L	0.676	0.99
185_L	191_K	0.673	0.99
17_Y	42_V	0.666	0.99
11_W	16_G	0.666	0.99
13_T	16_G	0.662	0.99
31_S	139_T	0.660	0.99
160_Q	164_V	0.660	0.99
83_G	90_K	0.658	0.99
29_I	119_H	0.655	0.99
68_Y	126_G	0.653	0.99
97_E	129_R	0.644	0.99
147_S	151_V	0.638	0.99
173_T	176_M	0.638	0.99
42_V	151_V	0.638	0.99
12_L	19_G	0.637	0.99
37_Y	40_Y	0.634	0.99
88_I	92_H	0.631	0.99
125_A	130_M	0.630	0.99
31_S	115_P	0.628	0.99
38_G	47_I	0.628	0.99
163_D	166_N	0.625	0.99
169_G	172_T	0.619	0.98
21_A	25_M	0.616	0.98
9_L	41_M	0.612	0.98
145_P	149_L	0.612	0.98
100_F	107_V	0.611	0.98
157_L	161_W	0.609	0.98
64_Q	132_F	0.609	0.98
181_V	188_V	0.608	0.98
91_H	94_D	0.607	0.98
92_H	96_S	0.607	0.98
68_Y	129_R	0.604	0.98
11_W	14_N	0.603	0.98
140_V	144_I	0.601	0.98
135_F	139_T	0.597	0.98
115_P	119_H	0.588	0.98
9_L	13_T	0.584	0.98
38_G	42_V	0.581	0.98
32_E	142_A	0.580	0.98
11_W	15_M	0.578	0.98
165_E	168_A	0.576	0.98
80_D	91_H	0.574	0.98
62_I	66_F	0.574	0.98
24_L	56_G	0.573	0.97
28_I	119_H	0.572	0.97
108_V	125_A	0.570	0.97
167_I	171_Y	0.568	0.97
155_I	159_S	0.566	0.97
82_Y	88_I	0.566	0.97
109_F	113_F	0.560	0.97
111_A	115_P	0.559	0.97
32_E	150_F	0.557	0.97
174_P	177_I	0.557	0.97
13_T	46_T	0.554	0.97
28_I	64_Q	0.554	0.97
185_L	190_K	0.552	0.97
179_A	183_I	0.552	0.97
29_I	33_I	0.550	0.97
134_K	138_L	0.549	0.97
67_I	115_P	0.548	0.97
95_M	98_N	0.546	0.97
27_E	119_H	0.544	0.97
37_Y	168_A	0.542	0.96
99_W	103_Y	0.541	0.96
24_L	119_H	0.537	0.96
118_R	143_I	0.536	0.96
112_R	139_T	0.536	0.96
28_I	122_S	0.533	0.96
28_I	139_T	0.532	0.96
27_E	112_R	0.531	0.96
75_G	78_F	0.531	0.96
49_F	148_I	0.528	0.96
66_F	69_W	0.526	0.96
35_L	147_S	0.524	0.96
43_S	46_T	0.522	0.96
167_I	174_P	0.521	0.96
20_I	55_A	0.515	0.95
60_G	119_H	0.514	0.95
134_K	137_V	0.513	0.95
38_G	151_V	0.512	0.95
65_I	140_V	0.511	0.95
166_N	169_G	0.510	0.95
99_W	102_K	0.510	0.95
82_Y	90_K	0.509	0.95
31_S	135_F	0.507	0.95
81_K	88_I	0.507	0.95
88_I	120_A	0.506	0.95
16_G	47_I	0.505	0.95
156_Q	160_Q	0.504	0.95
67_I	116_V	0.501	0.95
106_G	124_P	0.500	0.95

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
2m20A	2	0.1818	55.7	0.914	Contact Map
2l2tA	2	0.197	48.8	0.918	Contact Map
2ks1B	1	0.2222	47.9	0.918	Contact Map
2jwaA	2	0.2222	34.6	0.924	Contact Map
4dx5A	3	0.8081	29.5	0.927	Contact Map
2kluA	1	0.202	25.2	0.929	Contact Map
2kv5A	1	0.1667	24.9	0.93	Contact Map
3w9iA	3	0.7727	17.7	0.934	Contact Map
2rddB	1	0.1515	13.3	0.938	Contact Map
4mt1A	3	0.8131	11.5	0.94	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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